RetrogeneDB ID: retro_pabe_1877

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 22:19657580..19658642(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000011651
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ACTR2
• Ensembl ID: ENSPPYG00000012359
• Aliases: ACTR2, ARP2
• Description: actin-related protein 2 [Source:RefSeq peptide;Acc:NP_001126951]

Sequence

>retro_pabe_1877
ATCAGATCAACCACCAAAGTGGGAAACATTGAAATCAAGGATCTTATGTTTGGTGATGAGGCAAGTGAATTACGATCAAT
GTTAGAAGTTAACTACCCTATGGAAAATGGCATAGTACGAAATTGGGATGACACAAAACACCTGTGGGACTACACATTTG
GACCAGAGAAACTTAATATAGATACCAGAAATTGTAAAATCTTACTCACAGAACCTCCTATGAACCCAACCAAAAACAGA
GAGAAGATTGTAGAGGTAATGTTTGAAACTTACCAGTTTTCCGGTGTATATGTAGCCATCCAGGCAGTTCTGACTTTGTA
CGCTCAAGGTTTATTGACTGGTGTAGTGGTAGATTCTGGAGATGGTGTGACTCACATTTACCCAGTATATGAAGGCTTTT
CTCTCCCTCATCTTACCAGGAGACTGGATATTGCTGGGAGGAATATAACTAGATATCTTTTCAAGCTACTTCTGTTTCAA
GGATACACCTTCAACCACTCTGCTAATTTTGAAACGGTTCGCATGATTAAAGAAAAACTGTGTTACATGGGATATAATAT
TGTGCAAGAGCAGAAACTGGCCTTAGAAATCACAGTATTAGTTGAATCTTATACACTTCCAGATGGACGAATCATCAAAG
TTGGGGGAGAGAGATCTGAAACACCAGAAGCTTTATTTCAGCCTCACTTGATCAATCTTGAAGGAGCTGGTGTTGCTGAA
TTGCTTTTTAACACAATTCAGGCGGCTGACATTGATACCAGATCAGAATTCTACAAACACTTTGTGCTTTCTGGAGGGTC
TACTATGTATCCTGGCCTGCCATCACGGTTGGAATGAGAACTTAAACAGCTTTACTTAGAAAGAGTTTTGAAGGATGATG
TGGAAAAACTTTCTTAATTTAAGCTCTGCATTGAAGACCCACCCCGCAGAAAGCACATGGTATTCTTGGGTGGTGCATTT
CTAGCGGATACCATGAAAGACAAAGACAATTTTTGGATGACCCGACAGGAGTACCAAGAAAAGGGCATCCGTGTGCTAGA
GAAACTTGGTGTGACTGTTCGA

Alignment

ORF - retro_pabe_1877 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.94 %
• Parental protein coverage: 89.85 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IRSTTKVGNIEIKDLMVGDEASELRSMLEVNYPMENGIVRNWDDMKHLWDYTFGPEKLNIDTRNCKILLT
          IRSTTKVGNIEIKDLM.GDEASELRSMLEVNYPMENGIVRNWDD.KHLWDYTFGPEKLNIDTRNCKILLT
Retrocopy IRSTTKVGNIEIKDLMFGDEASELRSMLEVNYPMENGIVRNWDDTKHLWDYTFGPEKLNIDTRNCKILLT

Parental  EPPMNPTKNREKIVEVMFETYQFSGVYVAIQAVLTLYAQGLLTGVVVDSGDGVTHICPVYEGFSLPHLTR
          EPPMNPTKNREKIVEVMFETYQFSGVYVAIQAVLTLYAQGLLTGVVVDSGDGVTHI.PVYEGFSLPHLTR
Retrocopy EPPMNPTKNREKIVEVMFETYQFSGVYVAIQAVLTLYAQGLLTGVVVDSGDGVTHIYPVYEGFSLPHLTR

Parental  RLDIAGRDITRYLIKLLLLRGYAFNHSADFETVRMIKEKLCYVGYNIEQEQKLALETTVLVESYTLPDGR
          RLDIAGR.ITRYL.KLLL..GY.FNHSA.FETVRMIKEKLCY.GYNI.QEQKLALE.TVLVESYTLPDGR
Retrocopy RLDIAGRNITRYLFKLLLFQGYTFNHSANFETVRMIKEKLCYMGYNIVQEQKLALEITVLVESYTLPDGR

Parental  IIKVGGERFEAPEALFQPHLINVEGVGVAELLFNTIQAADIDTRSEFYKHIVLSGGSTMYPGLPSRLERE
          IIKVGGER.E.PEALFQPHLIN.EG.GVAELLFNTIQAADIDTRSEFYKH.VLSGGSTMYPGLPSRLE.E
Retrocopy IIKVGGERSETPEALFQPHLINLEGAGVAELLFNTIQAADIDTRSEFYKHFVLSGGSTMYPGLPSRLE*E

Parental  LKQLYLERVLKGDVEKLSKFKIRIEDPPRRKHMVFLGGAVLADIMKDKDNFWMTRQEYQEKGVRVLEKLG
          LKQLYLERVLK.DVEKLS.FK..IEDPPRRKHMVFLGGA.LAD.MKDKDNFWMTRQEYQEKG.RVLEKLG
Retrocopy LKQLYLERVLKDDVEKLS*FKLCIEDPPRRKHMVFLGGAFLADTMKDKDNFWMTRQEYQEKGIRVLEKLG

Parental  VTVR
          VTVR
Retrocopy VTVR

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	0.06 RPM	267.05 RPM
SRP007412_cerebellum	0.00 RPM	136.56 RPM
SRP007412_heart	0.03 RPM	55.09 RPM
SRP007412_kidney	0.03 RPM	136.76 RPM
SRP007412_liver	0.06 RPM	68.21 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1877 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1877 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1877 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009761	1 retrocopy	retro_btau_707,
Callithrix jacchus	ENSCJAG00000006722	1 retrocopy	retro_cjac_429,
Homo sapiens	ENSG00000138071	1 retrocopy	retro_hsap_1978,
Gorilla gorilla	ENSGGOG00000008505	1 retrocopy	retro_ggor_1435,
Monodelphis domestica	ENSMODG00000003364	2 retrocopies	retro_mdom_1082, retro_mdom_754,
Mus musculus	ENSMUSG00000020152	1 retrocopy	retro_mmus_2989,
Pongo abelii	ENSPPYG00000012359	1 retrocopy	retro_pabe_1877 ,
Pan troglodytes	ENSPTRG00000011990	1 retrocopy	retro_ptro_1320,