RetrogeneDB ID: retro_ggor_1078

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 14:1646877..1648691(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: XPO6
• Ensembl ID: ENSGGOG00000005609
• Aliases: None
• Description: None

Sequence

>retro_ggor_1078
ATGGCATCTGAAGAAGCCTCTCTCAGAGCATTGGAAAGGCTGATGACAGAACTTTTTCACGATGGTACGACCAATGAAAG
AAAACGTGAGATAGAGGAGCTTCTTAATAACTTTGCCCAGCAAATAGGAGCCTGGATATTCTTCCTGTACTTTCTCTCCA
GCACTAGGAATGGCTATGTAATGATGTACAGTTTAACAGTTTTTGAGAATCTGATCAATAAAATGTGGCTTGGGGTCCCA
TCTTAGGATGAGATGGAAATCCACAGCTGACTGCCCAAACTCCTTTTGGCTCACCATAAAACCTTTCCTTACTTTATCCA
GAGCAAGCTCTGCAAAGTTATTGTTGATATTGGACGTCAGGATTGGCCCATGTTCTACCATGACTTTTTTACTAACATTT
TGCAGTTGAACCAATCCCCTGTGACAACCCCCCTTGGGCCGATCATGTTGAAAACAATTTCAGAGGAGCTGGCTTGTCCC
CATGAGGACCTCAGTGTGGCTTGGAAGGAGGAGTTGCAGAAGCTGCTACTGGACCAGGTGCAGACAGTGCTTGGACTACT
GACGGGTATCTTGGAGACTGTCTGGGACAAACACAGTGTTACTGCTGCCACTCCACCACCCTCCCCGACCTCAGGAGAAA
GTGGTGACTTACTGAGTAACCTGTTGCAGAGTCCTAGTTCAGCCAAACTGTTGAATCAGCCAATTCCCATCCTTGATATG
GTGAGTGAGTATATCTGTTCCCTGGCCTTGGAGTGCCTGGCCCATCTGTTCAGTTGGATTCCTCTGTCTGCCGGCATCAC
CCCATCCCTCCTTACCACCACCTTCCACTTTGCATGATTTGGCTGTGACATCCGTGCCAGAAAGATGGCGTCAGTTAACG
GCAGCAGCCAGAACTGTGTCTCGGTTCAGGAGCGGAGCCAGCTGGGGGTCCTGGCCATGTCCTGCATCAATGAACTCATT
TCCAAGAGCTGTGTGCCGATAGAATTCGAGGAGTATTTACTGCTTATGTTCCAGCAGACTTTCTACCTCCTGCAGAAAAT
CACCAAGGATAACAATGCCCACACAGTGAAGAGCAGGCTAGAAGAGCTCGATGAGAGCTTTATTGAGAAGTTTACTGACT
TTCTTTGGCTCTTTGTGAGTGTTCACCTAAGAAGAATCGAGTCTTACTCCCAGTTCCCTGTGGCGGAGTTTTTGACACTT
TTGTTCAAGCACACATTTCATCAGCCTACTCATGAAGGTTAATTATCTTGTTTGGATAACTAGACACTCTTTTTGGACTA
TCTGACAAATAAAATTAAAAGTCATCTTGGAGACAAGGAAGCAGTTCTCAACAGGTACGAAGATGCCCTGGTGCTCCTCC
CCACAGAGGTGTTGAATCAAATCCAGTTCAGATACAACCAGGCCAGCCGGAGGAGTTGGATGACGAGACTCTGGATGACG
ATCAGCAGACGGAGTGACAGCGGTACTTATGGCAGAGCTTGGAGGTGGTGGCCAAAGTGATGGAGCTCCTGCCCACGCAC
GCCTTGTCCACACTGTTCCCAGTTCTTCAGGGCAATTTAGAAGTTTATTTGGGATTACAGCAATTTATAGTTACTTCAGG
GTCAGGACATAGGTTGAACATCATGGCGGAGAATGACTGCCGGTGGCTGCACTGCTCCCTGAGAGACTTGAGCTCCCTGC
TGCAGGCCATGGGCCACCTGGCTGGGTACTTTATTAGGGATGTGTTTGCTGCATGGTTCAATGATGCCCTCACAGTCGTG
GAGAGGTTGGTCAAAGTCACTCTGTACGGATCTCAGATAAAGTTGTACAACATT

Alignment

ORF - retro_ggor_1078 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.78 %
• Parental protein coverage: 53.78 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASEEASLRALESLMTEFFHDCTTNERKREIEELLNNFAQQIGAWRFCLYFLSSTRNDYVMMYSLTVFEN
          MASEEASLRALE.LMTE.FHD.TTNERKREIEELLNNFAQQIGAW.F.LYFLSSTRN.YVMMYSLTVFEN
Retrocopy MASEEASLRALERLMTELFHDGTTNERKREIEELLNNFAQQIGAWIFFLYFLSSTRNGYVMMYSLTVFEN

Parental  LINKMWLGVPSQDKMEIRSCLPKLLLAHHKTLPYFIRNKLCKVIVDIGRQDWPMFYHDFFTNILQLIQSP
          LINKMWLGVPS.D.MEI.S.LPKLLLAHHKT.PYFI..KLCKVIVDIGRQDWPMFYHDFFTNILQL.QSP
Retrocopy LINKMWLGVPS*DEMEIHS*LPKLLLAHHKTFPYFIQSKLCKVIVDIGRQDWPMFYHDFFTNILQLNQSP

Parental  VTTPLGLIMLKTTSEELACPREDLSVARKEELRKLLLDQVQTVLGLLTGILETVWDKHSVTAATPPPSPT
          VTTPLG.IMLKT.SEELACP.EDLSVA.KEEL.KLLLDQVQTVLGLLTGILETVWDKHSVTAATPPPSPT
Retrocopy VTTPLGPIMLKTISEELACPHEDLSVAWKEELQKLLLDQVQTVLGLLTGILETVWDKHSVTAATPPPSPT

Parental  SGESGDLLSNLLQSPSSAKLLNQPIPILDVESEYICSLALECLAHLFSWIPLSASITPSLLTTIFHFARF
          SGESGDLLSNLLQSPSSAKLLNQPIPILD..SEYICSLALECLAHLFSWIPLSA.ITPSLLTT.FHFA.F
Retrocopy SGESGDLLSNLLQSPSSAKLLNQPIPILDMVSEYICSLALECLAHLFSWIPLSAGITPSLLTTTFHFA*F

Parental  GCDIRARKMASVNGSSQNCVSGQERGRLGVLAMSCINELMSKNCVPMEFEEYLLRMFQQTFYLLQKITKD
          GCDIRARKMASVNGSSQNCVS.QER..LGVLAMSCINEL.SK.CVP.EFEEYLL.MFQQTFYLLQKITKD
Retrocopy GCDIRARKMASVNGSSQNCVSVQERSQLGVLAMSCINELISKSCVPIEFEEYLLLMFQQTFYLLQKITKD

Parental  NNAHTVKSRLEELDESYIEKFTDFLRLFVSVHLRRIESYSQFPVVEFLTLLFKYTFHQPTHEGYCSCLDI
          NNAHTVKSRLEELDES.IEKFTDFL.LFVSVHLRRIESYSQFPV.EFLTLLFK.TFHQPTHEG.......
Retrocopy NNAHTVKSRLEELDESFIEKFTDFLWLFVSVHLRRIESYSQFPVAEFLTLLFKHTFHQPTHEG*LXXXXX

Parental  WTLFLDYLTSKIKSRLGDKEAVLNRYEDALVLLLTEVLNRIQFRYNQA-QLEELDDETLDDDQQTEWQRY
          ..........KIKS.LGDKEAVLNRYEDALVLL.TEVLN.IQFRYNQA.Q.EELDDETLDDDQQTE.QRY
Retrocopy XXXXXXXXXNKIKSHLGDKEAVLNRYEDALVLLPTEVLNQIQFRYNQA<QPEELDDETLDDDQQTE*QRY

Parental  LRQSLEVVAKVMELLPTHAFSTLFPVLQDNLEVYLGLQQFIVTSGSGHRLNITAENDCRRLHCSLRDLSS
          L.QSLEVVAKVMELLPTHA.STLFPVLQ.NLEVYLGLQQFIVTSGSGHRLNI.AENDCR.LHCSLRDLSS
Retrocopy LWQSLEVVAKVMELLPTHALSTLFPVLQGNLEVYLGLQQFIVTSGSGHRLNIMAENDCRWLHCSLRDLSS

Parental  LLQAVGRLAEYFIGDVFAARFNDALTVVERLVKVTLYGSQIKLYNI
          LLQA.G.LA.YFI.DVFAA.FNDALTVVERLVKVTLYGSQIKLYNI
Retrocopy LLQAMGHLAGYFIRDVFAAWFNDALTVVERLVKVTLYGSQIKLYNI

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
SRP007412_brain_prefrontal_cortex	0.00 RPM	74.14 RPM
SRP007412_cerebellum	0.00 RPM	62.37 RPM
SRP007412_heart	0.00 RPM	14.92 RPM
SRP007412_kidney	0.00 RPM	44.73 RPM
SRP007412_liver	0.00 RPM	41.52 RPM
SRP007412_testis	0.10 RPM	183.79 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_1078 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1078 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1390
Pan troglodytes	retro_ptro_954

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000169180	1 retrocopy	retro_hsap_1390,
Gorilla gorilla	ENSGGOG00000005609	1 retrocopy	retro_ggor_1078 ,
Pan troglodytes	ENSPTRG00000007919	1 retrocopy	retro_ptro_954,