RetrogeneDB ID: retro_pabe_3281

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:110303608..110304225(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TARBP2
• Ensembl ID: ENSPPYG00000004583
• Aliases: None
• Description: TAR (HIV-1) RNA binding protein 2 [Source:HGNC Symbol;Acc:11569]

Sequence

>retro_pabe_3281
ATCCCTGTTGGTGCTCTTCAGAAACTGGTGGTGCAGAAAGGCTGGTGGTTGCCAGACTACACAGTGACCTAAGAGTCCAG
GCCAGATCACCACGAAGAATTGATCTGACGAGTGGAGCGTTTTATTGAGATTGGCAGTGGCACTTCCAAAAAATCAACAA
GTTGTAATGCGGTGACCAAAATGCTGCTTCGAGGGCACATGGTGTCTCTGGATGCCTGGGATGGCAATGAGGCAGAGCCT
GATGATGACTACTTCTCCATTGATGTGGGCTCCCGCCTGGATGGTCTTCAGAACTGGGGCCCAGGCTGCACCTGAGATTT
TCTACCAAATTCATTGGAGAGAAGATCCTGTCCTTCTGCAATTGCTCCCTGGGCTTCCTAGGTGCCCTGGGCCCTGCCTG
CTGCCGTGTCCTCAGTGAGCTCTCTGAGGAGCAGGCCTTCCACGTCAGTTACCTGGATGTTGAGGAGCTGAGCCTGAGTA
GACTCTGCCAGTGTCTGGTGGAACTGTCCCTCCAGCCGGCCACTGCGTATCATGGCTCTGCAACCACCAGGGAGGCAGCC
CGTGGTGAGGCTGCTTGCCGTGCCCTGCAGTACCACAAGATCATGGCGGGCAGCAAG

Alignment

ORF - retro_pabe_3281 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.08 %
• Parental protein coverage: 61.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VPSVVLTELVVQKGWRLPEYTVTQESGPAHRKEFTMTCRVEHFIEIGSGTSKKLAKRNAAAKMLLRVHTV
          .P...L..LVVQKGW.LP.YTVT.ES.P.H..E.....RVE.FIEIGSGTSKK....NA..KMLLR.H.V
Retrocopy IPVGALQKLVVQKGWWLPDYTVT*ESRPDHHEE--LI*RVERFIEIGSGTSKKSTSCNAVTKMLLRGHMV

Parental  PLDARDGNEVEPDDDHFSIGVGSRLDGLRNRGPGCTWDSLRNS-VGEKILSLRSCSLGSLGALGPACCRV
          .LDA.DGNE.EPDDD.FSI.VGSRLDGL.N.GPGCT.D.L.NS..GEKILS...CSLG.LGALGPACCRV
Retrocopy SLDAWDGNEAEPDDDYFSIDVGSRLDGLQNWGPGCT*DFLPNS<IGEKILSFCNCSLGFLGALGPACCRV

Parental  LSELSEEQAFHVSYLDIEELSLSGLCQCLVELSTQPATVCHGSATTREAARGEAARRALQYLKIMAGSK
          LSELSEEQAFHVSYLD.EELSLS.LCQCLVELS.QPAT..HGSATTREAARGEAA.RALQY.KIMAGSK
Retrocopy LSELSEEQAFHVSYLDVEELSLSRLCQCLVELSLQPATAYHGSATTREAARGEAACRALQYHKIMAGSK

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	7.57 RPM
SRP007412_cerebellum	0.00 RPM	10.34 RPM
SRP007412_heart	0.00 RPM	2.74 RPM
SRP007412_kidney	0.00 RPM	12.50 RPM
SRP007412_liver	0.00 RPM	6.40 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3281 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3281 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3281 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3995
Pan troglodytes	retro_ptro_2712
Gorilla gorilla	retro_ggor_2682

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018668	1 retrocopy	retro_cjac_1526,
Homo sapiens	ENSG00000139546	1 retrocopy	retro_hsap_3995,
Gorilla gorilla	ENSGGOG00000012637	1 retrocopy	retro_ggor_2682,
Mus musculus	ENSMUSG00000023051	1 retrocopy	retro_mmus_2820,
Nomascus leucogenys	ENSNLEG00000017690	1 retrocopy	retro_nleu_545,
Pongo abelii	ENSPPYG00000004583	1 retrocopy	retro_pabe_3281 ,
Pan troglodytes	ENSPTRG00000005020	1 retrocopy	retro_ptro_2712,