RetrogeneDB ID: retro_ptro_1567

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2A:110593438..110594047(+)
• Located in intron of: ENSPTRG00000012346

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACTR1A
• Ensembl ID: ENSPTRG00000002894
• Aliases: None
• Description: None

Sequence

>retro_ptro_1567
GTGGAGTCTTACGATACAATCACCAACCAGCCTGTCATGATCGACAATGAATCTGGTGTGATTAAAGCTGGTTTTGCTGG
TGATCAGATCCACAAATACTGCTTTCCAAAGTATGTGGGCCTACCCATGCATATTCGTATCATGGCAGGAGCCCTTGAAG
GTGACATCTTCATTGGCTTCAAAGCCAAGGAGCACCAAGGGCTGCTCTCGATCTGCTATCTCACGGAGCATGGCATTGTC
AAGGACTGGAATGACATGGAACACATCTGGCAATATGTCTATTCTAAGGACCAGCTGCAGACTTTCTCAGAGGAGCATCT
CGTGCTCCTCACTGAGGCACCTTTAAACCCACAAAGACACCAGGAATGAGCTGCCAACGTTTTCTTCAAGAGCTTCAATG
TGCCTGCTATTTTCATCTCCATGTAAGCTGTGCTCAGCCTTTATGCCACAGGCAGGACCACGGGGGTGGTGCTGGATTCT
GGGGATGGCATCACCCATGCTGTGCCCATCTATCAGGGCTTTGCCATGCCCCACTCCATCATGCGAATTGACATCGCAAG
CCGGAACATCTCTCGCTTCCTGCACCTCTACCTGCATAAGGAGGGCTAT

Alignment

ORF - retro_ptro_1567 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.27 %
• Parental protein coverage: 53.99 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MESYDVIANQPVVIDNGSGVIKAGFAGDQIPKYCFPNYVGRPKHVRVMAGALEGDIFIGPKAEEHRGLLS
          .ESYD.I.NQPV.IDN.SGVIKAGFAGDQI.KYCFP.YVG.P.H.R.MAGALEGDIFIG.KA.EH.GLLS
Retrocopy VESYDTITNQPVMIDNESGVIKAGFAGDQIHKYCFPKYVGLPMHIRIMAGALEGDIFIGFKAKEHQGLLS

Parental  IRYPMEHGIVKDWNDMERIWQYVYSKDQLQTFSEEHPVLLTEAPLNPRKNRERAAEVFFETFNVPALFIS
          I.Y..EHGIVKDWNDME.IWQYVYSKDQLQTFSEEH.VLLTEAPLNP....E.AA.VFF..FNVPA.FIS
Retrocopy ICYLTEHGIVKDWNDMEHIWQYVYSKDQLQTFSEEHLVLLTEAPLNPQRHQE*AANVFFKSFNVPAIFIS

Parental  MQAVLSLYATGRTTGVVLDSGDGVTHAVPIYEGFAMPHSIMRIDIAGRDVSRFLRLYLRKEGY
          M.AVLSLYATGRTTGVVLDSGDG.THAVPIY.GFAMPHSIMRIDIA.R..SRFL.LYL.KEGY
Retrocopy M*AVLSLYATGRTTGVVLDSGDGITHAVPIYQGFAMPHSIMRIDIASRNISRFLHLYLHKEGY

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	171.79 RPM
SRP007412_cerebellum	0.00 RPM	115.83 RPM
SRP007412_heart	0.03 RPM	53.25 RPM
SRP007412_kidney	0.03 RPM	80.70 RPM
SRP007412_liver	0.00 RPM	70.57 RPM
SRP007412_testis	0.00 RPM	71.34 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1567 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1567 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1567 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2141
Pongo abelii	retro_pabe_1930

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000138107	1 retrocopy	retro_hsap_2141,
Mus musculus	ENSMUSG00000025228	1 retrocopy	retro_mmus_2686,
Nomascus leucogenys	ENSNLEG00000015157	1 retrocopy	retro_nleu_2751,
Pongo abelii	ENSPPYG00000002605	1 retrocopy	retro_pabe_1930,
Pan troglodytes	ENSPTRG00000002894	1 retrocopy	retro_ptro_1567 ,
Pan troglodytes	ENSPTRG00000018890	27 retrocopies	retro_ptro_1042, retro_ptro_1051, retro_ptro_1076, retro_ptro_1143, retro_ptro_1272, retro_ptro_1515, retro_ptro_1756, retro_ptro_178, retro_ptro_2122, retro_ptro_2173, retro_ptro_2349, retro_ptro_2454, retro_ptro_263, retro_ptro_2805, retro_ptro_2854, retro_ptro_314, retro_ptro_3207, retro_ptro_3219, retro_ptro_3282, retro_ptro_3287, retro_ptro_3292, retro_ptro_3302, retro_ptro_3307, retro_ptro_387, retro_ptro_432, retro_ptro_53, retro_ptro_584,
Drosophila melanogaster	FBgn0011745	1 retrocopy	retro_dmel_80,