RetrogeneDB ID: retro_ptro_475

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 10:27734939..27735515(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM210B
• Ensembl ID: ENSPTRG00000013645
• Aliases: None
• Description: family with sequence similarity 210, member B [Source:HGNC Symbol;Acc:16102]

Sequence

>retro_ptro_475
ATGGCCGTGTTGCTGGCGGGGCTGGGCCCGGCAGGCAGGGTGGGCGCCTGGGTCCGGCCTTGCGCCACATGGCTCCTGGG
CGCGACCACCCCCTGTGCCCCGCTGCCCCTGGCCCTGGCCCTGCTCCTGCCCAGGCCAGATGCCCGGCTGCTCCGCACAG
CCGTGGGGACTGCCGCGGCACCCAGGACCTCAGCCAGGCCACGGAGACAACAGGCAGCAGCGTCAGCTGCACAGAGGAGA
AAAAGCAAAGCAAGTCACAGCAACTGAAAAAGATTTTTCAAGAATATGACACTGTTGGCGTGTCGTTGTACACTGGAATC
TCATTAATTTCCTTGGTCATATTTTACATGGTTGTGTCAAGTGGTGTGGACATGTCTGCAGTCCTGCTGAAACTCGGATT
TAAAGAGTCCCTGGTACAGTCAAAAATGGCAGCAGGCACAAGTACCTTTGTGGTGGCCTATGCAATCCACAAGCTGTTTG
CGCCAGTGAGAATCAGCATTACGTTAGTCTCTGTGCCCTTGATTGTCAGATAGTTTTGAAAAGTGGGATTTTTTAAAACC
TCCAGCTGCAAAACCT

Alignment

ORF - retro_ptro_475 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.69 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAGLLALLGPAGRVGARVRPRATWLLGATAPCAPPPLTLALLPPRPDARLLRTA-RGDCRGHQDPSQATG
          MA.LLA.LGPAGRVGA.VRP.ATWLLGAT.PCAP.PL.LALL.PRPDARLLRTA.RGDCRG.QD.SQAT.
Retrocopy MAVLLAGLGPAGRVGAWVRPCATWLLGATTPCAPLPLALALLLPRPDARLLRTA<RGDCRGTQDLSQATE

Parental  TTGSSVSCTEEKKQSKSQQLKKIFQEYGTVGVSLHIGISLISLGIFYMVVSSGVDMSAILLKLGFKESLV
          TTGSSVSCTEEKKQSKSQQLKKIFQEY.TVGVSL..GISLISL.IFYMVVSSGVDMSA.LLKLGFKESLV
Retrocopy TTGSSVSCTEEKKQSKSQQLKKIFQEYDTVGVSLYTGISLISLVIFYMVVSSGVDMSAVLLKLGFKESLV

Parental  QSKMAAGTSTFVVAYAIHKLFAPVRISITLVSVPLIVRYFRKVGFF-KPPAAKP
          QSKMAAGTSTFVVAYAIHKLFAPVRISITLVSVPLIVR.F.KVGFF.KPPAAKP
Retrocopy QSKMAAGTSTFVVAYAIHKLFAPVRISITLVSVPLIVR*F*KVGFF>KPPAAKP

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	26.38 RPM
SRP007412_cerebellum	0.00 RPM	29.68 RPM
SRP007412_heart	0.00 RPM	16.70 RPM
SRP007412_kidney	0.18 RPM	57.51 RPM
SRP007412_liver	0.00 RPM	48.12 RPM
SRP007412_testis	0.00 RPM	11.38 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_475 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_475 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_475 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000006630	1 retrocopy	retro_cpor_1046,
Homo sapiens	ENSG00000124098	1 retrocopy	retro_hsap_653,
Nomascus leucogenys	ENSNLEG00000007028	1 retrocopy	retro_nleu_1733,
Oryctolagus cuniculus	ENSOCUG00000017897	1 retrocopy	retro_ocun_1678,
Pongo abelii	ENSPPYG00000011147	2 retrocopies	retro_pabe_577, retro_pabe_659,
Pan troglodytes	ENSPTRG00000013645	1 retrocopy	retro_ptro_475 ,