LOCUS       KN122365             1008576 bp    DNA     linear   CON 04-SEP-2014
DEFINITION  Fukomys damarensis unplaced genomic scaffold scaffold242, whole
            genome shotgun sequence.
ACCESSION   KN122365 AYUG01000000
VERSION     KN122365.1
DBLINK      BioProject: PRJNA190641
            BioSample: SAMN02339281
KEYWORDS    WGS.
SOURCE      Fukomys damarensis (Damara mole-rat)
  ORGANISM  Fukomys damarensis
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia;
            Hystricomorpha; Bathyergidae; Fukomys.
REFERENCE   1  (bases 1 to 1008576)
  AUTHORS   Gladyshev,V.N. and Fang,X.
  TITLE     The Damaraland mole rat (Fukomys damarensis) genome and evolution
            of African mole rats
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 1008576)
  AUTHORS   Gladyshev,V.N. and Fang,X.
  TITLE     Direct Submission
  JOURNAL   Submitted (19-NOV-2013) Department of Science and Technology,
            Beijing Genomics Institute, Shenzhen, 2nd Office Building, Beishan
            Industrial Zone, BeishanRoad,Yantian District, Shenzhen, Guangdong
            518083, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method       :: SOAPdenovo v. 1.06
            Assembly Name         :: DMR_v1.0
            Genome Coverage       :: 140x
            Sequencing Technology :: Illumina Hiseq 2000
            ##Genome-Assembly-Data-END##
FEATURES             Location/Qualifiers
     source          1..1008576
                     /organism="Fukomys damarensis"
                     /mol_type="genomic DNA"
                     /submitter_seqid="scaffold242"
                     /db_xref="taxon:885580"
                     /chromosome="Unknown"
                     /sex="male"
                     /tissue_type="liver"
                     /geo_loc_name="USA"
                     /collection_date="Nov-2011"
     assembly_gap    20196..20291
                     /estimated_length=96
                     /gap_type="within scaffold"
                     /linkage_evidence="paired-ends"
     assembly_gap    31525..31695
                     /estimated_length=171
                     /gap_type="within scaffold"
                     /linkage_evidence="paired-ends"
     assembly_gap    108766..109515
                     /estimated_length=750
                     /gap_type="within scaffold"
                     /linkage_evidence="paired-ends"
     assembly_gap    157608..157790
                     /estimated_length=183
                     /gap_type="within scaffold"
                     /linkage_evidence="paired-ends"
     assembly_gap    186473..186580
                     /estimated_length=108
                     /gap_type="within scaffold"
                     /linkage_evidence="paired-ends"
     gene            <216935..>253681
                     /locus_tag="H920_07711"
     mRNA            join(<216935..217048,228859..228921,241078..241245,
                     242843..242999,243645..243728,252097..252206,
                     252845..252912,253642..>253681)
                     /locus_tag="H920_07711"
                     /product="Kit ligand"
     CDS             join(<216935..217048,228859..228921,241078..241245,
                     242843..242999,243645..243728,252097..252206,
                     252845..252912,253642..253681)
                     /locus_tag="H920_07711"
                     /note="GO_component: GO:0016020 - membrane [Evidence IEA];
                     GO_function: GO:0005173 - stem cell factor receptor
                     binding [Evidence IEA];
                     GO_process: GO:0007155 - cell adhesion [Evidence IEA]"
                     /codon_start=1
                     /product="Kit ligand"
                     /protein_id="KFO30884.1"
                     /db_xref="InterPro:IPR003452"
                     /db_xref="InterPro:IPR009079"
                     /db_xref="UniProtKB/Swiss-Prot:P21581"
                     /translation="TWIITCIYLQLLLFNPLVKTKEICGNPVTDNVKDITKLVANLPK
                     DYLITLNYVTGMDVLPSHCWLRQMVIQLSVSLTNLLDKFSNISEGLSNYSIIDKLGKI
                     VDDLVDCMETSFKNVKESSKRPEPRLFTPEEFFRIFNRSIDAFKDFMVASETSDCVIS
                     STLSTEKDSRVSVTKPFMLPPVAASSLKNDSSSSNSKAADSVGDPSLQWAAMALPAFF
                     SLVIGFAFGALYWKKKQPNLTRAGENIQINEEDNEISMLQEKEREFQEV"
     assembly_gap    291684..291747
                     /estimated_length=64
                     /gap_type="within scaffold"
                     /linkage_evidence="paired-ends"
     assembly_gap    379037..379077
                     /estimated_length=41
                     /gap_type="within scaffold"
                     /linkage_evidence="paired-ends"
     assembly_gap    403591..403607
                     /estimated_length=17
                     /gap_type="within scaffold"
                     /linkage_evidence="paired-ends"
     assembly_gap    470489..470655
                     /estimated_length=167
                     /gap_type="within scaffold"
                     /linkage_evidence="paired-ends"
     assembly_gap    475075..475294
                     /estimated_length=220
                     /gap_type="within scaffold"
                     /linkage_evidence="paired-ends"
     gene            complement(<485837..>521322)
                     /locus_tag="H920_07712"
     mRNA            complement(join(<485837..486645,488718..488944,
                     490430..490599,491881..491984,498948..499059,
                     500534..500654,503107..503255,509190..509442,
                     510809..510981,511541..511656,514440..514539,
                     521134..>521322))
                     /locus_tag="H920_07712"
                     /product="Transmembrane and TPR repeat-containing protein
                     3"
     CDS             complement(join(485837..486645,488718..488944,
                     490430..490599,491881..491984,498948..499059,
                     500534..500654,503107..503255,509190..509442,
                     510809..510981,511541..511656,514440..514539,
                     521134..521322))
                     /locus_tag="H920_07712"
                     /note="GO_function: GO:0005515 - protein binding [Evidence
                     IEA]"
                     /codon_start=1
                     /product="Transmembrane and TPR repeat-containing protein
                     3"
                     /protein_id="KFO30885.1"
                     /db_xref="InterPro:IPR001440"
                     /db_xref="InterPro:IPR013026"
                     /db_xref="InterPro:IPR013618"
                     /db_xref="InterPro:IPR019734"
                     /db_xref="UniProtKB/Swiss-Prot:Q6ZXV5"
                     /translation="MADINLKEVTLIVGVVTACYWNSLFCGFVFDDVSAILDNKDLHP
                     STPLKTLFQNDFWGTPMSEVTGVVGRAELLSSIFFLAAFLSYTKSKGPDNSIVWTPIA
                     LTVILVAVATLCKEQGITVVGICCVYEVFIAQGYTLPLLCTTAGQFLRGKSSIPFSLL
                     QTLIKLIVLMFSTLLLVVIRVQVIQSQLPVFTRFDNPAAVSPTPTRQLTFNYLLPVNA
                     WLLLNPSDLCCDWTMGTIPLIESFLDIRNLATFAFFCFLGILGIFSLRYPGDSSKTVL
                     MALCLIALPFIPASNLFFPVGFVVAERVLYVPSMGFCILVAHGWQKISNKSVFKKLSW
                     ACLSVVILTHALKTLHRNWDWESEYTLFMSALKVNKNNAKLWNNVGHALENEKNFERA
                     LKYFLQATHVQPDDIGAHMNVGRTYKNLNRTKEAEESYVMAKSLMPQIIPGKKYAARI
                     APNHLNVYINLANLIRANESRLEEADQLYRQAISMRPDFKQAYISRGELLLKMNKPLK
                     AKEAYLKALELDRNNADLWYNLAIVYIELREPNEALKNFNHALALNPRHKLALFNSAI
                     LMQESGEVKLRPEARKRLLNYVNEEPLDANGYFNLGMLAMDDKKDTEAEIWMKKAIKL
                     QADFRSALFNLALLYSQTAKELKALPILEELLKYYPDHVKGLILKGDILMNQKKDILG
                     AKKCFEKILEMDPTNVQGKHNLCVVYFEEKDLLKAERCLVETLALAPHEEYVQRHLNI
                     VRDKISSSGFVEQPVLPAGKSTGEEGENRIPTENVKEIRSESRPTQTTETTEDKSESK
                     HNKQLQKNKEAPQKTKDIKEIEKKRVAALKRLEEIERILNGE"
     assembly_gap    496647..496805
                     /estimated_length=159
                     /gap_type="within scaffold"
                     /linkage_evidence="paired-ends"
     assembly_gap    506385..506545
                     /estimated_length=161
                     /gap_type="within scaffold"
                     /linkage_evidence="paired-ends"
     assembly_gap    509501..509544
                     /estimated_length=44
                     /gap_type="within scaffold"
                     /linkage_evidence="paired-ends"
     assembly_gap    524608..525378
                     /estimated_length=771
                     /gap_type="within scaffold"
                     /linkage_evidence="paired-ends"
     gene            <532111..>610521
                     /locus_tag="H920_07713"
     mRNA            join(<532111..532212,532339..532416,533946..534015,
                     534309..534355,535778..535921,537076..537129,
                     537825..537977,538332..538514,539524..539613,
                     541783..541905,542662..542785,544707..544879,
                     545737..545899,547641..547747,547813..547900,
                     549038..549147,550683..550767,551220..551362,
                     554172..554336,554801..554950,557487..557602,
                     559309..559411,559500..559730,563023..563196,
                     567351..567462,571284..571489,572461..572612,
                     574377..574488,575192..575647,576516..576680,
                     577656..577763,577981..578115,579342..579608,
                     580216..580323,580905..581104,582166..582379,
                     583402..583539,585762..585983,586299..586421,
                     588541..588686,589006..589161,591624..591747,
                     595954..596088,596563..596640,597882..598046,
                     598654..598776,599739..599911,602983..603124,
                     604893..604966,605518..605612,609305..609384,
                     610291..>610521)
                     /locus_tag="H920_07713"
                     /product="Centrosomal protein of 290 kDa"
     CDS             join(532111..532212,532339..532416,533946..534015,
                     534309..534355,535778..535921,537076..537129,
                     537825..537977,538332..538514,539524..539613,
                     541783..541905,542662..542785,544707..544879,
                     545737..545899,547641..547747,547813..547900,
                     549038..549147,550683..550767,551220..551362,
                     554172..554336,554801..554950,557487..557602,
                     559309..559411,559500..559730,563023..563196,
                     567351..567462,571284..571489,572461..572612,
                     574377..574488,575192..575647,576516..576680,
                     577656..577763,577981..578115,579342..579608,
                     580216..580323,580905..581104,582166..582379,
                     583402..583539,585762..585983,586299..586421,
                     588541..588686,589006..589161,591624..591747,
                     595954..596088,596563..596640,597882..598046,
                     598654..598776,599739..599911,602983..603124,
                     604893..604966,605518..605612,609305..609384,
                     610291..610521)
                     /locus_tag="H920_07713"
                     /codon_start=1
                     /product="Centrosomal protein of 290 kDa"
                     /protein_id="KFO30886.1"
                     /db_xref="UniProtKB/Swiss-Prot:O15078"
                     /translation="MPPNIDFKELIKVDPDELPRQEELADNLLISLSKVEANDLKNEN
                     QENVIHLFRITQSLMKMKAQEVELALEEVEKAGEEQAKFENQLKTKVMKLENELEMAQ
                     QTTGGRDTRFLRDEIRQLEKQLEQKDRELEDIEKDLNKEKKVNEQLALRNEEAENENS
                     KLRRENEQLRQDIIDYQKQIDSQKESLLSRRGEDSDYRSQLSKKNYELVQYLDEIQTL
                     TEANEKIEVQNQEMRKNLEESVQEMEKMTDEYNRMKAVVHQTDNMMDQLKKENDHYRL
                     QVQELTDLLKAKNEEDDPIMVAVNAKVEEWKLILSTKDDEIIEYQQTLHNLREKLKNA
                     QLDADKSNIMALQQGVHKRDDQIKMLTEQVEQYTKEMEKNTFIIEDLKNELQRNKGTS
                     TLSQQTHYMKIQSKLQVLQEKTKEAERTAELAEGDARAKDKELIEALKRLKDYESGVY
                     GLEDAVIEIKNCKNQIKIRDREIEVLTKEINKLELKINDFLDENEALRERMGLEPKTM
                     IDLTEFRNSKRLKQQQYRAENQILLKEASIESLEEERLSLKRKIRQMAQERGKGNTTS
                     GLTTENLNLTEHFIQEHRTGEQKLNFVSLSMSEAQSKNEFLSRELIEKGRDLERSKTV
                     ITKFQNRLKELVEENKQLEEGMKEILQAIKEMQKDPDIKGGETSLIIPSLERLVNAIE
                     SKNAEGIFDASLHLKAQVDQLTGRNEELRQELKESRKEAMDYSQQLAKANLKIDHLEK
                     ETSLLRQSEGSHVVFKGLDLPDGVAPSSASIINSQNEYLIHLLQELENKEKKLKNLED
                     SLEDYNRKFAVIRHQQSLLYKEYLSEKENWKTESETIKDKKRKLEDQIQQDAIKVKEY
                     NNLLNALQMDSDEMKKTLSENSRKITVLQVNEKLLIRQYTALVEMERQLRKENGKQKK
                     DLMSMEAEVCEKIGCLQRFKEMAIFKIAALQKVIDNSVSLSELELANKQYNELTAKYR
                     DILQKDNMLVQRANNLEHLECENASLKEQIDSLNKELEITKEKLHTIEQAWEQDTQLR
                     NESNMDKAKKSITNSDIISISKKITMLEMKELNERQRAEHCQKMYEHLRTSLKQIEER
                     NFELETKFAELTKINLDAQKVEQMLRDELADSVSKPVSDADRQRILELEKSEMELKVE
                     VSKLREISDIAKRQVEILHTQQQSREKEVESLRMQLLDYQAQSDEKALIAKLHQHIVT
                     LQVSEAAAFGKLESVTSKLQKLEAYNLRLEQKLDEKEQALYYARLEGRNKAKHLRQTI
                     QSLRRQFSGALPLAQQEKFSKTMIQLQNDKLKIMQEMKNSQQQHRNMENKTLELELKL
                     KGLEELISTLKDARGAQKVISWHMKIEELRLQEFKLNRELIRDKEEIKYLNNIISEYE
                     HTISNLEEEIVQQNKFHEERQMAWDQREVELERQLDIFEHQQNEIINAAQKFEEATGS
                     MPDPSLPLPNQLEFALRKLKENIRVILETQATCKALEEKLKEKESALRLAEQNILSRD
                     RVITELRLRLPATAEREKLIAELGRKEVEPTSHHAMKIAHQTIANMQARLNQKEEVLK
                     KYQRLLEKAREEQREIVKKHEEDLHSLHHKLELQADSSLNKFKQTAWDLIKQSPATVP
                     TNKHFIRLAEMEQTVAEQDYSLSELLSKLKKVSQELERQKEITELKIKEFENMKLRLQ
                     ENHEGEVKKMKTEIEDLRCLLAQSQKESQSLKSELQAQKEANSRAPTTTMRNLVDRLK
                     SQLSLKEKQQKALSRALLELRAEMTAAAEEHIISVTSQKEANLNVQQIVDRQTRELKS
                     QIEDLNENLLKLREALKTSKNRENSLTDNLNDLNNDLQRKQKAYNKILREKDGIDQEN
                     EELKRQIKRLTTGLQSKPLIDNKQSLIEELQKKVKKLESQLERKVDEVDVKPMKEKSA
                     KEELIRWEEGKKWQTKIEGLRNKLKEKEGEVYTLTKQLTTLKDLFAKADKEKQTLQRK
                     LKTTGMTVDQVIGMRALESEKELEELKKRNLDLENDILCMRNHQALPRDSVVEDLRLQ
                     NRYLQEKLNALEKQFSKDEYSKPPTSGIESGDHYQKEQELQRANLKLSSENIELKFQL
                     EQANKDLPRLRNQVRDLKEMCEFFKKEKAEVERKLRGAGRSGKTIPELEKTIGLMKKV
                     VEKVQRENEQLKRASEIFTSEKTANIEQENEKLKSELEKFKVHLGRQLSMQYESKAKG
                     TEKVVAENERLRKELKKETEAAEKLRIAKNNLEILNEKMRVQLEETGKRLQLAECRGP
                     QLEGADSKSWKSIVVTRMYETKLKELETDTAKKNQSITDLKQLIREAAEREQKVKKYT
                     EDLEQQIEILKHVPDDAESEEGLKRELQLLRLAYSQLDKEKVELMHQLEVNKDQSGAE
                     STIPDAVQLKEAIKDLETQLKVSDLEKQHLKEEIRKLKKELENVDPSFFEEIEDLKYN
                     YKEEVKKNILLEEKFKKLSEQFGFELTSPVAASEQSENEEESPVNFPIY"
     assembly_gap    535076..535175
                     /estimated_length=100
                     /gap_type="within scaffold"
                     /linkage_evidence="paired-ends"
     assembly_gap    603754..604357
                     /estimated_length=604
                     /gap_type="within scaffold"
                     /linkage_evidence="paired-ends"
     gene            complement(<611366..>623212)
                     /locus_tag="H920_07714"
     mRNA            complement(join(<611366..611554,612957..613126,
                     614218..614415,615930..616046,616347..616442,
                     618810..618927,623123..>623212))
                     /locus_tag="H920_07714"
                     /product="hypothetical protein"
     CDS             complement(join(611366..611554,612957..613126,
                     614218..614415,615930..616046,616347..616442,
                     618810..618927,623123..623212))
                     /locus_tag="H920_07714"
                     /codon_start=1
                     /product="hypothetical protein"
                     /protein_id="KFO30887.1"
                     /db_xref="UniProtKB/Swiss-Prot:Q5RFG5"
                     /translation="MRRLGSVQRKMPCVFVTEVKDEPSAKREHQPFKVLATETISHKA
                     LDADIHSAIPTEKVDGTCCYVTTYKDQPYLWARLDRKPNKQADKRFKNFLRSKENSKE
                     FLWNVEEDFKPVPECWIPAKEIEQLKGNPVPDDNGHIPGWVPVEKSNKQYCWHSSVVN
                     YEFEMALVLKHHPDDPGLLQISAVPLSDLLEQTLELIGTNINGNPYGLGNKKHPIHLL
                     IPHGAFQIRNLPKLKLNDLLSWFEGCREGKIEGIVWHCSDGCLIKIHRHHLGLSWPIP
                     DTYMNSKPVVINMNLNKYDYTFDTKCLFNHFLKIDNQKFGRLRDIILDV"
     assembly_gap    615418..615468
                     /estimated_length=51
                     /gap_type="within scaffold"
                     /linkage_evidence="paired-ends"
     assembly_gap    627613..627721
                     /estimated_length=109
                     /gap_type="within scaffold"
                     /linkage_evidence="paired-ends"
     gene            <629285..>657599
                     /locus_tag="H920_07715"
     mRNA            join(<629285..629405,640146..640304,640940..641065,
                     641146..641256,643575..643685,648926..649033,
                     651953..652057,652559..652762,654332..654424,
                     657574..>657599)
                     /locus_tag="H920_07715"
                     /product="hypothetical protein"
     CDS             join(<629285..629405,640146..640304,640940..641065,
                     641146..641256,643575..643685,648926..649033,
                     651953..652057,652559..652762,654332..654424,
                     657574..657599)
                     /locus_tag="H920_07715"
                     /codon_start=1
                     /product="hypothetical protein"
                     /protein_id="KFO30888.1"
                     /db_xref="UniProtKB/Swiss-Prot:Q4R731"
                     /translation="QNCSISCFWETQPLGCVKISCIFYHSKPRNINGLFLPPSSNITI
                     QKDSQEGIPSPTQSQEPLKPQETISRPIHHPLVLKTNFEEEEEEEEEQNDYLDLGQFN
                     LKTICPIDASSLWTKTPEEIEEKRVIKEMCYKSGEYYRFHTPADISSKSTAPAVEKEL
                     EKPLENGSELQEGDGFTIPTKLSLSERQGETKISLDGKPKTDIAAFENGGGDCPIPQR
                     ISFLGVDESDGLTEEKEIHMSKCPNTKVNDVQPVKRPHFKGVKKRKWIYDEPKNFPGS
                     GMQRGVQSPNPKNKMNYHQHNKNKNAESASYIHVRRDAVKTVPLSAPRCSRPTNESYN
                     KADAKKEPKINVCPDKYMSTSYNGSAWRKRIPFSKTYSKTEKIYPEPRRNGSK"
     assembly_gap    678612..678948
                     /estimated_length=337
                     /gap_type="within scaffold"
                     /linkage_evidence="paired-ends"
     assembly_gap    692510..692628
                     /estimated_length=119
                     /gap_type="within scaffold"
                     /linkage_evidence="paired-ends"
     assembly_gap    734024..734143
                     /estimated_length=120
                     /gap_type="within scaffold"
                     /linkage_evidence="paired-ends"
     assembly_gap    745463..745545
                     /estimated_length=83
                     /gap_type="within scaffold"
                     /linkage_evidence="paired-ends"
     assembly_gap    790120..790169
                     /estimated_length=50
                     /gap_type="within scaffold"
                     /linkage_evidence="paired-ends"
     assembly_gap    797398..799169
                     /estimated_length=1772
                     /gap_type="within scaffold"
                     /linkage_evidence="paired-ends"
     assembly_gap    819425..819618
                     /estimated_length=194
                     /gap_type="within scaffold"
                     /linkage_evidence="paired-ends"
     assembly_gap    844672..846570
                     /estimated_length=1899
                     /gap_type="within scaffold"
                     /linkage_evidence="paired-ends"
     assembly_gap    968348..968722
                     /estimated_length=375
                     /gap_type="within scaffold"
                     /linkage_evidence="paired-ends"
     assembly_gap    980910..981114
                     /estimated_length=205
                     /gap_type="within scaffold"
                     /linkage_evidence="paired-ends"
     assembly_gap    990331..990516
                     /estimated_length=186
                     /gap_type="within scaffold"
                     /linkage_evidence="paired-ends"
     assembly_gap    1002548..1002619
                     /estimated_length=72
                     /gap_type="within scaffold"
                     /linkage_evidence="paired-ends"
CONTIG      join(AYUG01101867.1:1..20195,gap(96),AYUG01101868.1:1..11233,
            gap(171),AYUG01101869.1:1..77070,gap(750),AYUG01101870.1:1..48092,
            gap(183),AYUG01101871.1:1..28682,gap(108),AYUG01101872.1:1..105103,
            gap(64),AYUG01101873.1:1..87289,gap(41),AYUG01101874.1:1..24513,
            gap(17),AYUG01101875.1:1..66881,gap(167),AYUG01101876.1:1..4419,
            gap(220),AYUG01101877.1:1..21352,gap(159),AYUG01101878.1:1..9579,
            gap(161),AYUG01101879.1:1..2955,gap(44),AYUG01101880.1:1..15063,
            gap(771),AYUG01101881.1:1..9697,gap(100),AYUG01101882.1:1..68578,
            gap(604),AYUG01101883.1:1..11060,gap(51),AYUG01101884.1:1..12144,
            gap(109),AYUG01101885.1:1..50890,gap(337),AYUG01101886.1:1..13561,
            gap(119),AYUG01101887.1:1..41395,gap(120),AYUG01101888.1:1..11319,
            gap(83),AYUG01101889.1:1..44574,gap(50),AYUG01101890.1:1..7228,
            gap(1772),AYUG01101891.1:1..20255,gap(194),AYUG01101892.1:1..25053,
            gap(1899),AYUG01101893.1:1..121777,gap(375),
            AYUG01101894.1:1..12187,gap(205),AYUG01101895.1:1..9216,gap(186),
            AYUG01101896.1:1..12031,gap(72),AYUG01101897.1:1..5957)
//