RetrogeneDB ID: retro_pabe_40

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:79315497..79315770(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000000510
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RBM3
• Ensembl ID: ENSPPYG00000020314
• Aliases: None
• Description: RNA binding motif (RNP1, RRM) protein 3 [Source:RefSeq peptide;Acc:NP_001124733]

Sequence

>retro_pabe_40
ATGTCCACTAAAGAAGGAAAGCTCTTCGTGGGAGGGCTCAACGTTAACACCGACAAGCAGGTGCTGGAAGACCACTTCAG
CAGCTTCGGGCCTGTCTCTGAGGTGGTCATTGTCAAGGAGACTCAGCGGTCCAGGGGTTTTGGTTTTATCACCATCACCA
ACCCAGATGCCATGAGAGCCATGAACAGAGAGTCCCTGGATGGTCACCTGATCCGTGTGGATCATGCAGGCAAGTCTGCG
GGGGAACAAGAGGAGGTGCCTTTGGGGCCCATG

Alignment

ORF - retro_pabe_40 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.07 %
• Parental protein coverage: 54.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSSEEGKLFVGGLNFNTDEQALEDHFSSFGPISEVVVVKDRETQRSRGFGFITFTNPEHASVAMRAMNGE
          MS..EGKLFVGGLN.NTD.Q.LEDHFSSFGP.SEVV.VK..ETQRSRGFGFIT.TNP.....AMRAMN.E
Retrocopy MSTKEGKLFVGGLNVNTDKQVLEDHFSSFGPVSEVVIVK--ETQRSRGFGFITITNPD----AMRAMNRE

Parental  SLDGRQIRVDHAGKSA
          SLDG..IRVDHAGKSA
Retrocopy SLDGHLIRVDHAGKSA

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	14.10 RPM
SRP007412_cerebellum	0.00 RPM	13.50 RPM
SRP007412_heart	0.00 RPM	14.81 RPM
SRP007412_kidney	0.00 RPM	26.22 RPM
SRP007412_liver	0.00 RPM	19.46 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_40 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_40 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_40 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_265
Pan troglodytes	retro_ptro_222

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 51 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000013718	1 retrocopy	retro_acar_197,
Ailuropoda melanoleuca	ENSAMEG00000012653	1 retrocopy	retro_amel_519,
Bos taurus	ENSBTAG00000025848	1 retrocopy	retro_btau_1144,
Canis familiaris	ENSCAFG00000015485	2 retrocopies	retro_cfam_1475, retro_cfam_259,
Cavia porcellus	ENSCPOG00000003553	1 retrocopy	retro_cpor_950,
Dasypus novemcinctus	ENSDNOG00000010420	16 retrocopies	retro_dnov_1343, retro_dnov_1380, retro_dnov_1463, retro_dnov_151, retro_dnov_1718, retro_dnov_180, retro_dnov_2034, retro_dnov_2076, retro_dnov_212, retro_dnov_213, retro_dnov_2217, retro_dnov_2367, retro_dnov_2581, retro_dnov_733, retro_dnov_778, retro_dnov_974,
Dipodomys ordii	ENSDORG00000000182	1 retrocopy	retro_dord_547,
Equus caballus	ENSECAG00000024257	2 retrocopies	retro_ecab_130, retro_ecab_589,
Homo sapiens	ENSG00000102317	1 retrocopy	retro_hsap_265,
Gadus morhua	ENSGMOG00000012137	1 retrocopy	retro_gmor_4,
Loxodonta africana	ENSLAFG00000007003	1 retrocopy	retro_lafr_1091,
Myotis lucifugus	ENSMLUG00000003996	1 retrocopy	retro_mluc_1013,
Mus musculus	ENSMUSG00000031167	4 retrocopies	retro_mmus_2044, retro_mmus_2963, retro_mmus_3019, retro_mmus_501,
Nomascus leucogenys	ENSNLEG00000007841	2 retrocopies	retro_nleu_2591, retro_nleu_867,
Pongo abelii	ENSPPYG00000017728	1 retrocopy	retro_pabe_324,
Pongo abelii	ENSPPYG00000020314	1 retrocopy	retro_pabe_40 ,
Pongo abelii	ENSPPYG00000020771	3 retrocopies	retro_pabe_2548, retro_pabe_303, retro_pabe_766,
Pan troglodytes	ENSPTRG00000021864	1 retrocopy	retro_ptro_222,
Pteropus vampyrus	ENSPVAG00000015630	1 retrocopy	retro_pvam_953,
Sus scrofa	ENSSSCG00000021591	1 retrocopy	retro_sscr_842,
Ictidomys tridecemlineatus	ENSSTOG00000027493	1 retrocopy	retro_itri_142,
Tarsius syrichta	ENSTSYG00000008670	4 retrocopies	retro_tsyr_1733, retro_tsyr_197, retro_tsyr_2002, retro_tsyr_679,
Tursiops truncatus	ENSTTRG00000008587	3 retrocopies	retro_ttru_1898, retro_ttru_928, retro_ttru_938,