RetrogeneDB ID: retro_pabe_659

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 10_random:34428806..34429222(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM210B
• Ensembl ID: ENSPPYG00000011147
• Aliases: None
• Description: family with sequence similarity 210, member B [Source:HGNC Symbol;Acc:16102]

Sequence

>retro_pabe_659
AGGCCAGATGCCCGGCTGCTACGCACGGCTGTGGGGACTGCCGAGGCCGCCAGGACCTCAGCCAGGCCACGGAGGCAACA
GGCAGCAGCGTCAGCTGCACAGAGAAGAAAAAGCAAAGCAAGTCACAGCAATTGAAAAAGATTTTTCAAGAGTATGGCAC
TGTTGGCGTGTCGTTGTACACTGGAATCTCATTAATCTCCTTGGGCATATTTTACATGGTTGTGTCAAGTGGTGTGGACA
TGTTTGCAGTCCCGCTGAAACTCGGATTTAAAGAGTGCCTGGTACAGTCAAAAATGGCAGCAGGCACAAGTACCTTTGTG
GTGGCCTATGCAATCCACAAGCCGTTTGCGCCAGTGAGACTCAGCATTACGTTAGTCTCCGTGCCCTTGATTGTCAGATA
GTTTCGAAAAGTGGGA

Alignment

ORF - retro_pabe_659 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.43 %
• Parental protein coverage: 72.4 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RPDARVLRTARGY-CRGHQDPSQATETTGSSVSCTEEKKQSKSQQLKKIFQEYGTVGVSLHIGISLISLG
          RPDAR.LRTA.G..CRG.QD.SQATE.TGSSVSCTE.KKQSKSQQLKKIFQEYGTVGVSL..GISLISLG
Retrocopy RPDARLLRTAVGT<CRGRQDLSQATEATGSSVSCTEKKKQSKSQQLKKIFQEYGTVGVSLYTGISLISLG

Parental  IFYMVVSSGVDMSAILLKLGFEESLVQSKMAAGASTFVVAYAIHKLFAPVRISITLVSVPLIVRYFRKVG
          IFYMVVSSGVDM.A..LKLGF.E.LVQSKMAAG.STFVVAYAIHK.FAPVR.SITLVSVPLIVR.FRKVG
Retrocopy IFYMVVSSGVDMFAVPLKLGFKECLVQSKMAAGTSTFVVAYAIHKPFAPVRLSITLVSVPLIVR*FRKVG

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	0.06 RPM	24.00 RPM
SRP007412_cerebellum	0.12 RPM	43.65 RPM
SRP007412_heart	0.00 RPM	41.63 RPM
SRP007412_kidney	0.00 RPM	46.27 RPM
SRP007412_liver	0.00 RPM	51.10 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_659 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_659 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_659 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,