RetrogeneDB ID: retro_pabe_1227

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 15:31273793..31274310(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000006323
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: U2AF1
• Ensembl ID: ENSPPYG00000011463
• Aliases: None
• Description: U2 small nuclear RNA auxiliary factor 1 [Source:HGNC Symbol;Acc:12453]

Sequence

>retro_pabe_1227
CCGACGTTTAGCCAGACCATTGCCCTCTTGAACATTTCCTGTAACCCTCAAAACTCTTCCCAGTCGGCCGACGGTTTGCG
CCGTGTCGTGAGCGATGTTGAGATGCGGGAACACTATGATGAATTTTTTGAGGAGGTTTTTATAGAATTGGGGGAGAAGT
ATGGGGAAGTTGAGGAGATGAACGTCTGTGACAACCTGGGAGACCACCTGGTGGGGAACGTGTACGTCAAGCTTCCCGGT
GAGAAAGATGCGGAAAAGGCTGTGATTGACTTGAACAAACCGTTGGTTTAACGGACAGCCGATCCACGCCGAGCTGTTAC
CTGTGATGGACTTCAGGGGAGCCTGCTGCCGTCAGTATGAGATGGGAGAATGCACACGAGGCGGCTTCTGCAACTTCATG
CATTTGAAGCCCATTTCCAGAGAGCTGCGGCGGGAGCTGTGTGGGCAGCGTCGCAAGAAGCGTAGATGAAGATCCCGATC
CCGGGAGCGTCGTTCTCGGTCTAGAGACCGTGGTCGT

Alignment

ORF - retro_pabe_1227 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.44 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PTFSQTIALLNIYRNPQNSSQSADGLRCAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHL
          PTFSQTIALLNI..NPQNSSQSADGLR..VSDVEM.EHYDEFFEEVF.E..EKYGEVEEMNVCDNLGDHL
Retrocopy PTFSQTIALLNISCNPQNSSQSADGLRRVVSDVEMREHYDEFFEEVFIELGEKYGEVEEMNVCDNLGDHL

Parental  VGNVYVKFRREEDAEKAVIDLN-NRWFNGQPIHAELSPVTDFREACCRQYEMGECTRGGFCNFMHLKPIS
          VGNVYVK...E.DAEKAVIDLN.NRWFNGQPIHAEL.PV.DFR.ACCRQYEMGECTRGGFCNFMHLKPIS
Retrocopy VGNVYVKLPGEKDAEKAVIDLN>NRWFNGQPIHAELLPVMDFRGACCRQYEMGECTRGGFCNFMHLKPIS

Parental  RELRRELYGRRRKKHRSRSRSRERRSRSRDRGR
          RELRREL.G.RRKK.R.RSRSRERRSRSRDRGR
Retrocopy RELRRELCGQRRKKRR*RSRSRERRSRSRDRGR

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	26.26 RPM
SRP007412_cerebellum	0.00 RPM	30.28 RPM
SRP007412_heart	0.00 RPM	13.79 RPM
SRP007412_kidney	0.03 RPM	30.73 RPM
SRP007412_liver	0.06 RPM	29.26 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1227 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1227 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1227 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1478
Pan troglodytes	retro_ptro_1000
Gorilla gorilla	retro_ggor_150

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000015558	1 retrocopy	retro_ecab_1081,
Homo sapiens	ENSG00000160201	2 retrocopies	retro_hsap_1478, retro_hsap_790,
Loxodonta africana	ENSLAFG00000011460	1 retrocopy	retro_lafr_1135,
Macaca mulatta	ENSMMUG00000022769	2 retrocopies	retro_mmul_1071, retro_mmul_2126,
Mus musculus	ENSMUSG00000061613	3 retrocopies	retro_mmus_1602, retro_mmus_1787, retro_mmus_2955,
Nomascus leucogenys	ENSNLEG00000014737	1 retrocopy	retro_nleu_2382,
Otolemur garnettii	ENSOGAG00000016504	1 retrocopy	retro_ogar_241,
Pongo abelii	ENSPPYG00000011463	2 retrocopies	retro_pabe_1227 , retro_pabe_703,