RetrogeneDB ID: retro_ecab_345

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 15:16899445..16902387(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: IPO7
• Ensembl ID: ENSECAG00000015965
• Aliases: None
• Description: importin 7 [Source:HGNC Symbol;Acc:9852]

Sequence

>retro_ecab_345
GGTGTTATCTGTTTGAAAAATATGATAACACAGTATTGACCTGATCGGGAAACAGCACCAGGGGATATATCCGCTTATAC
TATTCCCGAAGAAGATCGACATTGTATTCGAGAAAATATTGTAGAAGCCATTATCTACTCTCCTGAACTTATCAGGGTAC
AACTTACTACTTGCATTCATCATATCATCAAACATGATTATCCAAGCCGCTGGGCTGCCATTGTGGACAAAATTGACTTT
TATCTTCAGTCTGATAACAGTGCTTGTTGGCTAGGAATTCTTCTTTGCCTTTACCAGCTTGTGAAAAATTATGAGTACAA
GAAACCAGAAGAATGGAATCCATTGGTGCAGCAATGCAGCATTTCCTGCCAATTCTAAAGGACCATTCTATCCAGCTTCT
TTCTGATCAGTCTGATCAATCTGTCCTCATTCAGAAAAAAATTTTCAAGATCTTCTTTGCTCTTGTTCAGTATACACTAC
CACTGGAGCTGATAAACCAACAGAACCTGACAGAATGGATAGAAATTTTAAAAACTGTTGTGAACAGGGATGTACCTAAT
GAAACACTTCAAGTTGAAGAAGATGATAGACCTGAGTTACTGTGGTGGAAATGTAAGAAGTGGGATTTACATATCTTAGC
AAGGCTTTTTGAAGGCTATGGAATCCCTGGCAATGTATGCAAGGAGTATAATGAATTTGCCGAAGTATTTCTGAAGGCGT
TTGCTGTTGGTGTCCAGCAAGTTTTATTGAAGGTGTTGTATCAGTACAAGGAAAAGCATATATGGCTCCTCGAGTTTTAC
AGCAGACATTAAATTATATTAATCAAGGAGTTTCTCATGCCCTCACCTGGAAGAATCTGAAGCCTCATATACAAGGCATT
ATCCAAGATGTTATTTTTCCATTGATGTGCTAGACAGATGCTGATGAGGAACTTGGGAGGAAGACCCTTATGAATATATA
CGCATGAAGTTTGATGTGTTTGAAGATTTCATTTCTCCTACCACTGCTGCCCAGACACTTTTGTTTACAGCCTGTAGTAA
GAGAAAAGAGGTGCTACAAAAGACTATGGGATTCTGCTACCAGATTCTTACTGAACCAAATGCCGATCCTCGAAAAAAAG
AAGGAGCCCTGCATATGGTTGGCTCTTTAGCTGAAATACTTTTGAAGAAAAAGATCTACAAAGATCAGATGGAATACATG
TTGCAGAATCATGTATTCCTTCTCTTCAGCAGTGAACTAGGCTACATGAGAGCAAGGGCTTGCTTGGTCCTTCATTATTT
TTGTGAAGTGAAGTTCAAAAGTGTCCAGAACCTGCAAACAGCTTTAGAGCTGACACGAAGATGTCTGATTGATGATAGGG
AAATGCCTGTGAAAGTGGAAGCTGCCATTGCACTTCAAGTGTTGATCAGCAATCAAGAAAAAGCTGAAGAATATATCACA
CCGTTCATCAGACCTGTAATGCAGGCTCTTCTTCATATTATAAGAGAAACAGAAAATGATGATCTTACCAATGTCATTCA
GAAAATGATCTGCGAGTATAGTGAAGAAGTTACTCCTATTGCAGTAGAAATGACCCAACATTTGGCAATGACATTTAATC
AAGTAATCCAGACTGGGCCAGATGAAGAAGGAAGTGATGACAAAGCAGTTACTGTTATGGGAATCCTGAATACCATCGAC
ACACTTCTTAGTGTAGTTGAAGATCATAAAGAGATAACCCAGCAGCTTGAGGCAATCTGCTTACAGGTCATTGGAACTGT
TTTACAACAGCGTGTCTTAGAATTCTATGAGGAGATCTCTTTAGCACATAGTTTGACATGTCAGCAGGTGTCTCTGCAGA
TATGGCAGCTAGTACCTCTGGTATTTGAAGTTTTTCAGCAAGATTGCTTTGATTACGTCACAGATATGATGCCTCTGCTC
CATAATTATGTAACAGTTGATACAGACACACTTCTGTCTGATACCAACTATCTTGAAATGATATACAGTATGTGCAAAAA
AGGTTCTTACAGGAGTTGCAGGAGAAGATGCAGAGTGCCATGCAGCAAAATTGTTAGAGGTCATCATTCTACAGTGCAAA
GGGCATGGCATTGATCAGTGAATTCCCTTATTTGTGGAAGCAGCTTTAGAGAGACTGACAAGAGAAGTGAAGACAAGTGA
ACTTCGAACAATGTGCCTGCAAGTTGCCATTGCAGCTTTGTATTATAATCCACACCTGCTTCTCAATACCTTAGAAAATC
TTCGCTTCCCTAATAATGTTGAACCAGTTACAAATCATTTTATCACACAGTGGCTTAATGATGTTGATTGTTTCTTGGGG
CTTCATGACAGAAAGATGTGTGTTCTGGGCCTGTGTGCTTTTATTGATATGGAACAAATACCACAAGTTTTAAATCAGGT
TTCTGGACAGATTTTTGCCAGCTTTTATCCTTTTATTTAATGGATTAAAAAGAGCTTATGCCTGCCATGCAGAACACGAG
AATGACAGTGACGACGATGATGAAGCTGAAGATGATGATGAAACGGAGGAACTGGGGAGTGATGAAGATGACATTGATGA
AGATGGGCGGGAATATTTGGAGATGCTGGCTAAACAAGCAGGTGAAGATGGAGATGATGAAGACTGGGAAGAAGATGATG
CTGAGGAGACTGCTCTGGAAGGCTATTCTACAATCATTGATGACGAAGATAATCCTGTTGATGAGTATCAGATATTTAAA
GCTATATTTCAAACTATACAAAGTCGTAATCCTGTGTGGTATCAGGCTCTGACTCATGGTCTTAATGAAGAACAAAGAAA
ACAGTTACAGGATATAGCAACTCTGGCTGATCAAAGAGCAGCCCGTGAATCCAAAATGATAGAAAAGCGTGGAGGATACA
AATTCAGTGCTCCAGTTGTGCCAAATTCTTTCAATTTTGGAGGCCCAGCACCAGGGATGAAT

Alignment

ORF - retro_ecab_345 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.94 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  GVIYLKNMITQYWPDRETAPGDISPYTIPEEDRHCIRENIVEAIIHSPELIRVQLTTCIHHIIKHDYPSR
          GVI.LKNMITQY.PDRETAPGDIS.YTIPEEDRHCIRENIVEAII.SPELIRVQLTTCIHHIIKHDYPSR
Retrocopy GVICLKNMITQY*PDRETAPGDISAYTIPEEDRHCIRENIVEAIIYSPELIRVQLTTCIHHIIKHDYPSR

Parental  WTAIVDKIGFYLQSDNSACWLGILLCLYQLVKNYEYKKPEERNPLV-AAMQHFLPVLKDRFIQLLSDQSD
          W.AIVDKI.FYLQSDNSACWLGILLCLYQLVKNYEYKKPEE.NPLV.AAMQHFLP.LKD..IQLLSDQSD
Retrocopy WAAIVDKIDFYLQSDNSACWLGILLCLYQLVKNYEYKKPEEWNPLV<AAMQHFLPILKDHSIQLLSDQSD

Parental  QSVLIQKQIFKIFYALVQYTLPLELINQQNLTEWIEILKTVVNRDVPNETLQVEEDDRPELPWWKCKKWA
          QSVLIQK.IFKIF.ALVQYTLPLELINQQNLTEWIEILKTVVNRDVPNETLQVEEDDRPEL.WWKCKKW.
Retrocopy QSVLIQKKIFKIFFALVQYTLPLELINQQNLTEWIEILKTVVNRDVPNETLQVEEDDRPELLWWKCKKWD

Parental  LHILARLFERYGSPGNVSKEYNEFAEVFLKAFAVGVQQVLLKVLYQYKEKQ-YMAPRVLQQTLNYINQGV
          LHILARLFE.YG.PGNV.KEYNEFAEVFLKAFAVGVQQVLLKVLYQYKEK..YMAPRVLQQTLNYINQGV
Retrocopy LHILARLFEGYGIPGNVCKEYNEFAEVFLKAFAVGVQQVLLKVLYQYKEKH<YMAPRVLQQTLNYINQGV

Parental  SHALTWKNLKPHIQGIIQDVIFPLMCYTDADEEL-WQEDPYEYIRMKFDVFEDFISPTTAAQTLLFTACS
          SHALTWKNLKPHIQGIIQDVIFPLMC.TDADEEL.W.EDPYEYIRMKFDVFEDFISPTTAAQTLLFTACS
Retrocopy SHALTWKNLKPHIQGIIQDVIFPLMC*TDADEEL<WEEDPYEYIRMKFDVFEDFISPTTAAQTLLFTACS

Parental  KRKEVLQKTMGFCYQILTEPNADPRKKDGALHMIGSLAEILLKKKIYKDQMEYMLQNHVFPLFSSELGYM
          KRKEVLQKTMGFCYQILTEPNADPRKK.GALHM.GSLAEILLKKKIYKDQMEYMLQNHVF.LFSSELGYM
Retrocopy KRKEVLQKTMGFCYQILTEPNADPRKKEGALHMVGSLAEILLKKKIYKDQMEYMLQNHVFLLFSSELGYM

Parental  RARACWVLHYFCEVKFKSDQNLQTALELTRRCLIDDREMPVKVEAAIALQVLISNQEKAKEYITPFIRPV
          RARAC.VLHYFCEVKFKS.QNLQTALELTRRCLIDDREMPVKVEAAIALQVLISNQEKA.EYITPFIRPV
Retrocopy RARACLVLHYFCEVKFKSVQNLQTALELTRRCLIDDREMPVKVEAAIALQVLISNQEKAEEYITPFIRPV

Parental  MQALLHIIRETENDDLTNVIQKMICEYSEEVTPIAVEMTQHLAMTFNQVIQTGPDEEGSDDKAVTAMGIL
          MQALLHIIRETENDDLTNVIQKMICEYSEEVTPIAVEMTQHLAMTFNQVIQTGPDEEGSDDKAVT.MGIL
Retrocopy MQALLHIIRETENDDLTNVIQKMICEYSEEVTPIAVEMTQHLAMTFNQVIQTGPDEEGSDDKAVTVMGIL

Parental  NTIDTLLSVVEDHKEITQQLEGICLQVIGTVLQQHVLEFYEEIFSLAHSLTCQQVSPQMWQLLPLVFEVF
          NTIDTLLSVVEDHKEITQQLE.ICLQVIGTVLQQ.VLEFYEEI.SLAHSLTCQQVS.Q.WQL.PLVFEVF
Retrocopy NTIDTLLSVVEDHKEITQQLEAICLQVIGTVLQQRVLEFYEEI-SLAHSLTCQQVSLQIWQLVPLVFEVF

Parental  QQDGFDYFTDMMPLLHNYVTVDTDTLLSDTKYLEMIYSMC-KKVLTGVAGEDAECHAAKLLEVIILQCKG
          QQD.FDY.TDMMPLLHNYVTVDTDTLLSDT.YLEMIYSMC.KKVLTGVAGEDAECHAAKLLEVIILQCKG
Retrocopy QQDCFDYVTDMMPLLHNYVTVDTDTLLSDTNYLEMIYSMC>KKVLTGVAGEDAECHAAKLLEVIILQCKG

Parental  RGIDQCIPLFVEAALERLTREVKTSELRTMCLQVAIAALYYNPHLLLNTLENLRFPNNVEPVTNHFITQW
          .GIDQ.IPLFVEAALERLTREVKTSELRTMCLQVAIAALYYNPHLLLNTLENLRFPNNVEPVTNHFITQW
Retrocopy HGIDQ*IPLFVEAALERLTREVKTSELRTMCLQVAIAALYYNPHLLLNTLENLRFPNNVEPVTNHFITQW

Parental  LNDVDCFLGLHDRKMCVLGLCALIDMEQIPQVLNQVSGQI-LPAFILLFNGLKRAYACHAEHENDSDDDD
          LNDVDCFLGLHDRKMCVLGLCA.IDMEQIPQVLNQVSGQI.LPAFILLFNGLKRAYACHAEHENDSDDDD
Retrocopy LNDVDCFLGLHDRKMCVLGLCAFIDMEQIPQVLNQVSGQI>LPAFILLFNGLKRAYACHAEHENDSDDDD

Parental  EAEDDDETEELGSDEDDIDEDGQEYLEILAKQAGEDGDDEDWEEDDAEETALEGYSTIIDDEDNPVDEYQ
          EAEDDDETEELGSDEDDIDEDG.EYLE.LAKQAGEDGDDEDWEEDDAEETALEGYSTIIDDEDNPVDEYQ
Retrocopy EAEDDDETEELGSDEDDIDEDGREYLEMLAKQAGEDGDDEDWEEDDAEETALEGYSTIIDDEDNPVDEYQ

Parental  IFKAIFQTIQSRNPVWYQALTHGLNEEQRKQLQDIATLADQRRAAHESKMIEKHGGYKFSAPVVPSSFNF
          IFKAIFQTIQSRNPVWYQALTHGLNEEQRKQLQDIATLADQ.RAA.ESKMIEK.GGYKFSAPVVP.SFNF
Retrocopy IFKAIFQTIQSRNPVWYQALTHGLNEEQRKQLQDIATLADQ-RAARESKMIEKRGGYKFSAPVVPNSFNF

Parental  GGPAPGMN
          GGPAPGMN
Retrocopy GGPAPGMN

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	0.47 RPM	44.27 RPM
SRP021940_cerebellum	0.10 RPM	20.41 RPM
SRP021940_embryo	0.49 RPM	59.84 RPM
SRP021940_placental_villous	0.53 RPM	43.06 RPM
SRP021940_synovial_membrane	0.22 RPM	28.25 RPM
SRP021940_testis	0.13 RPM	10.10 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_345 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_345 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_345 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000015965	1 retrocopy	retro_ecab_345 ,
Homo sapiens	ENSG00000205339	1 retrocopy	retro_hsap_501,
Gorilla gorilla	ENSGGOG00000002260	1 retrocopy	retro_ggor_973,
Macaca mulatta	ENSMMUG00000023636	1 retrocopy	retro_mmul_437,
Pongo abelii	ENSPPYG00000029652	1 retrocopy	retro_pabe_1036,