RetrogeneDB ID: retro_ptro_148

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:52583595..52584292(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDCL2
• Ensembl ID: ENSPTRG00000016073
• Aliases: None
• Description: phosducin-like 2 [Source:HGNC Symbol;Acc:29524]

Sequence

>retro_ptro_148
ATGCAGGACCCCAACGCAGACACTGAATGGAGTGATATCTTACACAAAAAGGGCATCTTAAAGTCTGAAAGAATTGGAAG
AGGAGGCGGAAGATGAGCAGCGCATCCTCCAGCAGTCAATCGTGACAACATAGGAAGATATGACTTTGGAAGAGCTGGAG
GATCGTGAAGACAAGTTTAATGAGGAGGATGAATGTGCTATTGAAATGTACAGACAGCAGAGACTGGCTGAGTGGAAAGC
AACTAAATTGAAGAATAAATTTGAAGAAGTTTTGGAGATCTCAGGGAAGGATTATGTTCAAGAAGTTACCAAAGCCAGTG
AGGGTTTGTGGGTCATCTTGCACCTTTACAAACAAGGAATTCCCCTCTGTGCCCTGATAAATCAGCACCTCAGTGGAGTT
GCCAGGAAGTTTCCTGATTTCAAATTTATCAAAGCCATTTCAACAACCTGCATACCCAGTTATCCTGATAGGAATCTGCC
CATGATATTTGTTTACCTGGAAGGAGATATCAAGGCTCAGTTTATTGGTCCTCTGGTGTTTGGCGGCATGAGCCTGACAA
GAGATGAGTTGGAGTGAAAACTGTCTGAATCTGGAGCAATTAAGAGGGACCTGGAGGAAAACCTTAAGAAGCCAGTTGAA
GATGTATTGCTGTCCTCAGTGCAATGCTCTGTCCCCATGAAGAGGGACAGTGATTCT

Alignment

ORF - retro_ptro_148 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.77 %
• Parental protein coverage: 96.68 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MQDPNEDTEWNDILRDFGILPP-KEESKDEIEEMVLRLQKEAMVKPFEKMTLAQLKEAEDEFDEEDMQAI
          MQDPN.DTEW.DIL...GIL...KE.......E...R......V...E.MTL..L...ED.F.EED..AI
Retrocopy MQDPNADTEWSDILHKKGILKS>KELEEEAEDEQ--RILQQSIVTT*EDMTLEELEDREDKFNEEDECAI

Parental  ETYRKKRLQEWKALKKKQKFGELREISGNQYVNEVTNAEEDVWVITHLYRSSIPMCLLVNQHLSLLARKF
          E.YR..RL.EWKA.K.K.KF.E..EISG..YV.EVT.A.E..WVI.HLY...IP.C.L.NQHLS..ARKF
Retrocopy EMYRQQRLAEWKATKLKNKFEEVLEISGKDYVQEVTKASEGLWVILHLYKQGIPLCALINQHLSGVARKF

Parental  PETKFVKAIVNSCIQHYHDNCLPTIFVYKNGQIEAKFIGIIECGGINLKLEELEWKLAEVGAIQTDLEEN
          P..KF.KAI...CI..Y.D..LP.IFVY..G.I.A.FIG....GG..L...ELE.KL.E.GAI..DLEEN
Retrocopy PDFKFIKAISTTCIPSYPDRNLPMIFVYLEGDIKAQFIGPLVFGGMSLTRDELE*KLSESGAIKRDLEEN

Parental  PRKDIVDMMVSSIR-NTSIHDDSDS
          ..K...D...SS.........DSDS
Retrocopy LKKPVEDVLLSSVQCSVPMKRDSDS

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	0.18 RPM	0.00 RPM
SRP007412_cerebellum	0.11 RPM	0.00 RPM
SRP007412_heart	0.03 RPM	0.06 RPM
SRP007412_kidney	0.08 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.53 RPM	45.53 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_148 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_148 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_148 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_151

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012692	3 retrocopies	retro_chof_1554, retro_chof_562, retro_chof_737,
Echinops telfairi	ENSETEG00000000666	1 retrocopy	retro_etel_1568,
Gorilla gorilla	ENSGGOG00000007908	1 retrocopy	retro_ggor_2890,
Monodelphis domestica	ENSMODG00000020680	2 retrocopies	retro_mdom_1048, retro_mdom_993,
Pan troglodytes	ENSPTRG00000016073	7 retrocopies	retro_ptro_148 , retro_ptro_1810, retro_ptro_1865, retro_ptro_2402, retro_ptro_2690, retro_ptro_2784, retro_ptro_675,