RetrogeneDB ID: retro_ptro_222

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:150206961..150207410(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBM3
• Ensembl ID: ENSPTRG00000021864
• Aliases: None
• Description: None

Sequence

>retro_ptro_222
ATGTCCACTAAAGAAGGAAAGATCTTCGTGGGAGGGCTCAACATTAACACCGACGAGCAGGTGCTGGAAGACGACTTCAG
CAGCTTCGGGCCTGTCTCTGAGGTGGTCATTGTCAAGGAGACTCAGCGGTCCAGGGGTTTTGGTTTCATCACCATCACCA
ACCCAGACGCCATGAGAGCCATGAACAGAGAGTCCCTGGATGGTCACCAGATCCGCGTGGATCATGCAGGCAAGTCTGCT
GGGGAACCAGAGGAGGTGCCTTTGGGGCCCATGGGCGTGGTCACAGCTACTCTAGAGGTGGTGGGAACCAGGACTATGGG
AGTGGCAGGTATGACAGTTGACCTGGAGGGTATAGATATGGATATGGACAGTCCAGAGACTATAATGTCAGAAGCCCGGG
TGGTTATGACTGCTACTCAGAAGGAAATTACAGAAGCAATTATGACAAC

Alignment

ORF - retro_ptro_222 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.48 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSSEEGKLFVGGLNFNTDEQALEDHFSSFGPISEVVVVKDRETQRSRGFGFITFTNPEHASVAMRAMNGE
          MS..EGK.FVGGLN.NTDEQ.LED.FSSFGP.SEVV.VK..ETQRSRGFGFIT.TNP.....AMRAMN.E
Retrocopy MSTKEGKIFVGGLNINTDEQVLEDDFSSFGPVSEVVIVK--ETQRSRGFGFITITNPD----AMRAMNRE

Parental  SLDGRQIRVDHAGKSAR-GTRGGGFGAHGRGRSYSRGGGDQGYGSGRYYDSRPGGYGYGYGRSRDYNGRN
          SLDG.QIRVDHAGKSA..GTRGG.FGAHGRG.SYSRGGG.Q.YGSGR.YDS.PGGY.YGYG.SRDYN.R.
Retrocopy SLDGHQIRVDHAGKSAG<GTRGGAFGAHGRGHSYSRGGGNQDYGSGR-YDS*PGGYRYGYGQSRDYNVRS

Parental  QGGYDRYSGGNYRDNYDN
          .GGYD.YS.GNYR.NYDN
Retrocopy PGGYDCYSEGNYRSNYDN

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	29.92 RPM
SRP007412_cerebellum	0.00 RPM	99.41 RPM
SRP007412_heart	0.00 RPM	138.79 RPM
SRP007412_kidney	0.00 RPM	141.77 RPM
SRP007412_liver	0.00 RPM	197.68 RPM
SRP007412_testis	0.00 RPM	30.98 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_222 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_222 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_222 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_265
Pongo abelii	retro_pabe_40

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 31 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,
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	ENSPPYG00000020314	1 retrocopy	retro_pabe_40,
Pan troglodytes	ENSPTRG00000018988	1 retrocopy	retro_ptro_299,
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,