RetrogeneDB ID: retro_ptro_488

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 10:57475647..57476723(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRAF6
• Ensembl ID: ENSPTRG00000003510
• Aliases: None
• Description: None

Sequence

>retro_ptro_488
ATAAGTCTGCTAAACTGTGAAAACAGCTGTGGATCCAGCCAGTCTCAAAGTGACTACTGTGTGGCCATGGCCAGCTCCTG
TAGCGCAGCAACAAAAAATGATAGTGTGGGCAGAACTGCCAGCACGGGGAACCTCTCCAGCTCCTTTATGGAGGAGATCC
AGGGATATGATGTAGAGTTTGGCCCACCCCTGGAAAGCAAGTATGAATGCCCCATCTGCTTGATGGCATTACGAGAAGCA
GTGCAAACTCCATGCAGCCATAGGTTCTGCAAAGCCTGCATCATAAAATCAATAAGGGATGCAGGTCACAAATATCCAGT
TGACAATGAAATACTGCTGGAAAATAAACTATTTCCAGACAATTTTGCAAAACGTGAGATTATTTCTCTGATAGTGAAGT
GTCCAAATGAAGGTTGTTTGCACAAGACGGAACTGAGACATCTTGAGGATCATCAAACACATTGTGAGTTTGCTCTTATG
GATTGTCCCCAATGCCAGCCTCCCTTCCAAAAATTCCATATTAATATTCACATTATGAAGGGTTGTCCAAGGAGGCAGGT
ATCTTGTGACAACTGTACTGCATCAATGGCATTTGAAGATAAAAAGATCCATGACCAGAACTGCCCTTTGGCAAATGTCA
TCTGTGAGTACTGCAATACTATACTCATCAGAGAACAGATGCCTAACTTTATGACCTAGACCGCCCTACAGCCCCAATTC
CATGCACATTCCGTACTTTTCGTAGCCATGAAAAGATGCAGAGGAATCACTTGGCACGCCACCTACAAGAGAACACCCAA
TCAAACATGAGAATGTTGGCCCAGGCTGTTCATAGTTTGAGCCTTATACCCTACTCTGGGTATATCTCAGAGGTCCGGAA
TTTCCAGGAAAGTATTCACCAGTTAGAGGGTCGCCTTGTAAGACAATGTCATCAAATCCGGGAGCTGACTGATAAAATGG
AAACTCAGAGTATGTATGTAAGTGAGCTCAAATGAACCATTCGAACCCTTGAGGACAAAGTTGCTGAAATTGAAGCACAG
CAGTGCAATGGAATTTACATTTGGAAGATTGGGAAT

Alignment

ORF - retro_ptro_488 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.67 %
• Parental protein coverage: 68.77 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSLLNCENSCGSSQSESDCCVAMASSCSAATKDDSVGGTASTGNLSSSFMEEIQGYDVEFDPPLESKYEC
          .SLLNCENSCGSSQS.SD.CVAMASSCSAATK.DSVG.TASTGNLSSSFMEEIQGYDVEF.PPLESKYEC
Retrocopy ISLLNCENSCGSSQSQSDYCVAMASSCSAATKNDSVGRTASTGNLSSSFMEEIQGYDVEFGPPLESKYEC

Parental  PICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQLFPDNFAKREILSLMVKCPNEGCL
          PICLMALREAVQTPC.HRFCKACIIKSIRDAGHK.PVDNEILLEN.LFPDNFAKREI.SL.VKCPNEGCL
Retrocopy PICLMALREAVQTPCSHRFCKACIIKSIRDAGHKYPVDNEILLENKLFPDNFAKREIISLIVKCPNEGCL

Parental  HKMELRHLEDHQAHCEFALMDCPQCQRPFQKFHINIHILKDCPRRQVSCDNCAASMAFEDKEIHDQNCPL
          HK.ELRHLEDHQ.HCEFALMDCPQCQ.PFQKFHINIHI.K.CPRRQVSCDNC.ASMAFEDK.IHDQNCPL
Retrocopy HKTELRHLEDHQTHCEFALMDCPQCQPPFQKFHINIHIMKGCPRRQVSCDNCTASMAFEDKKIHDQNCPL

Parental  ANVICEYCNTILIREQMPNH-YDLDCPTAPIPCTFSTFGCHEKMQRNHLARHLQENTQSHMRMLAQAVHS
          ANVICEYCNTILIREQMPN..YDLD.PTAPIPCTF.TF..HEKMQRNHLARHLQENTQS.MRMLAQAVHS
Retrocopy ANVICEYCNTILIREQMPNF<YDLDRPTAPIPCTFRTFRSHEKMQRNHLARHLQENTQSNMRMLAQAVHS

Parental  LSLIPDSGYISEVRNFQETIHQLEGRLVRQDHQIRELTAKMETQSMYVSELKRTIRTLEDKVAEIEAQQC
          LSLIP.SGYISEVRNFQE.IHQLEGRLVRQ.HQIRELT.KMETQSMYVSELK.TIRTLEDKVAEIEAQQC
Retrocopy LSLIPYSGYISEVRNFQESIHQLEGRLVRQCHQIRELTDKMETQSMYVSELK*TIRTLEDKVAEIEAQQC

Parental  NGIYIWKIGN
          NGIYIWKIGN
Retrocopy NGIYIWKIGN

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	0.02 RPM	6.08 RPM
SRP007412_cerebellum	0.00 RPM	7.99 RPM
SRP007412_heart	0.00 RPM	7.75 RPM
SRP007412_kidney	0.08 RPM	10.43 RPM
SRP007412_liver	0.00 RPM	6.51 RPM
SRP007412_testis	0.11 RPM	12.54 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_488 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_488 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_488 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_680
Gorilla gorilla	retro_ggor_586

---

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 ,