RetrogeneDB ID: retro_ptro_2712

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:101977790..101978717(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TARBP2
• Ensembl ID: ENSPTRG00000005020
• Aliases: None
• Description: None

Sequence

>retro_ptro_2712
AGGGCCCACCAGCCTAATTTCACCTTCTGGGTCACTGTTGGCAACACCAGCTGCACTGCTCAGGGCCCCAGGAAGAAGGT
AGTCAAGCACAAGGCAGCTGAGGTGGCCCTCAGACACCTCAAAGTGGAGAGCATGTTGGAGCCGGCCCCGGAGGACAGCA
GTTCTTTTTCTCCCCTAGACTCTTCACTGCCTGAGGACTTTCCAGTTTTTACTGCTTCAGCAGCTGCTACCCCAGTTTCA
TCTGTTTTCCTAACCAGGAGCACCCCCATGGAAAAGCAGCCCCCGCTCCTCCCTTCAGCAGTCGGAGTGCATCCCTGTTG
GTGCTCTTCAGAAACTGGTGGTGCAGAAAGGCTGGTGGTTGCCAGAGCACACAGTGACCTAGGAGTCCAGGCCAGATCAA
CACGAAGAATTGACCTGACGAGTGGAGCGTTTCATTGAGATTGGCAGTGGCACTTCCAAAAAATCAACAAGTTGTAATGC
AGTGACCAAAATGCTGCTTAGAGTGCACACGGTGTCTGTGGATGCCTGGGATGGCAATGAGGCAGAGCCTGATGATGACT
ACTTCTCCATTGATGTGGGCTCCCGCCTGGATGGTCTTCAGAACCGGGGCCCAGGCTGCACCTGAGATTTTCTACCAAAT
TCATGGGAGAGAAGATCCTGTCCTTCTGCAATTGCTCCCTGGGCTCCATAGGTGCCCTGGGCCCTGCCTGCTGCCGTGTC
CTCAGTGAGCTCTCTGAAAAGCAGGTCTTCCATGTCAGTTACCTGGATGTTGAGGAGCTGAGCCTGAGTAGACTCTGCCA
GTGTCTGGTGGAACTGTCCTTCCAGCTGGCCACTGCATATCATGGCTCTGCAACCACCAGGGAGGCAGCCCATGGTGAGG
CTGCTTGCCGTGCCCTGCAGTACCACAAGATCATGGCGGGCAGCAAG

Alignment

ORF - retro_ptro_2712 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.59 %
• Parental protein coverage: 84.97 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QAHQPNFTFRVTVGDTSCTGQGPSKKAAKHKAAEVALKHLKGGSMLEPALEDSSSFSPLDSSLPEDIPVF
          .AHQPNFTF.VTVG.TSCT.QGP.KK..KHKAAEVAL.HLK..SMLEPA.EDSSSFSPLDSSLPED.PVF
Retrocopy RAHQPNFTFWVTVGNTSCTAQGPRKKVVKHKAAEVALRHLKVESMLEPAPEDSSSFSPLDSSLPEDFPVF

Parental  TAAAAATPVPSVVLTRSPPMELQPPVSP-QQSECNPVGALQELVVQKGWRLPEYTVTQESGPAHRKEFTM
          TA.AAATPV.SV.LTRS.PME.QPP..P.QQSEC.PVGALQ.LVVQKGW.LPE.TVT.ES.P....E...
Retrocopy TASAAATPVSSVFLTRSTPMEKQPPLLP>QQSECIPVGALQKLVVQKGWWLPEHTVT*ESRPDQHEE--L

Parental  TCRVERFIEIGSGTSKKLAKRNAAAKMLLRVHTVPLDARDGNEVEPDDDHFSIGVGSRLDGLRNRGPGCT
          T.RVERFIEIGSGTSKK....NA..KMLLRVHTV..DA.DGNE.EPDDD.FSI.VGSRLDGL.NRGPGCT
Retrocopy T*RVERFIEIGSGTSKKSTSCNAVTKMLLRVHTVSVDAWDGNEAEPDDDYFSIDVGSRLDGLQNRGPGCT

Parental  WDSLRNS-VGEKILSLRSCSLGSLGALGPACCRVLSELSEEQAFHVSYLDIEELSLSGLCQCLVELSTQP
          .D.L.NS..GEKILS...CSLGS.GALGPACCRVLSELSE.Q.FHVSYLD.EELSLS.LCQCLVELS.Q.
Retrocopy *DFLPNS<MGEKILSFCNCSLGSIGALGPACCRVLSELSEKQVFHVSYLDVEELSLSRLCQCLVELSFQL

Parental  ATVCHGSATTREAARGEAARRALQYLKIMAGSK
          AT..HGSATTREAA.GEAA.RALQY.KIMAGSK
Retrocopy ATAYHGSATTREAAHGEAACRALQYHKIMAGSK

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	0.05 RPM	14.26 RPM
SRP007412_cerebellum	0.11 RPM	40.62 RPM
SRP007412_heart	0.00 RPM	4.02 RPM
SRP007412_kidney	0.00 RPM	24.22 RPM
SRP007412_liver	0.00 RPM	18.13 RPM
SRP007412_testis	0.00 RPM	4.85 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2712 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2712 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2712 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3995
Gorilla gorilla	retro_ggor_2682
Pongo abelii	retro_pabe_3281

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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 ,