RetrogeneDB ID: retro_ptro_2078

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:115332402..115332726(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: WRB
• Ensembl ID: ENSPTRG00000013915
• Aliases: None
• Description: Pan troglodytes tryptophan rich basic protein (WRB), mRNA. [Source:RefSeq mRNA;Acc:NM_001251919]

Sequence

>retro_ptro_2078
GTGGGCACGGCTAAGGCTAACCACTGGGCGTGGCTGCTGGTGCTCAGATTCCTGTTTGGGTGCAGTGTCCTTCAGATCCT
ACTCCCGTCCTTCTCTTTTATGTCCAGGGTGCAGCGCAAGGATGCAGAACAGGAGTCGCAGATCAAAGCAGAGATCCAGG
ATATGAAGCAAGAGTTATCCGCGGTCAATATGATGGACAAGTTTGCCAGATCTGCCAGGCTGGAAAGAAAGATCAACAAG
ATGACGAATAAGCTCAAAACTCATGTGAAAGTACAGACAGCTCAATCAGGAATGCTAAAATGGGTTATAAGTGTTGCTTT
CTAC

Alignment

ORF - retro_ptro_2078 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.98 %
• Parental protein coverage: 62.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSSAAADHWAWLLVLSFVFGCNVLRILLPSFSSFMSRVLQKDAEQESQMRAEIQDMKQELSTVNMMDEFA
          ...A.A.HWAWLLVL.F.FGC.VL.ILLPSFS.FMSRV..KDAEQESQ..AEIQDMKQELS.VNMMD.FA
Retrocopy VGTAKANHWAWLLVLRFLFGCSVLQILLPSFS-FMSRVQRKDAEQESQIKAEIQDMKQELSAVNMMDKFA

Parental  RYARLERKINKMTDKLKTHVKARTAQLAKIKWVISVAFY
          R.ARLERKINKMT.KLKTHVK..TAQ....KWVISVAFY
Retrocopy RSARLERKINKMTNKLKTHVKVQTAQSGMLKWVISVAFY

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	0.05 RPM	44.20 RPM
SRP007412_cerebellum	0.00 RPM	41.44 RPM
SRP007412_heart	0.12 RPM	19.62 RPM
SRP007412_kidney	0.03 RPM	26.75 RPM
SRP007412_liver	0.00 RPM	14.34 RPM
SRP007412_testis	0.00 RPM	43.63 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2078 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2078 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2078 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3080
Pongo abelii	retro_pabe_2552
Macaca mulatta	retro_mmul_1966

---

Parental genes homology:

Parental genes homology involve 13 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005714	2 retrocopies	retro_cjac_2153, retro_cjac_3208,
Dasypus novemcinctus	ENSDNOG00000024987	1 retrocopy	retro_dnov_1496,
Homo sapiens	ENSG00000182093	1 retrocopy	retro_hsap_3080,
Gorilla gorilla	ENSGGOG00000013144	1 retrocopy	retro_ggor_2116,
Microcebus murinus	ENSMICG00000015808	1 retrocopy	retro_mmur_1275,
Macaca mulatta	ENSMMUG00000020654	2 retrocopies	retro_mmul_1966, retro_mmul_853,
Mus musculus	ENSMUSG00000023147	1 retrocopy	retro_mmus_1452,
Nomascus leucogenys	ENSNLEG00000013146	1 retrocopy	retro_nleu_2014,
Otolemur garnettii	ENSOGAG00000026761	1 retrocopy	retro_ogar_2691,
Pongo abelii	ENSPPYG00000011427	1 retrocopy	retro_pabe_2552,
Pan troglodytes	ENSPTRG00000013915	1 retrocopy	retro_ptro_2078 ,
Ictidomys tridecemlineatus	ENSSTOG00000012736	1 retrocopy	retro_itri_1744,
Tursiops truncatus	ENSTTRG00000015373	1 retrocopy	retro_ttru_1711,