RetrogeneDB ID: retro_ecab_37

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 23:27294517..27297835(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000006243
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: IPO5
• Ensembl ID: ENSECAG00000014808
• Aliases: IPO5, RANBP5
• Description: importin 5 [Source:HGNC Symbol;Acc:6402]

Sequence

>retro_ecab_37
ATGGCGGCGACCGGGTCTGCAGGGATACCGGCGACCGTGTCGGGAAAGCAAGAGTTTTACCAGCTTTTGAAGAACCTGAT
AAATCCAAGCTGTATGGTCCGGAGGCAGGCAGAGGAAATCTATGAAAATATCCCAGGTCTGTGTAAGACTACATTCCTCT
TAGATGCTGTCAGAAATAGAAGAGCAGGTTATGAGGTGAGACAAATGGCAGCCGCACTGCTACGACGGCTTTTGTCCTCT
GGGTTTGAGGAAGTCTATCCAAATCTCCCCTCTGATGTTCAGAGGGACGTCAAGATTGAACTGATCCTGGCTGTTAAATT
AGAAACACATGCTAGCATGAGGAAAAAACTTTGTGATATTTTTGCAGTGCTGGCCAGGAATTTGATAGACGAGGATGGCA
CTAACCACTGGCCTGAAGGTCTGAAGTTCCTTATTGATTCAATCTACTCTAAAAATGTGGTTCTCTGGGAGGTTGCACTT
CACGTTTTCTGGCACTTTCCTGGGATTTTTGGGAACCAAGAGCGGCACGATTTGGATATCATCAAACGGTTGTTGGACCA
GTGTATTCAAGATCAAGAACATCCAGCAATCAGGACGTTATCTGCTAGAGCCGCCGCTGCATTTGTACTTGCTAATGAGA
ATAATATTGCTCTTTTCAAAGACTTTGCAGACTTGCTTCCTGGAATCTTACAGGCTGTGAATGATTCATGCTACCAGGAT
GATGATTCTGTGCTAGAATCCCTTGTTGAGATTGCAGATACTGTACCTAAATACTTGGGTCCTTATTTAGAAGATACTCT
GCAGTTGAGTCTAAAGTTGTGTGGAGACTCTAGACTTAGTAATCTGCAACGCCAACTGGCCCTTGAAGTTATAGTGACCT
TGTCTGAAACTGCAACCCCAATGTTAAAAAAACATACAAATATTATTGCACAAGCAATTCCTCATATATTAGCAATGATG
GTTGATCTACAAGATGATGAGGACTGGGTAAATGCTGATGAAATGGAAGAAGATGATTTTGACAGCAATGCAGTTGCTGC
TGAGAGTGCACTAGACAGATTGGCTTGTGGGCTCGGAGGAAAACTTGTTTTACCAATGACTAAGGAGCATATCATGCAGA
TGCTTCAGAGCCCAGACTGGAAATATCGACATGCTGGATTAATGGCCTTATCTGCCATTGGAGAAGGATGCCATCAGCAA
ATGGAATCAATTCTAGATGAAACAGTTAACTCTGTTTTGCTTTTTCTTCAGGATCCGCATCCTAGGGTGAGGGCTGCAGC
CTGTACTACACTTGGACAGATGGCCACAGATTTTGCACCTAACTTCCAAAAGAAATTCCATGAAACAGTGATTGCAGCTC
TGTTGCGTACCATGGAGAATCAAGGTAATCAGCGTGTGCAATCACATGCAGCTTCCGCGCTTATTATTTTTATTGAAGAC
TGCCCCAAATCATTGCTAGTTCTATATTTGGATAGTATGGTGAGAAATCTGCATTCCATCTTGGTGATTAAACTTCAAGA
GTTGATTCGGAATGGAACTAAGTTGGCCTTGGAACAGCTTGTGACAACCATTGCCTCAGTTGCGGATACTATAGAAGAAA
AGTTTGTTCCCTATTATGACATATTTATGCCCTCACTAAAGCACATTGTTGAACTCGCTGTTCAAAAGGAACTCAAGCTT
CTGAAAGGAAAAACTATTGAATGTATTAGTCATGTTGGTCTTGCTGTTGGGAAGGAAAAATTTATGCAGGATGCATCAAA
TGTGATGCAGCTATTATTGAAGACACAATCAGACTTAAATAATATGGAAGATGATGACCCTCAGACCTCTTACATGATTT
CAGCATGGGCTCGAATGTGTAAAATTCTTGGAAATGATTTTCAGCAGTACCTTCCATTGGTTATTGAGCCTCTTATTAAG
ACTGCTTCAGCTAAACCTGATGTCGCTCTCTTAGACACACAAGACGTGGAGAATATGAGTGATGATGATGGATGGCAATT
TGTAAATCTTGGAGACCAGCAAAGTTTTGGAATTAAAACTTCAGGACTTGAAGCAAAAGCAACTGCTTGCCAGATGTTGG
TTTACTATGCTAAGGAGTTAAGGGAAGGCTTTGTGGAATATACAGAACAAGTTGTAAAGCTGATGGTTCCTTTACTGAAA
TTTTATTTCCATGACAATGTTCGAGTGGCAGCAGCAGAGTCCATGCCTTTTCTCCTGGAATGTGCAAGAACTCGTGGCCC
AGAGTATCTTGCACAGATGTGGCAATTCATATGTGATCCCTTAATCAAGGCTATTGGGACTGAACCTGATACAGATGTAC
TGTCAGAAATAATGAATTCTTTTGCAAAGTCCATTGAAGTAATGGGAGATGGGTGCCTTAATGATGAACACTTGGAAGAA
CTGGGAGAAATATTGAAAGCAAAACTTGAAGGGCACTTTAAAAATCAAGAATTGAGACAGGTTAAAAGACAGGAAGAAAA
CTATGACCAGCAGGTTGAAATGTCTCTGCAAGATGAAGATGAATGTGATGTTTATATTCTGACCAAAGTATCAGATATTT
TGCACTCATTATTTAGTACTTATAAGGAAAAGATTTTACCATGGTTTGAACAGCTGCTCCCATTAATTGTAAATCTAATT
TGTTCCAGTAGGCCATGGCCAGACAGACAGTGGGGATTGTGCATATTTGACGATATCATAGAGCACTGCAGTCCAACCTC
TTTTAAATATGTAGAATATTTTCGGTGGCCAATGCTACTAAATATGCGAGACAACAACCCTGAAGTCAGGCAAGCTGCTG
CTTATGGCCTGGGTGTTATGGCACAGTTTGGTGGAGATGACTATCGTTCTTTATGTTCAGAAGCTGTTCCACTGCTGGTA
AAAGTTATTAAGTGTGCAAATTCCAAAACCAAAAAAAATGTCATTGCTACAGAGAACTGTATCTCAGCAGTAGGGAAGAT
TTTGAGGTTTAAGCCTAACTGTGTAAATGTAGATGAAGTTCTTCCACACTGGTTATCATGGCTTCCACTGCATGAAGATA
AAGAGGAAGCTATTCAGACTTTGAGTTTTCTCTGTGACTTAATTGAAAGTAACCATCCAGTTGTACTTGGTCCAAATAAT
TCCAATCTTCCCAAAATAATCAGTATAATTGCAGAAGGAAAAATTAATGAGACTATTAACTATGAAGATCCTTGTGCCAA
ACGCCTAGCTAATGTCGTGCGTCAGGTACAGACTTCTGAAGAACTCTGGTTGGAATGCGTATCCCAACTTGATAATGAGC
AGCAGGAAGCCTTACAGGAGTTGCTAAATTTTGCTTGA

Alignment

ORF - retro_ecab_37 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.24 %
• Parental protein coverage: 99.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VRKQAEETYENIPGQSKITFLLQAIRNTTAAEEARQMAAVLLRRLLSSAFDEVYPTLPSDVQTAIKSELL
          VR.QAEE.YENIPG..K.TFLL.A.RN..A..E.RQMAA.LLRRLLSS.F.EVYP.LPSDVQ...K.EL.
Retrocopy VRRQAEEIYENIPGLCKTTFLLDAVRNRRAGYEVRQMAAALLRRLLSSGFEEVYPNLPSDVQRDVKIELI

Parental  MIIQMETQSSMRKKICDIAAELARNLIDEDGNNQWPEGLKFLFDSVSSQNMGLREAALHIFWNFPGIFGN
          .....ET..SMRKK.CDI.A.LARNLIDEDG.N.WPEGLKFL.DS..S.N..L.E.ALH.FW.FPGIFGN
Retrocopy LAVKLETHASMRKKLCDIFAVLARNLIDEDGTNHWPEGLKFLIDSIYSKNVVLWEVALHVFWHFPGIFGN

Parental  QQQHYLDVIKRMLVQCMQDQEHPSIRTLSARATAAFILANEHNVALFKHFADLLPGFLQAVNDSCYQNDD
          Q..H.LD.IKR.L.QC.QDQEHP.IRTLSARA.AAF.LANE.N.ALFK.FADLLPG.LQAVNDSCYQ.DD
Retrocopy QERHDLDIIKRLLDQCIQDQEHPAIRTLSARAAAAFVLANENNIALFKDFADLLPGILQAVNDSCYQDDD

Parental  SVLKSLVEIADTVPKYLRPHLEATLQLSLKLCGDTSLNNMQRQLALEVIVTLSETAAAMLRKHTNIVAQT
          SVL.SLVEIADTVPKYL.P.LE.TLQLSLKLCGD..L.N.QRQLALEVIVTLSETA..ML.KHTNI.AQ.
Retrocopy SVLESLVEIADTVPKYLGPYLEDTLQLSLKLCGDSRLSNLQRQLALEVIVTLSETATPMLKKHTNIIAQA

Parental  IPQMLAMMVDLEEDEDWANADELEDDDFDSNAVAGESALDRMACGLGGKLVLPMIKEHIMQMLQNPDWKY
          IP..LAMMVDL..DEDW.NADE.E.DDFDSNAVA.ESALDR.ACGLGGKLVLPM.KEHIMQMLQ.PDWKY
Retrocopy IPHILAMMVDLQDDEDWVNADEMEEDDFDSNAVAAESALDRLACGLGGKLVLPMTKEHIMQMLQSPDWKY

Parental  RHAGLMALSAIGEGCHQQMEGILNEIVNFVLLFLQDPHPRVRYAACNAVGQMATDFAPGFQKKFHEKVIA
          RHAGLMALSAIGEGCHQQME.IL.E.VN.VLLFLQDPHPRVR.AAC...GQMATDFAP.FQKKFHE.VIA
Retrocopy RHAGLMALSAIGEGCHQQMESILDETVNSVLLFLQDPHPRVRAAACTTLGQMATDFAPNFQKKFHETVIA

Parental  ALLQTMEDQGNQRVQAHAAAALINFTEDCPKSLLIPYLDNLVKHLHSIMVLKLQELIQKGTKLVLEQVVT
          ALL.TME.QGNQRVQ.HAA.ALI.F.EDCPKSLL..YLD..V..LHSI.V.KLQELI..GTKL.LEQ.VT
Retrocopy ALLRTMENQGNQRVQSHAASALIIFIEDCPKSLLVLYLDSMVRNLHSILVIKLQELIRNGTKLALEQLVT

Parental  SIASVADTAEEKFVPYYDLFMPSLKHIVENAVQKELRLLRGKTIECISLIGLAVGKEKFMQDASDVMQLL
          .IASVADT.EEKFVPYYD.FMPSLKHIVE.AVQKEL.LL.GKTIECIS..GLAVGKEKFMQDAS.VMQLL
Retrocopy TIASVADTIEEKFVPYYDIFMPSLKHIVELAVQKELKLLKGKTIECISHVGLAVGKEKFMQDASNVMQLL

Parental  LKTQTDFSDMEDDDPQISYMISAWARMCKILGKEFQQYLPVVMGPLMKTASIKPEVALLDTQDMENMSDD
          LKTQ.D...MEDDDPQ.SYMISAWARMCKILG..FQQYLP.V..PL.KTAS.KP.VALLDTQD.ENMSDD
Retrocopy LKTQSDLNNMEDDDPQTSYMISAWARMCKILGNDFQQYLPLVIEPLIKTASAKPDVALLDTQDVENMSDD

Parental  DGWEFVNLGDQQSFGIKTAGLEEKSTACQMLVCYAKELKEGFVEYTEQVVKLMVPLLKFYFHDGVRVAAA
          DGW.FVNLGDQQSFGIKT.GLE.K.TACQMLV.YAKEL.EGFVEYTEQVVKLMVPLLKFYFHD.VRVAAA
Retrocopy DGWQFVNLGDQQSFGIKTSGLEAKATACQMLVYYAKELREGFVEYTEQVVKLMVPLLKFYFHDNVRVAAA

Parental  ESMPLLLECARVRGPEYLTQMWHFMCDALIKAIGTEPDSDVLSEIMHSFAKCIEVMGDGCLNNEHFEELG
          ESMP.LLECAR.RGPEYL.QMW.F.CD.LIKAIGTEPD.DVLSEIM.SFAK.IEVMGDGCLN.EH.EELG
Retrocopy ESMPFLLECARTRGPEYLAQMWQFICDPLIKAIGTEPDTDVLSEIMNSFAKSIEVMGDGCLNDEHLEELG

Parental  GILKAKLEEHFKNQELRQVKRQDEDYDEQVEESLQDEDDNDVYILTKVSDILHSIFSSYKEKVLPWFEQL
          .ILKAKLE.HFKNQELRQVKRQ.E.YD.QVE.SLQDED..DVYILTKVSDILHS.FS.YKEK.LPWFEQL
Retrocopy EILKAKLEGHFKNQELRQVKRQEENYDQQVEMSLQDEDECDVYILTKVSDILHSLFSTYKEKILPWFEQL

Parental  LPLIVNLICPHRPWPDRQWGLCIFDDVIEHCSPASFKYAEYFLRPMLQYVCDNSPEVRQAAAYGLGVMAQ
          LPLIVNLIC..RPWPDRQWGLCIFDD.IEHCSP.SFKY.EYF..PML....DN.PEVRQAAAYGLGVMAQ
Retrocopy LPLIVNLICSSRPWPDRQWGLCIFDDIIEHCSPTSFKYVEYFRWPMLLNMRDNNPEVRQAAAYGLGVMAQ

Parental  YGGDNYRPFCTEALPLLVRVIQSADSKTKENVNATENCISAVGKIMKFKPDCVNVEEVLPHWLSWLPLHE
          .GGD.YR..C.EA.PLLV.VI..A.SKTK.NV.ATENCISAVGKI..FKP.CVNV.EVLPHWLSWLPLHE
Retrocopy FGGDDYRSLCSEAVPLLVKVIKCANSKTKKNVIATENCISAVGKILRFKPNCVNVDEVLPHWLSWLPLHE

Parental  DKEEAVQTFSYLCDLIESNHPIVLGPNNTNLPKIFSIIAEGEMHEAIKHEDPCAKRLANVVRQVQTSGGL
          DKEEA.QT.S.LCDLIESNHP.VLGPNN.NLPKI.SIIAEG...E.I..EDPCAKRLANVVRQVQTS..L
Retrocopy DKEEAIQTLSFLCDLIESNHPVVLGPNNSNLPKIISIIAEGKINETINYEDPCAKRLANVVRQVQTSEEL

Parental  WTECIAQLSPEQQAAIQELLNSA
          W.EC..QL..EQQ.A.QELLN.A
Retrocopy WLECVSQLDNEQQEALQELLNFA

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
SRP021940_articular_cartilage	10.21 RPM	126.50 RPM
SRP021940_cerebellum	5.61 RPM	114.04 RPM
SRP021940_embryo	22.53 RPM	212.07 RPM
SRP021940_placental_villous	9.14 RPM	116.43 RPM
SRP021940_synovial_membrane	6.70 RPM	103.19 RPM
SRP021940_testis	1.73 RPM	863.94 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_37 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_37 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_37 has 0 orthologous retrocopies within eutheria group .

---

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,