RetrogeneDB ID: retro_ptro_3118

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:68500969..68501997(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACTR3
• Ensembl ID: ENSPTRG00000012388
• Aliases: None
• Description: None

Sequence

>retro_ptro_3118
ATGGTGGGAGGGCTGCAGGCCTGTGTGGTGGACTGTAGCATGGGGTATACAAAACTAGGATATGCCAGAAATATAGAACC
ACAGTTGATCATCCTTTCCTGTATTGCTACTAAGGAGTCACCAAAAGTGGGTGATCAATCTCAAAGGAGGGTGATGAAAG
GTATTGATGACCAAGACTTCTTCATTGGTGATGAAGCAGTAGAAAAAACCTACATATGCAACAAAGTGGCCAATCCACCA
TGGTATAGTTGAAGTTGGACCTGACAAAAAGGTTTATGGAGCAAGTCATCCTAAATATTTAAGGGCAGAAACTGAAGACC
GTTATTTTATTTTGTCTGAACCTCGACTGAATACTCCAGAAAACAGGGAATATACTGCTGAAGTAATGTTTGAGTCCTTC
AGTGTTCCGGGCTTGTACATTGCTGTGCAGGCTGTTCTTGCCTTAGCTGCATCTTGGACCTCCAGACACGTAGGAGGACG
GACGTTTACAGGTACAGTAATAGACAGTGGAGATGGTGTCACTCATGTCATTGCTATGGCTGAAGGGTATTTGATTGCCA
ACTGTATTAAACACATTCCAATCCCAGGACGAAATATAACATATTTTATTCCGCAACTGCTGAGAGACCGAGAAGTAGGA
ATCCCTCGAAAACAATCCCTGGAAACTGCTAAGACAATAAAGGAGCACTATAGTTATGTCTGCCCAGATTTAGTAAAGGA
ATTTAACAAGTATGACACAGATGGGTCAAAATGGATTAAGCAGTATACCAGAATCAATGATATCTCAAAGAAAGAATTTT
CCATTGGTGTTGTTTCTGAGAGATTTTTGGGATTTGAAATCTTTTTTTCATCCAGAGTTTGCCAATCCAGACTTTACATA
ACCTATCTCAGAAATTGTATGTGAAGTAATTCAGAATTGTCCTATTGATGTCAGACGGCCTCTCTATAAGAATATGGTCC
TCTCTGTAGGTTCAAGCATGTTCAGTGACTTTGGATATCACTTGCAAAGAGATTTGAAAAGAACTGTA

Alignment

ORF - retro_ptro_3118 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.9 %
• Parental protein coverage: 82.06 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MAGRLPACVVDCGTGYTKLGYAGNTEPQFIIPSCIAIKESAKVGDQAQRRVMKGVDDLDFFIGDEAIEK-
          M.G.L.ACVVDC..GYTKLGYA.N.EPQ.II.SCIA.KES.KVGDQ.QRRVMKG.DD.DFFIGDEA.EK.
Retrocopy MVGGLQACVVDCSMGYTKLGYARNIEPQLIILSCIATKESPKVGDQSQRRVMKGIDDQDFFIGDEAVEK>

Parental  PTYATKWPIRHGIVE-DW-DLMERFMEQVIF-KYLRAEPEDHYFLLTEPPLNTPENREYTAEIMFESFNV
          PTYATKWPI.HGIVE..W.DL..RFMEQVI..KYLRAE.ED.YF.L.EP.LNTPENREYTAE.MFESF.V
Retrocopy PTYATKWPIHHGIVE<SW<DLTKRFMEQVIL<KYLRAETEDRYFILSEPRLNTPENREYTAEVMFESFSV

Parental  PGLYIAVQAVLALAASWTSRQVGERTLTGTVIDSGDGVTHVIPVAEGYVIGSCIKHIPIAGRDITYFIQQ
          PGLYIAVQAVLALAASWTSR.VG.RT.TGTVIDSGDGVTHVI..AEGY.I..CIKHIPI.GR.ITYFI.Q
Retrocopy PGLYIAVQAVLALAASWTSRHVGGRTFTGTVIDSGDGVTHVIAMAEGYLIANCIKHIPIPGRNITYFIPQ

Parental  LLRDREVGIPPEQSLETAKAVKERYSYVCPDLVKEFNKYDTDGSKWIKQYTGINAISKKEFSIDVGYERF
          LLRDREVGIP..QSLETAK..KE.YSYVCPDLVKEFNKYDTDGSKWIKQYT.IN.ISKKEFSI.V..ERF
Retrocopy LLRDREVGIPRKQSLETAKTIKEHYSYVCPDLVKEFNKYDTDGSKWIKQYTRINDISKKEFSIGVVSERF

Parental  LGPEI-FFHPEFANPDFTQPISEVVDEVIQNCPIDVRRPLYKNIVLSGGSTMFRDFGRRLQRDLKRTV
          LG.EI.FFHPEFANPDFT.PISE.V.EVIQNCPIDVRRPLYKN.VLS.GS.MF.DFG..LQRDLKRTV
Retrocopy LGFEI>FFHPEFANPDFT*PISEIVCEVIQNCPIDVRRPLYKNMVLSVGSSMFSDFGYHLQRDLKRTV

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	55.07 RPM
SRP007412_cerebellum	0.00 RPM	70.91 RPM
SRP007412_heart	0.00 RPM	64.12 RPM
SRP007412_kidney	0.00 RPM	65.93 RPM
SRP007412_liver	0.00 RPM	54.54 RPM
SRP007412_testis	0.00 RPM	165.35 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3118 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3118 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3118 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003401	1 retrocopy	retro_btau_672,
Callithrix jacchus	ENSCJAG00000014091	4 retrocopies	retro_cjac_3602, retro_cjac_3813, retro_cjac_385, retro_cjac_4005,
Homo sapiens	ENSG00000115091	2 retrocopies	retro_hsap_1391, retro_hsap_4694,
Gorilla gorilla	ENSGGOG00000011346	1 retrocopy	retro_ggor_2921,
Mustela putorius furo	ENSMPUG00000010717	1 retrocopy	retro_mputfur_1275,
Mus musculus	ENSMUSG00000026341	1 retrocopy	retro_mmus_3653,
Nomascus leucogenys	ENSNLEG00000011619	2 retrocopies	retro_nleu_1077, retro_nleu_2364,
Pongo abelii	ENSPPYG00000012798	1 retrocopy	retro_pabe_3647,
Pan troglodytes	ENSPTRG00000012388	2 retrocopies	retro_ptro_3118 , retro_ptro_955,
Pan troglodytes	ENSPTRG00000019897	8 retrocopies	retro_ptro_1137, retro_ptro_1479, retro_ptro_2007, retro_ptro_2952, retro_ptro_2961, retro_ptro_3052, retro_ptro_3281, retro_ptro_420,
Vicugna pacos	ENSVPAG00000009479	1 retrocopy	retro_vpac_468,