RetrogeneDB ID: retro_ggor_2486

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 6:147733530..147734303(-)
• Located in intron of: ENSGGOG00000001069

Retrocopy information

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

Parental gene information

• Parental gene symbol: C15ORF29
• Ensembl ID: ENSGGOG00000014230
• Aliases: None
• Description: None

Sequence

>retro_ggor_2486
ATGGCATCGGAAACTCACAATGTTAAAAAACGGAACTTTTGTAATAAGATTGAGGATCATTTCATTGATCTTCCTAGAAA
AAAAGATCTCTAATTTCACTGATAAGAACATGAAGGAGGTTAAGAAGTCTCCAAAACAGTTGGCTGCTTACATAAATAGA
ACAGTTGGACAAACTGTGAAAAGCCCAGATAAACTTCGTAAAGTGATCTATCGCAGAAAGAAAGTTCATCATCCCTTTCC
AAATCTTTGTTGCAGAAAAAAACAGCCCCCTGGAAGGTCGGGGCTGTGACATGGCAAATAAAGAAAATGAACTGGCTTGT
GCAGGCCACCAGACTGAAAAATTACACCATGACAGTCGAACATATTTGGTTAACTCCAGTGATTCTGGTTCTTCACAGAC
AGAAAGCCCATCATCAAAATATAGTGGGTTTTTTTCTGAGGTTTCTCAGGACCATGAAACAATGGTCCAAGTTTTGTTCA
GCAGGAATAGGAGATTGAATGTAGCTTTAATTTTCTGGAGAAAGAGAAGTATAAGTGAACTTGTAGCTTATTTGTTGAGG
ATAGAAGATCTTGGCGTTGTGGTAGATTGCCTTCCTGTGCTCACCAATTGTTTACAGGAAGAAAAACAATATATCTCACT
TGGCTGCTGTGTAGACTTGTTGCCTCTAGTAAAGTCACTACTTAAAAGCAAATTTGAAGAATATGTTATAGTTGGTTTAA
ACTGGCTTCAAGCAGTCATTAAAAGGTGGTGGTCAGAACTATCATCCAAAACA

Alignment

ORF - retro_ggor_2486 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.14 %
• Parental protein coverage: 84.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MASETHNVKKRNFCNKIEDHFIDLPRKK-ISNFTDKNMKEVKKSPKQLAAYINRTVGQTVKSPDKLRKVI
          MASETHNVKKRNFCNKIEDHFIDLPRKK.ISNFTDKNMKEVKKSPKQLAAYINRTVGQTVKSPDKLRKVI
Retrocopy MASETHNVKKRNFCNKIEDHFIDLPRKK>ISNFTDKNMKEVKKSPKQLAAYINRTVGQTVKSPDKLRKVI

Parental  YRRKKVHHPFPNPCYRKKQSPGRSG-CDMANKENELACAGHLPEKLHHDSRTYLVNSSDSGSSQTESPSS
          YRRKKVHHPFPN.C.RKKQ.PGRSG.CDMANKENELACAGH..EKLHHDSRTYLVNSSDSGSSQTESPSS
Retrocopy YRRKKVHHPFPNLCCRKKQPPGRSG>CDMANKENELACAGHQTEKLHHDSRTYLVNSSDSGSSQTESPSS

Parental  KYSGFFSEVSQDHETMAQVLFSRNMRLNVALTFWRKRSISELVAYLLRIEDLGVVVDCLPVLTNCLQEEK
          KYSGFFSEVSQDHETM.QVLFSRN.RLNVAL.FWRKRSISELVAYLLRIEDLGVVVDCLPVLTNCLQEEK
Retrocopy KYSGFFSEVSQDHETMVQVLFSRNRRLNVALIFWRKRSISELVAYLLRIEDLGVVVDCLPVLTNCLQEEK

Parental  QYISLGCCVDLLPLVKSLLKSKFEEYVIVGLNWLQAVIKRWWSELSSKT
          QYISLGCCVDLLPLVKSLLKSKFEEYVIVGLNWLQAVIKRWWSELSSKT
Retrocopy QYISLGCCVDLLPLVKSLLKSKFEEYVIVGLNWLQAVIKRWWSELSSKT

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	2.40 RPM
SRP007412_cerebellum	0.00 RPM	2.84 RPM
SRP007412_heart	0.00 RPM	0.44 RPM
SRP007412_kidney	0.00 RPM	3.72 RPM
SRP007412_liver	0.00 RPM	2.66 RPM
SRP007412_testis	0.00 RPM	6.22 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_2486 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2486 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3677
Pan troglodytes	retro_ptro_2491

---

Parental genes homology:

Parental genes homology involve 24 parental genes, and 63 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006413	2 retrocopies	retro_btau_1198, retro_btau_1776,
Callithrix jacchus	ENSCJAG00000021110	3 retrocopies	retro_cjac_1971, retro_cjac_265, retro_cjac_2971,
Cavia porcellus	ENSCPOG00000011153	2 retrocopies	retro_cpor_1374, retro_cpor_1410,
Dasypus novemcinctus	ENSDNOG00000016279	5 retrocopies	retro_dnov_1586, retro_dnov_2201, retro_dnov_2253, retro_dnov_248, retro_dnov_957,
Dipodomys ordii	ENSDORG00000013172	2 retrocopies	retro_dord_378, retro_dord_730,
Equus caballus	ENSECAG00000023450	1 retrocopy	retro_ecab_841,
Echinops telfairi	ENSETEG00000001640	7 retrocopies	retro_etel_1169, retro_etel_1341, retro_etel_2032, retro_etel_2062, retro_etel_319, retro_etel_518, retro_etel_635,
Homo sapiens	ENSG00000134152	3 retrocopies	retro_hsap_3171, retro_hsap_3677, retro_hsap_425,
Gorilla gorilla	ENSGGOG00000014230	3 retrocopies	retro_ggor_1347, retro_ggor_2486 , retro_ggor_415,
Macropus eugenii	ENSMEUG00000015610	4 retrocopies	retro_meug_1035, retro_meug_1899, retro_meug_1900, retro_meug_646,
Myotis lucifugus	ENSMLUG00000001532	2 retrocopies	retro_mluc_214, retro_mluc_633,
Macaca mulatta	ENSMMUG00000000013	1 retrocopy	retro_mmul_2005,
Mustela putorius furo	ENSMPUG00000008019	1 retrocopy	retro_mputfur_1258,
Nomascus leucogenys	ENSNLEG00000010772	2 retrocopies	retro_nleu_1020, retro_nleu_2679,
Oryctolagus cuniculus	ENSOCUG00000017654	5 retrocopies	retro_ocun_1065, retro_ocun_343, retro_ocun_614, retro_ocun_877, retro_ocun_975,
Otolemur garnettii	ENSOGAG00000015633	3 retrocopies	retro_ogar_1643, retro_ogar_2219, retro_ogar_3301,
Ochotona princeps	ENSOPRG00000010379	1 retrocopy	retro_opri_446,
Pongo abelii	ENSPPYG00000006309	2 retrocopies	retro_pabe_2634, retro_pabe_646,
Pan troglodytes	ENSPTRG00000006877	3 retrocopies	retro_ptro_2271, retro_ptro_2491, retro_ptro_323,
Sorex araneus	ENSSARG00000007891	1 retrocopy	retro_sara_345,
Ictidomys tridecemlineatus	ENSSTOG00000003813	1 retrocopy	retro_itri_1292,
Tupaia belangeri	ENSTBEG00000001614	7 retrocopies	retro_tbel_1267, retro_tbel_127, retro_tbel_1362, retro_tbel_2139, retro_tbel_3276, retro_tbel_4552, retro_tbel_984,
Tarsius syrichta	ENSTSYG00000011059	1 retrocopy	retro_tsyr_2135,
Vicugna pacos	ENSVPAG00000007170	1 retrocopy	retro_vpac_632,