RetrogeneDB ID: retro_pabe_2285

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:10382833..10383195(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000013488
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HNRNPA1L2
• Ensembl ID: ENSPPYG00000025850
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein A1-like 2 [Source:HGNC Symbol;Acc:27067]

Sequence

>retro_pabe_2285
GGTTATGAAGGAGGCAGCCCTGGTTGCTCTGGAGGAAGCAGAGGCTATGGAAATGGTGGACAGGATTCTGGAAACCAGGG
CAGTGGCTATGATGGGGGTGGCAGCCATGACAGCTATAACAATGGAGTAGGCATAAGTGACTTTGGTGGTGAGAGTGGAA
GCAATTTGGGAGGGGGTGGAAGCTACAGTGATTTCTGAAAAAACAACAATCAATCTTAAAATTTGGACTCATGAAGGGAG
GGAACTTTGGAGGCAGAATCTCTGGCCCCTATGGTGGTGGAGACCAATACTTTGCCAAACCACAAAACCAAGGTGGCTAT
GGCAGTTCCAGCAACAGCAGTAGCTATGGCAATGGCAGAAGA

Alignment

ORF - retro_pabe_2285 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.87 %
• Parental protein coverage: 61.54 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GYGGGGPGYSGGSRGYGSGGQGYGNQGSGYGGSGSYDSYNNGGG-GCFGGGSGSNFGGGGSYNDFGNYNN
          GY.GG.PG.SGGSRGYG.GGQ..GNQGSGY.G.GS.DSYNNG.G...FGG.SGSN.GGGGSY.DF...NN
Retrocopy GYEGGSPGCSGGSRGYGNGGQDSGNQGSGYDGGGSHDSYNNGVGISDFGGESGSNLGGGGSYSDF*KNNN

Parental  QSSN-FGPMKGGNFGGRSSGPYGGGGQYFAKPRNQGGYGSSSSSSSYGSGRR
          QS.N.FG.MKGGNFGGR.SGPYGGG.QYFAKP.NQGGYGSSS.SSSYG.GRR
Retrocopy QS*N<FGLMKGGNFGGRISGPYGGGDQYFAKPQNQGGYGSSSNSSSYGNGRR

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	57.06 RPM
SRP007412_cerebellum	0.00 RPM	45.97 RPM
SRP007412_heart	0.00 RPM	44.37 RPM
SRP007412_kidney	0.00 RPM	78.09 RPM
SRP007412_liver	0.00 RPM	46.97 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2285 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2285 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2285 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_1427

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000009228	7 retrocopies	retro_dnov_1059, retro_dnov_1670, retro_dnov_1944, retro_dnov_2081, retro_dnov_250, retro_dnov_320, retro_dnov_374,
Loxodonta africana	ENSLAFG00000029587	5 retrocopies	retro_lafr_1202, retro_lafr_1208, retro_lafr_192, retro_lafr_747, retro_lafr_961,
Mustela putorius furo	ENSMPUG00000004620	1 retrocopy	retro_mputfur_34,
Mustela putorius furo	ENSMPUG00000005735	2 retrocopies	retro_mputfur_1378, retro_mputfur_653,
Oryctolagus cuniculus	ENSOCUG00000013350	1 retrocopy	retro_ocun_1675,
Oreochromis niloticus	ENSONIG00000012248	1 retrocopy	retro_onil_38,
Procavia capensis	ENSPCAG00000001867	5 retrocopies	retro_pcap_111, retro_pcap_162, retro_pcap_377, retro_pcap_424, retro_pcap_435,
Pongo abelii	ENSPPYG00000012967	1 retrocopy	retro_pabe_450,
Pongo abelii	ENSPPYG00000016107	1 retrocopy	retro_pabe_821,
Pongo abelii	ENSPPYG00000025850	4 retrocopies	retro_pabe_1765, retro_pabe_2285 , retro_pabe_3492, retro_pabe_3835,