RetrogeneDB ID: retro_ptro_2383

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:118558513..118558973(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAP1B
• Ensembl ID: ENSPTRG00000005197
• Aliases: None
• Description: Pan troglodytes RAP1B, member of RAS oncogene family (RAP1B), mRNA. [Source:RefSeq mRNA;Acc:NM_001098545]

Sequence

>retro_ptro_2383
ATGCTTGAGTATAAATTAGTCATTCTTGGCTCAGGAGCTGTTGGAAATTCTGCTTTGACTGTACAATTTGTACAAAGAAT
TTTGTTGAAAAACATGGTCCTACAATAAAAGATATTACAGAAAGCAAGTGGAAATAGATGCACAACTCTGTATGCTTGAC
ATATTGGATACTGCAGGAACAGAACAATTTACAGCAATAAAGGGTTTGTACGTAAAAAATGGACAAGGCTTGGTATTAGC
ATATACCATCCCAGCACAGTCCACATTTTATGATTTACAAGATCTGAGAGAACAGATTCTTTAAGTTAAAGACACTGATA
TTGTCCCAGTGATTGTTGGTAATAAGTGTGACTTGGAAGATAAAAGAGTTGTAGGGAAGGAACAAGGTCAAAATCTAGCA
AGACAATGGAACAACTGTGCATTCTTAGAATCTTCTGCAAAATAAAAAATAAATCTTAAT

Alignment

ORF - retro_ptro_2383 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.62 %
• Parental protein coverage: 84.24 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MREYKLVVLGSGGVGKSALTVQFVQGI-FVEKYDPTIEDS-YRKQVEVDAQQCMLEILDTAGTEQFTAMR
          M.EYKLV.LGSG.VG.SALTVQFVQ.I.FVEK..PTI.D..YRKQVE.DAQ.CML.ILDTAGTEQFTA..
Retrocopy MLEYKLVILGSGAVGNSALTVQFVQRI<FVEKHGPTIKDI<YRKQVEIDAQLCMLDILDTAGTEQFTAIK

Parental  DLYMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTDDVPMILVGNKCDLEDERVVGKEQGQNLARQW
          .LY.KNGQG..L.Y.I.AQSTF.DLQDLREQIL.VKDTD.VP...VGNKCDLED.RVVGKEQGQNLARQW
Retrocopy GLYVKNGQGLVLAYTIPAQSTFYDLQDLREQIL*VKDTDIVP-VIVGNKCDLEDKRVVGKEQGQNLARQW

Parental  NNCAFLESSAKSKINVN
          NNCAFLESSAK.KIN.N
Retrocopy NNCAFLESSAK*KINLN

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	19.66 RPM
SRP007412_cerebellum	0.00 RPM	18.82 RPM
SRP007412_heart	0.00 RPM	31.92 RPM
SRP007412_kidney	0.00 RPM	67.97 RPM
SRP007412_liver	0.00 RPM	50.28 RPM
SRP007412_testis	0.00 RPM	82.09 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2383 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2383 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2383 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_1863

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 50 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008637	1 retrocopy	retro_amel_103,
Cavia porcellus	ENSCPOG00000008272	4 retrocopies	retro_cpor_1194, retro_cpor_632, retro_cpor_739, retro_cpor_85,
Dasypus novemcinctus	ENSDNOG00000019724	18 retrocopies	retro_dnov_1243, retro_dnov_1249, retro_dnov_1323, retro_dnov_1395, retro_dnov_1574, retro_dnov_1710, retro_dnov_1763, retro_dnov_1841, retro_dnov_186, retro_dnov_1976, retro_dnov_2033, retro_dnov_217, retro_dnov_2679, retro_dnov_298, retro_dnov_318, retro_dnov_719, retro_dnov_761, retro_dnov_84,
Erinaceus europaeus	ENSEEUG00000010052	1 retrocopy	retro_eeur_327,
Echinops telfairi	ENSETEG00000000242	1 retrocopy	retro_etel_11,
Gorilla gorilla	ENSGGOG00000025649	1 retrocopy	retro_ggor_2836,
Loxodonta africana	ENSLAFG00000016460	1 retrocopy	retro_lafr_482,
Microcebus murinus	ENSMICG00000013148	1 retrocopy	retro_mmur_116,
Macaca mulatta	ENSMMUG00000011442	2 retrocopies	retro_mmul_1151, retro_mmul_1863,
Oryctolagus cuniculus	ENSOCUG00000029552	5 retrocopies	retro_ocun_1132, retro_ocun_1200, retro_ocun_597, retro_ocun_636, retro_ocun_796,
Otolemur garnettii	ENSOGAG00000005746	2 retrocopies	retro_ogar_2260, retro_ogar_272,
Pongo abelii	ENSPPYG00000004751	1 retrocopy	retro_pabe_3403,
Pan troglodytes	ENSPTRG00000001102	1 retrocopy	retro_ptro_937,
Pan troglodytes	ENSPTRG00000005197	3 retrocopies	retro_ptro_1812, retro_ptro_2383 , retro_ptro_2877,
Pan troglodytes	ENSPTRG00000019108	1 retrocopy	retro_ptro_2511,
Rattus norvegicus	ENSRNOG00000007048	4 retrocopies	retro_rnor_2479, retro_rnor_870, retro_rnor_871, retro_rnor_872,
Sus scrofa	ENSSSCG00000021148	1 retrocopy	retro_sscr_1125,
Sus scrofa	ENSSSCG00000030014	2 retrocopies	retro_sscr_435, retro_sscr_909,