RetrogeneDB ID: retro_ggor_586

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 10:71355752..71356828(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000023215
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TRAF6
• Ensembl ID: ENSGGOG00000005854
• Aliases: None
• Description: None

Sequence

>retro_ggor_586
ATAAGTCTGCTAAACTGTGAAAACAGCTGTGGATCCAGCCAGTCTCAAAGTGACTACTGTGTGGCCATGGCCAGCTCCTG
TAGCGCGGCAACAAAAAATGATAGTGTGGGCAGAACTGCCAGCACGGGGAACCTCTCCAGCTCCTTTATGGAGGAGATCC
AGGGATATGATGCAGAGTTTGGCCCACCCCTGGAAAGCAAGTATGAATGCCCCATCTGCTTGATGGCATTACGAGAAGCA
GTGCAAACGCCATGCAGCCATAGGTTCTGCAAAGCCTGCATCATAAAATCAATAAGGGATGCAGGTCACAAATATCCAGT
TGACAATGAAATACTGCTGGAAAATAAACTATTTCCAGACAATTTTGCAAAACATGAGATTCTTTCTCTGATAGTGAAGT
GTCCAAATGAAGGTTGTTTGCACAAGATGGAACTGAGACATCTTGAAGATCATCAAACACATTGTGAGTTTGCTCTTATG
GATTGTCCCCAATGCCAGCCTCCCTTCCAAAAATTCCATATTAATATTCACATTCTGAAGGGTTGTCCAAGGAGGCAGGT
ATCTTGTGACAACTGTGCTGCATCAATGTCATTTGAAGATAAAAAGATCCATGACCAGAACTGTCCTTTGGCAAATGTCA
TCTGTGAGTACTGCAATACTATACTCATCAGAGAACAGATGCCTAACTTTATGACCTAGACCGCCCTACAGCCCCAATTC
CATGCACATTCCGTACTTTTCGTAGCCATGAAAAGATGCGGAGGAATCACTTGGCACGCCACCTACAAGAGAACACCCAA
TCAAACATGAGAATGTTGGCCCAGGCTGTTCATAGTTTGAGCCTTATAACCGAGTCTGGGTATATCTCAGAGGTCCGGAA
TTTCCAGGAAAGTATTCACCAGTTAGAGGGTCGCCTTGTAAGACAAGGTCATCAAATCCGGGAGCTGACTGATAAAATGG
AAACTCAGAGTATGTATGTAAGTGAGCTCAAACGAACCATTCGAACCCTTGAGGACAAAGTTGCTGAAATTGAAGAACAG
CAGTGCAATGGAATTTACATTTGGAAGATTGGGAAT

Alignment

ORF - retro_ggor_586 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.39 %
• Parental protein coverage: 68.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSLLNCENSCGSSQSESDCCVAMASSCSAATKDDSVGGTASTGNLSSSFMEEIQGYDVEFDPPLESKYEC
          .SLLNCENSCGSSQS.SD.CVAMASSCSAATK.DSVG.TASTGNLSSSFMEEIQGYD.EF.PPLESKYEC
Retrocopy ISLLNCENSCGSSQSQSDYCVAMASSCSAATKNDSVGRTASTGNLSSSFMEEIQGYDAEFGPPLESKYEC

Parental  PICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQLFPDNFAKREILSLMVKCPNEGCL
          PICLMALREAVQTPC.HRFCKACIIKSIRDAGHK.PVDNEILLEN.LFPDNFAK.EILSL.VKCPNEGCL
Retrocopy PICLMALREAVQTPCSHRFCKACIIKSIRDAGHKYPVDNEILLENKLFPDNFAKHEILSLIVKCPNEGCL

Parental  HKMELRHLELYQVRHYQGYFIVRCIQC-IYFSFCMLNITFGELQPRQMMSKVDTGVPPQDKRMQIHDQNC
          HKMELRHLE..Q...........C.QC...F.....NI......PR...S..............IHDQNC
Retrocopy HKMELRHLEDHQT--HCEFALMDCPQCQPPFQKFHINIHILKGCPRRQVSCDNCAASMSFEDKKIHDQNC

Parental  PLANVICEYCNTILIREQMPNH-YDLDCPTAPIPCTFSTFGCHEKMQRNHLARHLQENTQSHMRMLAQAV
          PLANVICEYCNTILIREQMPN..YDLD.PTAPIPCTF.TF..HEKM.RNHLARHLQENTQS.MRMLAQAV
Retrocopy PLANVICEYCNTILIREQMPNF<YDLDRPTAPIPCTFRTFRSHEKMRRNHLARHLQENTQSNMRMLAQAV

Parental  HSLSLIPDSGYISEVRNFQETIHQLEGRLVRQDHQIRELTAKMETQSMYVSELKRTIRTLEDKVAEIEAQ
          HSLSLI..SGYISEVRNFQE.IHQLEGRLVRQ.HQIRELT.KMETQSMYVSELKRTIRTLEDKVAEIE.Q
Retrocopy HSLSLITESGYISEVRNFQESIHQLEGRLVRQGHQIRELTDKMETQSMYVSELKRTIRTLEDKVAEIEEQ

Parental  QCNGIYIWKIGN
          QCNGIYIWKIGN
Retrocopy QCNGIYIWKIGN

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	0.62 RPM	5.56 RPM
SRP007412_cerebellum	0.43 RPM	5.28 RPM
SRP007412_heart	0.09 RPM	2.16 RPM
SRP007412_kidney	0.90 RPM	6.50 RPM
SRP007412_liver	0.37 RPM	4.99 RPM
SRP007412_testis	2.59 RPM	14.50 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_586 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_586 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_680
Pan troglodytes	retro_ptro_488

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000036009	1 retrocopy	retro_btau_391,
Homo sapiens	ENSG00000175104	1 retrocopy	retro_hsap_680,
Gorilla gorilla	ENSGGOG00000005854	1 retrocopy	retro_ggor_586 ,
Nomascus leucogenys	ENSNLEG00000017949	1 retrocopy	retro_nleu_782,
Pan troglodytes	ENSPTRG00000003510	1 retrocopy	retro_ptro_488,