RetrogeneDB ID: retro_cfam_452

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 11:27046884..27050145(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000031402
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: IPO5
• Ensembl ID: ENSCAFG00000005561
• Aliases: IPO5, RANBP5
• Description: importin 5 [Source:HGNC Symbol;Acc:6402]

Sequence

>retro_cfam_452
TTTTATCAGCTTCTGAAGAACTTGATCAATCCAAGCTGTATGGTGCGGAGGCAGGCAGAGGAAATCTATGAAAATATCCC
AGGTCTGTGTAAGACTACATTCCTCTTAGATGCTGTCAGAAATAGAAGAGCAGGTTATGAGGTGAGACAAATGGCTGCCG
CACTGCTACGACGGCTTTTGTCCTCTGGGTTTGAGGAAGTCTATCCAAATCTGCCTTCTGATGTTCAGAGGGACGTCAAG
ATTGAACTGATACTGGCTGTTAAGTTAGAAACACATGCTAGCATGAGGAAAAAACTTTGTGATATTTTTGCAGTGCTGGC
CAGGAATTTGATAGATGAGGATGGCACTAACCACTGGCCCGAAGGTCTGAAGTTCCTTATCGATTCAATCTACTCTAAAA
ATGTAGTTCTATGGGAAGTTGCACTTCATGTTTTCTGGCACTTTCCTGGGATCTTTGGGAACCAAGAGCGGCACGATTTG
GATATCATCAAACGGTTGTTGGACCAGTGCATTCAGGATCAAGAACATCCAGCAATCAGGACATTATCTGCTAGAGCTGC
AGCTGCATTTGTACTTGCTAATGAGAATAATATTGCTCTTTTCAAAGACTTTTCAGACTTGCTTCCTGGAATCTTACAGG
CTGTGAGTGACTCATGCTACCAGGATGATGATTCAGTGCTAGAATCCCTTGTTGAGATTGCAGATACTGTACCTAAATAC
TTGGGTCCTTATTTAGAAGACACTCTGCAGTTGAGTCTGAAGTTATGTGGAGACTCTAGACTTAGTAATCTGCAACGCCA
GCTGGCCCTTGAAATAATAGTGACCTTGTCTGAAACTGCAACCCCAATGTTGAAAAAACATACAAATATAATTGCACAGG
CAGTTCCTCATATATTAGCAATGATGGTTGATCTACAAGATGATGAGGACTGGGTAAATGCTGATGAGATGGAAGAAGAT
GATTTTGACAGCAATGCAGTTGCTGCTGAGAGTGCACTAGACAGACTGGCTTGTGGGCTCGGTGGAAAACTTGTTTTACC
AATGACTAAGGAGCACATCATGCAGATGCTTCAGAGCCCTGACTGGAAATATCGACATGCTGGATTAATGGCCTTATCTG
CCATTGGAGAAGGATGCCATCAGCAAATGGAATCAATTCTAGATGAAACAGTTAACTCTGTTTTGCTTTTTCTTCAGGAT
CCTCACCCAAGGGTGAGGGCTGCAGCCTGTACTACGCTTGGACAGATGGCTACAGATTTTGCGCCTAACTTCCAAAAGAA
ATTCCATGAAACAGTGATTGCAGCTCTGTTGCGTACCATGGAAAATCAAGGTAATCAGCGTGTGCAATCACATGCGGCTT
CTGCACTTATTATTTTTATAGAAGACTGCCCCAAAGCATTGCTAGTTCTATATTTGGATAGTATGGTGAGAAATCTACAT
TCCATCTTGGTGATTAAACTTCAAGAGTTGATTCGGAATGGAACTAAATTGGCCTTGGAACAGCTTGTGACAACCATTGC
CTCAGTTGCAGATACAATAGAAGAAAAATTTGTTCCATATTATGATATATTTATGCCATCACTAAAGCACATTGTTGAGC
TTGCTATTCAAAAGGAACTCAAGCTTCTGAAAGGAAAAACTATTGAGTGCATTAGCCATGTTGGTCTTGCTGTTGGGAAG
GAAAAATTTATGCAAGATGCATCAAATGTGATGCAGCTATTGTTGAAGACACAATCAGACTTAAATAATATGGAAGATGA
TGACCCTCAGACATCTTACATGGTTTCAGCATGGGCCAGAATGTGTAAAATTCTTGGAAGTGATTTTCAACAGTATCTTC
CACTGGTTATTGAGCCTCTCATTAAGACTGCTTCAGCAAAACCTGATGTTGCTCTCTTAGACACACAAGATGTGGAAAAT
ATGAGTGATGATGATGGATGGCAATTTGTAAATCTTGGAGACCAACAAAGTTTTGGAATTAAAACTTCAGGACTTGAAGC
AAAAGCAACTGCTTGTCAAATGTTGGTTTACTATGCTAAGGAATTAGGGGAAGGATTTGTGGAATATACAGAACAAGTTG
TAAAGCTTATGGTTCCTTTATTGAAATTTTATTTCCATGACAATGTTCGAGTGGCAGCAGCAGAGTCTATGCCTTTTCTC
CTGGAATGTGCAAGAATTCGTGGCCCAGAGTATCTTGCACAGATGTGGCAATTCATATGTGATCCTTTAATCAAGGCTAT
TGGGACTGAACCTGATACAGATGTACTCTCAGAAGTAATGAATTCTTTTGCAAAATCCATTGAAGTAATGGGAGATGGGT
GCCTTAATGATGAACACTTGGAAGAACTAGGAGAAATACTGAAAGCAAAACTTGAAGGGCATTTTAAAAACCAAGAATTG
AGACAGGTTAAAAGACAGGAAGAAAACTATGACCAACAGGTTGAAATGTCTCTACAAGATGAGGATGAATGTGATGTTTA
TATTCTGACCAAAGTATCAGATATTTTGCACTCATTATTTAGTACTTATAAGGAAAAGATTTTACCGTGGTTTGAACAGC
TGCTTCCATTAATTGTAAATCTAATTTGTTCAAGTAGGCCATGGCCAGACAGACAGTGGGGATTGTGCATTTTTGATGAT
ATTATAGAGCACTGCAGTCCAACCTCATTTAAATATGTAGAATATTTTAGGTGGCCAATGCTACTAAATATGCGAGACAA
TAACCCTGAAGTCAGACAAGCTGCTGCTTATGGCCTGGGTGTTATGGCACAGTTTGGTGGAGATGATTATCGTTCTTTAT
GTTCGGAAGCTGTTCCACTGCTGGTAAAAGTTATTAAGTGTGCAAATTCCAAAACCAAAAAAAATGTCATTGCTACAGAG
AACTGTATTTCAGCAGTAGGGAAGATTCTGAGGTTTAAGCCTAACTGTGTAAATGTAGATGAAGTTCTTCCACATTGGTT
ATCATGGCTTCCACTGCATGAGGATAAAGAGGAAGCTATTCAGTCTTTGAGTTTTCTCTGTGACTTAATTGAAAGTAATC
ATCCAGTTGTACTTGGTCCAAATAATTCCAATCTTCCCAAAATAATCAGTATAATTGCAGAAGGAAAAGTTAATGAGACT
ATTAACTATGAAGATCCTTGTGCCAAACGCCTAGCTAATGTTGTGCGTCAGGTACAGACTTCTGAAGAATTATGGTTGGA
ATGCATATCCCAACTTGATGATGAGCAGCAGGAAGCTTTACAGGAGCTGCTAAATTTTGCT

Alignment

ORF - retro_cfam_452 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.05 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FHLLSLGLLSRETKILKCAHETYENIPGQSKITFLLQAIRNTTAAEEARQMAAVLLRRLLSSAFDEVYPT
          F..L...L..........A.E.YENIPG..K.TFLL.A.RN..A..E.RQMAA.LLRRLLSS.F.EVYP.
Retrocopy FYQLLKNLINPSCMVRRQAEEIYENIPGLCKTTFLLDAVRNRRAGYEVRQMAAALLRRLLSSGFEEVYPN

Parental  LPSDVQTAIKSELLMIIQMETQSSMRKKICDIAAELARNLIDEDGNNQWPEGLKFLFDSVSSQNMGLREA
          LPSDVQ...K.EL......ET..SMRKK.CDI.A.LARNLIDEDG.N.WPEGLKFL.DS..S.N..L.E.
Retrocopy LPSDVQRDVKIELILAVKLETHASMRKKLCDIFAVLARNLIDEDGTNHWPEGLKFLIDSIYSKNVVLWEV

Parental  ALHIFWNFPGIFGNQQQHYLDVIKRMLVQCMQDQEHPSIRTLSARATAAFILANEHNVALFKHFADLLPG
          ALH.FW.FPGIFGNQ..H.LD.IKR.L.QC.QDQEHP.IRTLSARA.AAF.LANE.N.ALFK.F.DLLPG
Retrocopy ALHVFWHFPGIFGNQERHDLDIIKRLLDQCIQDQEHPAIRTLSARAAAAFVLANENNIALFKDFSDLLPG

Parental  FLQAVNDSCYQNDDSVLKSLVEIADTVPKYLRPHLEATLQLSLKLCGDTNLNNMQRQLALEVIVTLSETA
          .LQAV.DSCYQ.DDSVL.SLVEIADTVPKYL.P.LE.TLQLSLKLCGD..L.N.QRQLALE.IVTLSETA
Retrocopy ILQAVSDSCYQDDDSVLESLVEIADTVPKYLGPYLEDTLQLSLKLCGDSRLSNLQRQLALEIIVTLSETA

Parental  AAMLRKHTNIVAQTIPQMLAMMVDLEEDEDWANADELEDDDFDSNAVAGESALDRMACGLGGKLVLPMIK
          ..ML.KHTNI.AQ..P..LAMMVDL..DEDW.NADE.E.DDFDSNAVA.ESALDR.ACGLGGKLVLPM.K
Retrocopy TPMLKKHTNIIAQAVPHILAMMVDLQDDEDWVNADEMEEDDFDSNAVAAESALDRLACGLGGKLVLPMTK

Parental  EHIMQMLQNPDWKYRHAGLMALSAIGEGCHQQMEGILNEIVNFVLLFLQDPHPRVRYAACNAVGQMATDF
          EHIMQMLQ.PDWKYRHAGLMALSAIGEGCHQQME.IL.E.VN.VLLFLQDPHPRVR.AAC...GQMATDF
Retrocopy EHIMQMLQSPDWKYRHAGLMALSAIGEGCHQQMESILDETVNSVLLFLQDPHPRVRAAACTTLGQMATDF

Parental  APGFQKKFHEKVIAALLQTMEDQGNQRVQAHAAAALINFTEDCPKSLLIPYLDNLVKHLHSIMVLKLQEL
          AP.FQKKFHE.VIAALL.TME.QGNQRVQ.HAA.ALI.F.EDCPK.LL..YLD..V..LHSI.V.KLQEL
Retrocopy APNFQKKFHETVIAALLRTMENQGNQRVQSHAASALIIFIEDCPKALLVLYLDSMVRNLHSILVIKLQEL

Parental  IQKGTKLVLEQVVTSIASVADTAEEKFVPYYDLFMPSLKHIVENAVQKELRLLRGKTIECISLIGLAVGK
          I..GTKL.LEQ.VT.IASVADT.EEKFVPYYD.FMPSLKHIVE.A.QKEL.LL.GKTIECIS..GLAVGK
Retrocopy IRNGTKLALEQLVTTIASVADTIEEKFVPYYDIFMPSLKHIVELAIQKELKLLKGKTIECISHVGLAVGK

Parental  EKFMQDASDVMQLLLKTQTDFSDMEDDDPQISYMISAWARMCKILGKEFQQYLPVVMGPLMKTASIKPEV
          EKFMQDAS.VMQLLLKTQ.D...MEDDDPQ.SYM.SAWARMCKILG..FQQYLP.V..PL.KTAS.KP.V
Retrocopy EKFMQDASNVMQLLLKTQSDLNNMEDDDPQTSYMVSAWARMCKILGSDFQQYLPLVIEPLIKTASAKPDV

Parental  ALLDTQDMENMSDDDGWEFVNLGDQQSFGIKTAGLEEKSTACQMLVCYAKELKEGFVEYTEQVVKLMVPL
          ALLDTQD.ENMSDDDGW.FVNLGDQQSFGIKT.GLE.K.TACQMLV.YAKEL.EGFVEYTEQVVKLMVPL
Retrocopy ALLDTQDVENMSDDDGWQFVNLGDQQSFGIKTSGLEAKATACQMLVYYAKELGEGFVEYTEQVVKLMVPL

Parental  LKFYFHDNKRVRVAAAESMPLLLECARVRGPEYLTQMWHFMCDALIKAIGTEPDSDVLSEIMHSFAKCIE
          LKFYFHDN..VRVAAAESMP.LLECAR.RGPEYL.QMW.F.CD.LIKAIGTEPD.DVLSE.M.SFAK.IE
Retrocopy LKFYFHDN--VRVAAAESMPFLLECARIRGPEYLAQMWQFICDPLIKAIGTEPDTDVLSEVMNSFAKSIE

Parental  VMGDGCLNNEHFEELGGILKAKLEEHFKNQELRQVKRQDEDYDEQVEESLQDEDDNDVYILTKVSDILHS
          VMGDGCLN.EH.EELG.ILKAKLE.HFKNQELRQVKRQ.E.YD.QVE.SLQDED..DVYILTKVSDILHS
Retrocopy VMGDGCLNDEHLEELGEILKAKLEGHFKNQELRQVKRQEENYDQQVEMSLQDEDECDVYILTKVSDILHS

Parental  IFSSYKEKVLPWFEQLLPLIVNLICPHRPWPDRQWGLCIFDDVIEHCSPASFKYAEYFLRPMLQYVCDNS
          .FS.YKEK.LPWFEQLLPLIVNLIC..RPWPDRQWGLCIFDD.IEHCSP.SFKY.EYF..PML....DN.
Retrocopy LFSTYKEKILPWFEQLLPLIVNLICSSRPWPDRQWGLCIFDDIIEHCSPTSFKYVEYFRWPMLLNMRDNN

Parental  PEVRQAAAYGLGVMAQYGGDNYRPFCTEALPLLVRVIQSADSKTKENVNATENCISAVGKIMKFKPDCVN
          PEVRQAAAYGLGVMAQ.GGD.YR..C.EA.PLLV.VI..A.SKT...V.ATENCISAVGKI..FKP.CVN
Retrocopy PEVRQAAAYGLGVMAQFGGDDYRSLCSEAVPLLVKVIKCANSKTXXXVIATENCISAVGKILRFKPNCVN

Parental  VEEVLPHWLSWLPLHEDKEEAVQTFNYLCDLIESNHPIVLGPNNTNLPKIFSIIAEGEMHEAIKHEDPCA
          V.EVLPHWLSWLPLHEDKEEA.Q....LCDLIESNHP.VLGPNN.NLPKI.SIIAEG...E.I..EDPCA
Retrocopy VDEVLPHWLSWLPLHEDKEEAIQSLSFLCDLIESNHPVVLGPNNSNLPKIISIIAEGKVNETINYEDPCA

Parental  KRLANVVRQVQTSGGLWTECIAQLSPEQQAAIQELLNSA
          KRLANVVRQVQTS..LW.ECI.QL..EQQ.A.QELLN.A
Retrocopy KRLANVVRQVQTSEELWLECISQLDDEQQEALQELLNFA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP012049_cerebellum	29.44 RPM	99.12 RPM
SRP017611_brain	51.68 RPM	85.66 RPM
SRP017611_kidney	17.04 RPM	205.77 RPM
SRP017611_liver	6.82 RPM	47.57 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_452 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_452 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_452 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Sus scrofa	retro_sscr_24

---

Parental genes homology:

Parental genes homology involve 21 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003784	1 retrocopy	retro_amel_3,
Bos taurus	ENSBTAG00000039374	1 retrocopy	retro_btau_104,
Canis familiaris	ENSCAFG00000005561	1 retrocopy	retro_cfam_452 ,
Choloepus hoffmanni	ENSCHOG00000006061	1 retrocopy	retro_chof_11,
Cavia porcellus	ENSCPOG00000004827	2 retrocopies	retro_cpor_265, retro_cpor_57,
Equus caballus	ENSECAG00000014808	1 retrocopy	retro_ecab_37,
Felis catus	ENSFCAG00000025657	1 retrocopy	retro_fcat_24,
Homo sapiens	ENSG00000065150	1 retrocopy	retro_hsap_57,
Gorilla gorilla	ENSGGOG00000008742	1 retrocopy	retro_ggor_47,
Loxodonta africana	ENSLAFG00000016190	1 retrocopy	retro_lafr_22,
Myotis lucifugus	ENSMLUG00000006500	1 retrocopy	retro_mluc_295,
Mus musculus	ENSMUSG00000030662	2 retrocopies	retro_mmus_251, retro_mmus_3683,
Nomascus leucogenys	ENSNLEG00000007831	2 retrocopies	retro_nleu_1610, retro_nleu_2482,
Oryctolagus cuniculus	ENSOCUG00000003898	1 retrocopy	retro_ocun_143,
Otolemur garnettii	ENSOGAG00000007570	1 retrocopy	retro_ogar_169,
Pongo abelii	ENSPPYG00000005458	1 retrocopy	retro_pabe_172,
Pan troglodytes	ENSPTRG00000005984	2 retrocopies	retro_ptro_49, retro_ptro_745,
Pteropus vampyrus	ENSPVAG00000004516	1 retrocopy	retro_pvam_8,
Rattus norvegicus	ENSRNOG00000010989	1 retrocopy	retro_rnor_240,
Sus scrofa	ENSSSCG00000009509	1 retrocopy	retro_sscr_24,
Ictidomys tridecemlineatus	ENSSTOG00000011164	1 retrocopy	retro_itri_32,