RetrogeneDB ID: retro_ggor_1336

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 17:21865405..21866538(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ENSG00000110934
• Ensembl ID: ENSGGOG00000009423
• Aliases: None
• Description: None

Sequence

>retro_ggor_1336
TACTTCACCCAGTTCAGTGAGATTGAGGAGAGAATTGCCAAGTGGGGTTGAAAACTCGTGGATTATGATGGTGCCCAACA
TCACCTGGATGCAGTGCAGAATGCCAAGAAGAAAGATGAGGCCAAGACTGCCAAGGCAGAGGAAGAGTTCAACAAAGCCC
AGACTATGTTTGAAGATCTGAACCAAAAACTACTAGAGGAGCTGCCTATTCTTTATAATAGTCATATTGGCTGCTATGTG
ACCATCTTCCAAAACATTTCCAATTTGAGGGATGTCTTCTACAGGGAAATGAGCAAGCTGAACTGCAATCTCTATGAGGT
GATGAGCAAACTGCAGAAGCAACATTCCAATAAAGTCTTTGTGGTGAAGGGACTATCAAGCAGCAGCAGGCTCTCTTTAG
TCATTTATCCCCCAGTTCGAACATCTATGGCCTCCAGTCCTCTTACCTCACCTACTAGTCCCTCTACACTTTCCTTGAAG
AGTGAGAGTGAATCTGTCACAACAACTGAAGATCTGGCACCTGATGCAGCCCGGGGGAAGATAATTCTGAGATCAAGGAG
CACTTAGAAGATGAGGAAATAGAGAAGGAAGGATCTGACGCAAGCTCCTCTGAGGAAGAAGAGCCTCTACCAGCCTGCAG
TGGCCCTGCCTAGGCCCAGCCCTCTCCTACCATTGGGAGTGGCAAGTCCCAGGAGGAAGTTCTCCCTAGCTCCCCAGCTC
TATCACCAGGCAGAACCCTGAGCCCTTCAGGGCAGCCTTCATCATCTGCCACAGAAGTAGTCCTCCAAACCCGCACAGAA
AGTGAAGGATCTGAACAACCAAAGAAGAAAACCTATATCCAGAGGACCTCAGCACTCCCTAGTAGGCCTCCTCCACCCAG
AGCCACTCCAAACCCCAGGACCTCCTCAGGGAACATACCCTCCAGTCCTCCAGCCTCTGGAGGGGGTTCAACCACTGGCC
CTAGGGTCTCCTTGGGGACTGAGACTCCAAGTCCTAGGACCTCCCTAGAGTTCTCCCCTAATCCAGAACTACAAGAGAAG
CCAGTAAGAACTCCTGAGGTCAAAGAAAATGAAAACATCCACAATCAGAACCCCAAAGAACTTTGCACTTTTCCCACCTT
AATGACATCTCAG

Alignment

ORF - retro_ggor_1336 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.96 %
• Parental protein coverage: 70.26 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YVAQFSEIKERIAKRGRKLVDYDSARHHLEAVQNAKKKDEAKTAKAEEEFNKAQTVFEDLNQELLEELPI
          Y..QFSEI.ERIAK.G.KLVDYD.A.HHL.AVQNAKKKDEAKTAKAEEEFNKAQT.FEDLNQ.LLEELPI
Retrocopy YFTQFSEIEERIAKWG*KLVDYDGAQHHLDAVQNAKKKDEAKTAKAEEEFNKAQTMFEDLNQKLLEELPI

Parental  LYNSRIGCYVTIFQNISNLRDVFYREMSKLNHNLYEVMSKLEKQHSNKVFVVKGLSSSSRRSLVISPPVR
          LYNS.IGCYVTIFQNISNLRDVFYREMSKLN.NLYEVMSKL.KQHSNKVFVVKGLSSSSR.SLVI.PPVR
Retrocopy LYNSHIGCYVTIFQNISNLRDVFYREMSKLNCNLYEVMSKLQKQHSNKVFVVKGLSSSSRLSLVIYPPVR

Parental  TATVSSPLTSPTSPSTLSLKSESESVSATEDLAPDAAQG-EDNSEIKELLEEEEIEKEGSEASSSEEDEP
          T...SSPLTSPTSPSTLSLKSESESV..TEDLAPDAA.G.EDNSEIKE.LE.EEIEKEGS.ASSSEE.EP
Retrocopy TSMASSPLTSPTSPSTLSLKSESESVTTTEDLAPDAARG<EDNSEIKEHLEDEEIEKEGSDASSSEEEEP

Parental  LPACNGPAQAQPSPTTESAKSQEEVLPSSPAPSPGGALSPSGQPSSSAAEVVLRTRTASEGSEQPKKRAS
          LPAC.GPA.AQPSPT..S.KSQEEVLPSSPA.SPG..LSPSGQPSSSA.EVVL.TRT.SEGSEQPKK...
Retrocopy LPACSGPA*AQPSPTIGSGKSQEEVLPSSPALSPGRTLSPSGQPSSSATEVVLQTRTESEGSEQPKKKTY

Parental  IQRTSAPPSRPPPPRATASPRPSSGNIPSSPTASGGGSPTSPRASLRTGTPSPRTSLEVFPNPEPPEKPV
          IQRTSA.PSRPPPPRAT..PR.SSGNIPSSP.ASGGGS.T.PR.SL.T.TPSPRTSLE..PNPE..EKPV
Retrocopy IQRTSALPSRPPPPRATPNPRTSSGNIPSSPPASGGGSTTGPRVSLGTETPSPRTSLEFSPNPELQEKPV

Parental  RTPEAKENENIHNQNPEELCTSPTLMTSQ
          RTPE.KENENIHNQNP.ELCT.PTLMTSQ
Retrocopy RTPEVKENENIHNQNPKELCTFPTLMTSQ

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	0.05 RPM	3.26 RPM
SRP007412_cerebellum	0.00 RPM	0.95 RPM
SRP007412_heart	0.00 RPM	1.28 RPM
SRP007412_kidney	0.00 RPM	4.33 RPM
SRP007412_liver	0.11 RPM	10.18 RPM
SRP007412_testis	0.21 RPM	21.45 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_1336 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1336 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3192
Pan troglodytes	retro_ptro_2251
Pongo abelii	retro_pabe_2648
Macaca mulatta	retro_mmul_2013

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000110934	2 retrocopies	retro_hsap_2952, retro_hsap_3192,
Gorilla gorilla	ENSGGOG00000009423	1 retrocopy	retro_ggor_1336 ,
Loxodonta africana	ENSLAFG00000002387	1 retrocopy	retro_lafr_1163,
Nomascus leucogenys	ENSNLEG00000017774	1 retrocopy	retro_nleu_1636,
Pongo abelii	ENSPPYG00000004526	2 retrocopies	retro_pabe_2448, retro_pabe_2648,
Pan troglodytes	ENSPTRG00000004954	2 retrocopies	retro_ptro_2049, retro_ptro_2251,