RetrogeneDB ID: retro_pabe_3647

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:66406752..66407781(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACTR3
• Ensembl ID: ENSPPYG00000012798
• Aliases: ACTR3, ARP3
• Description: Actin-related protein 3 [Source:UniProtKB/Swiss-Prot;Acc:Q5R8R1]

Sequence

>retro_pabe_3647
ATGGTGGGAGGGCTGCAGGCCTGTGTGGTGGACTGTAGCATGGGGTATACAAAACTAGGATATGCCAGAAATATAGAACC
ACAGTTGATAATCCTTTCCCGTATTGCTACTAAGGAGTCACCAAAAGTGGGTGATCAATCTCAAAAGAGGGTGATGAAAG
GTATTGATGACCGAGACTTCTTCACTGGTGATGAAGCAGTAGAAAAAACCTACATATGCAACAAAGTGGCCAATCCACCA
TGGTATAGTTGAAGTTGGACCTGACAAAAAGGTTTATGGAGCAAGTCATCCTAAATATTTAAGGGCAGAAACTGAAGACC
ATTATTTTATTTTGTCTGAACCTCAACTTAATACTCCAGAAAACAGGGAATATACCGCTGAAGTAATGTTTGAGTCCCTC
AGTGTTCCAGGCTTGTACATTGCTGTGCAGCCTGTTCTTGCCTTAGCTGCATCTTGGACCTCCAGACAAGTAGGAGGACG
GACATTTACAGGTACAGTAATAGACAGTGGAGATGGTGTCACTCATGTCATTGTTATGGCTGAAGGGTATTTGATTGGCA
ACTGTATTAAACACATTCCAATCCCAGGATGAGATATAACATATTTTATTCCGCAACTGCTGAGAGACTGAGAAGTAGGA
ATCCCTCGAAAACAATCCCTGGAAACTGCTAAGACAATAAAGGAGCACTATAGTTATGTCTTCCCAGATTTAGTAAAAGA
ATTTAACAAGTATGACGCAGATGGGTCAAAATGGATTAAGCAGTATACCAGAATCAATGCTATCTCAAAGAAAGAATTTT
CCATTGGTGTTATTTCTGAGAGATTTTTGGGATTTGGAATCTTATTTTTCATCTGGAGTTTGCCAATCCAGACTTTACAT
AACCTATCTCAGAAACTGTAGATGAAGTAATTCAGAATTGTCCTATTGATGTCAGATGGCCTCTCTATAAGAATACGGTC
CTCTCTGTAGGTTCAACCACGTTCAGTGACTTTGGATATCACTTGCAAAGAGATTTGAAAATAACTGTA

Alignment

ORF - retro_pabe_3647 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.79 %
• Parental protein coverage: 82.06 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MAGRLPACVVDCGTGYTKLGYAGNTEPQFIIPSCIAIKESAKVGDQAQRRVMKGVDDLDFFIGDEAIEK-
          M.G.L.ACVVDC..GYTKLGYA.N.EPQ.II.S.IA.KES.KVGDQ.Q.RVMKG.DD.DFF.GDEA.EK.
Retrocopy MVGGLQACVVDCSMGYTKLGYARNIEPQLIILSRIATKESPKVGDQSQKRVMKGIDDRDFFTGDEAVEK>

Parental  PTYATKWPIRHGIVE-DW-DLMERFMEQVIF-KYLRAEPEDHYFLLTEPPLNTPENREYTAEIMFESFNV
          PTYATKWPI.HGIVE..W.DL..RFMEQVI..KYLRAE.EDHYF.L.EP.LNTPENREYTAE.MFES..V
Retrocopy PTYATKWPIHHGIVE<SW<DLTKRFMEQVIL<KYLRAETEDHYFILSEPQLNTPENREYTAEVMFESLSV

Parental  PGLYIAVQAVLALAASWTSRQVGERTLTGTVIDSGDGVTHVIPVAEGYVIGSCIKHIPIAGRDITYFIQQ
          PGLYIAVQ.VLALAASWTSRQVG.RT.TGTVIDSGDGVTHVI..AEGY.IG.CIKHIPI.G.DITYFI.Q
Retrocopy PGLYIAVQPVLALAASWTSRQVGGRTFTGTVIDSGDGVTHVIVMAEGYLIGNCIKHIPIPG*DITYFIPQ

Parental  LLRDREVGIPPEQSLETAKAVKERYSYVCPDLVKEFNKYDTDGSKWIKQYTGINAIS-KKEFSIDVGYER
          LLRD.EVGIP..QSLETAK..KE.YSYV.PDLVKEFNKYD.DGSKWIKQYT.INAIS..K.F........
Retrocopy LLRD*EVGIPRKQSLETAKTIKEHYSYVFPDLVKEFNKYDADGSKWIKQYTRINAIS>RKNFPLVLFLRD

Parental  FLGPE-IFFHPEFANPDFTQPISEVVDEVIQNCPIDVRRPLYKNIVLSGGSTMFRDFGRRLQRDLKRTV
          F...E...FH.EFANPDFT.PISE.VDEVIQNCPIDVR.PLYKN.VLS.GST.F.DFG..LQRDLK.TV
Retrocopy FWDLE>LIFHLEFANPDFT*PISETVDEVIQNCPIDVRWPLYKNTVLSVGSTTFSDFGYHLQRDLKITV

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	55.51 RPM
SRP007412_cerebellum	0.00 RPM	50.71 RPM
SRP007412_heart	0.00 RPM	41.18 RPM
SRP007412_kidney	0.00 RPM	62.95 RPM
SRP007412_liver	0.00 RPM	64.36 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3647 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3647 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3647 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 17 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 ,
Pongo abelii	ENSPPYG00000018206	1 retrocopy	retro_pabe_2460,
Pan troglodytes	ENSPTRG00000012388	2 retrocopies	retro_ptro_3118, retro_ptro_955,
Vicugna pacos	ENSVPAG00000009479	1 retrocopy	retro_vpac_468,