RetrogeneDB ID: retro_ggor_2836

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 9:19092113..19092665(-)
• Located in intron of: ENSGGOG00000010914

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAP1B
• Ensembl ID: ENSGGOG00000025649
• Aliases: None
• Description: None

Sequence

>retro_ggor_2836
ATGCATGAGTATAAGCTAGTTATTCTTGGCCCAGGAGGCGTTGGAAAGTCTGCTTTGAATGTACAATTTGTTCAAGGAAT
TTTTGTTGAAAAATATGTCCTATGATAGAAGATTCTTATACAAAGCAAGTTGAAGTAGATGCACAACAGTGTATGCTTGC
AATCTTGGATACTGCAAGAATGGAACAACGTATAGCAAGGAGGGATTTGTACATGAGAAATGGACAAGGCTTTGCATTAG
TTTATTCCATCACAGCACAGTCCACATTTAATGATTTGCAAGACTTGAGAGAACAGATTGTTTGAGTTAAAGACACTGAT
GATGTTCCAATGACTCTTGTTGGTAATAAGTATGACTTGGAAGATGAAAGAGCTGTACGGAAGGAACAAGGTCAAAAATC
TAGCAAGACAATGGAACAACTGTGCATTCTTAGATTCTTCTACAAAATCAAAAATAAATGTTAATGAGATCTTTTATGAC
CTAGTGCGGCAGATTAACAGAAAAACTCCAGTGCCTGGGAAGGCTCGCAAAAAGTCATCATGTCAGCTGCTT

Alignment

ORF - retro_ggor_2836 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.1 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MREYKLVVLGSGGVGKSALTVQFVQGIFVEKYD-PTIEDSYRKQVEVDAQQCMLEILDTAGTEQFTAMRD
          M.EYKLV.LG.GGVGKSAL.VQFVQGIFVEKY..P.IEDSY.KQVEVDAQQCML.ILDTA..EQ..A.RD
Retrocopy MHEYKLVILGPGGVGKSALNVQFVQGIFVEKYV<PMIEDSYTKQVEVDAQQCMLAILDTARMEQRIARRD

Parental  LYMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTDDVPMILVGNKCDLEDERVVGKEQGQ-NLARQW
          LYM.NGQGFALVYSITAQSTFNDLQDLREQI..VKDTDDVPM.LVGNK.DLEDER.V.KEQGQ.NLARQW
Retrocopy LYMRNGQGFALVYSITAQSTFNDLQDLREQIV*VKDTDDVPMTLVGNKYDLEDERAVRKEQGQ>NLARQW

Parental  NNCAFLESSAKSKINVNEIFYDLVRQINRKTPVPGKARKKSSCQLL
          NNCAFL.SS.KSKINVNEIFYDLVRQINRKTPVPGKARKKSSCQLL
Retrocopy NNCAFLDSSTKSKINVNEIFYDLVRQINRKTPVPGKARKKSSCQLL

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	16.26 RPM
SRP007412_cerebellum	0.00 RPM	19.42 RPM
SRP007412_heart	0.00 RPM	7.97 RPM
SRP007412_kidney	0.04 RPM	77.85 RPM
SRP007412_liver	0.00 RPM	55.50 RPM
SRP007412_testis	0.00 RPM	78.01 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2836 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2836 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4234
Pan troglodytes	retro_ptro_2877
Pongo abelii	retro_pabe_3403
Macaca mulatta	retro_mmul_1151
Callithrix jacchus	retro_cjac_607

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 58 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008637	1 retrocopy	retro_amel_103,
Callithrix jacchus	ENSCJAG00000007261	3 retrocopies	retro_cjac_1435, retro_cjac_2371, retro_cjac_607,
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,
Gorilla gorilla	ENSGGOG00000001648	1 retrocopy	retro_ggor_79,
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,
Mus musculus	ENSMUSG00000052681	1 retrocopy	retro_mmus_1370,
Nomascus leucogenys	ENSNLEG00000003573	2 retrocopies	retro_nleu_1034, retro_nleu_481,
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,
Pan troglodytes	ENSPTRG00000005197	3 retrocopies	retro_ptro_1812, retro_ptro_2383, retro_ptro_2877,
Rattus norvegicus	ENSRNOG00000007048	4 retrocopies	retro_rnor_2479, retro_rnor_870, retro_rnor_871, retro_rnor_872,
Sarcophilus harrisii	ENSSHAG00000011497	1 retrocopy	retro_shar_425,
Sus scrofa	ENSSSCG00000030014	2 retrocopies	retro_sscr_435, retro_sscr_909,
Tupaia belangeri	ENSTBEG00000013380	4 retrocopies	retro_tbel_2145, retro_tbel_4650, retro_tbel_4658, retro_tbel_613,
Tarsius syrichta	ENSTSYG00000000192	1 retrocopy	retro_tsyr_910,