RetrogeneDB ID: retro_hsap_653

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 10:27638643..27639219(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000213770
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FAM210B
• Ensembl ID: ENSG00000124098
• Aliases: FAM210B, 5A3, C20orf108, dJ1167H4.1
• Description: family with sequence similarity 210, member B [Source:HGNC Symbol;Acc:16102]

Sequence

>retro_hsap_653
ATGGCCGTGTTGCTGGCGGGGCTGGGCCCGGCAGGCAGGGTGGGCGCCTGGGTCCGGCCTTGCGCCACATGGCTCCTGGG
CGCGACCACCCCCTGTGCCCCGCTGCCCCTGGCCCTGGCCCTGCTCCTGCCCAGGCCAGATGCCCGGCTGCTCCGCACAG
CCGTGGGGACTGCCGCGGCAGCCAGGACCTCAGCCAGGCCACGGAGAGAACAGGCAGCAGCGTCAGCTGCACAGAGGAGA
AAAAGCAAAGCAAGTCACAGCAACTGAAAAAGATTTTTCAAGAATATGACACTGTTGGCGTGTCGTTGTACACTGGAATC
TCATTCATTTCCTTGGTCATATTTTACATGGTTGTGTCAAGTGGTGTGGACATGTCTGCAGTCCTGCTGAAACTCGGATT
TAAAGAGTCCCTCGTACAGTCAAAAATGGCAGCAGGCACAAGTACCTTTGTGGTGGCCTATGCAATCCACAAGCTGTTTG
CGCCAGTGAGAATCAGCATTACGTTAGTCTCTGTGCCCTTGATCGTCAGATAGTTTCGAAAAGTGGGATTTTTTAAAACC
TCCAGCTGCAAAACCT

Alignment

ORF - retro_hsap_653 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.66 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAGLLALLGPAGRVGARVRPRATWLLGATAPCAPPPLALALLPPRLDARLLRTA-RGDCRGHQDPSQATG
          MA.LLA.LGPAGRVGA.VRP.ATWLLGAT.PCAP.PLALALL.PR.DARLLRTA.RGDCRG.QD.SQAT.
Retrocopy MAVLLAGLGPAGRVGAWVRPCATWLLGATTPCAPLPLALALLLPRPDARLLRTA<RGDCRGSQDLSQATE

Parental  TTGSSVSCTEEKKQSKSQQLKKIFQEYGTVGVSLHIGISLISLGIFYMVVSSGVDMPAILLKLGFKESLV
          .TGSSVSCTEEKKQSKSQQLKKIFQEY.TVGVSL..GIS.ISL.IFYMVVSSGVDM.A.LLKLGFKESLV
Retrocopy RTGSSVSCTEEKKQSKSQQLKKIFQEYDTVGVSLYTGISFISLVIFYMVVSSGVDMSAVLLKLGFKESLV

Parental  QSKMAAGTSTFVVAYAIHKLFAPVRISITLVSVPLIVRYFRKVGFF-KPPAAKP
          QSKMAAGTSTFVVAYAIHKLFAPVRISITLVSVPLIVR.FRKVGFF.KPPAAKP
Retrocopy QSKMAAGTSTFVVAYAIHKLFAPVRISITLVSVPLIVR*FRKVGFF>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
bodymap2_adipose	0.00 RPM	67.66 RPM
bodymap2_adrenal	0.04 RPM	44.32 RPM
bodymap2_brain	0.00 RPM	24.99 RPM
bodymap2_breast	0.04 RPM	100.76 RPM
bodymap2_colon	0.00 RPM	109.52 RPM
bodymap2_heart	0.00 RPM	67.24 RPM
bodymap2_kidney	0.00 RPM	49.16 RPM
bodymap2_liver	0.00 RPM	74.80 RPM
bodymap2_lung	0.00 RPM	60.30 RPM
bodymap2_lymph_node	0.04 RPM	54.00 RPM
bodymap2_ovary	0.00 RPM	157.05 RPM
bodymap2_prostate	0.28 RPM	136.88 RPM
bodymap2_skeletal_muscle	0.00 RPM	66.02 RPM
bodymap2_testis	0.00 RPM	88.65 RPM
bodymap2_thyroid	0.00 RPM	54.27 RPM
bodymap2_white_blood_cells	0.00 RPM	62.53 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_653 was not detected

EST

No EST(s) were mapped for retro_hsap_653 retrocopy.

TSS

No TSS is located nearby retro_hsap_653 retrocopy 5' end.

Lab

retro_hsap_653 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_653 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,