RetrogeneDB ID: retro_ggor_1296

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 17:36136143..36137220(+)
• Located in intron of: ENSGGOG00000003300

Retrocopy information

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

Parental gene information

• Parental gene symbol: GNL3L
• Ensembl ID: ENSGGOG00000007550
• Aliases: None
• Description: None

Sequence

>retro_ggor_1296
GCTTTCAAGGCCAGGACCCAGCATCAGGTCAGCTTTGGAGCTGAAAACCTCATGAGGGTTCTGGGGAACTATTGCTGCCT
TGGTGAAGTGCGCACCCACATCCATATGGACGTTGTAGGCCTTCCCAATATTGGGAAGAGCAGCCTGATTAAAAGCCTGA
AGCACAGCCATGCATGCAGTGTGGGAGCCATTCCTGGGGTCACGAAATTCATGCAGGAGGTCTACCTGGACAAGTTCATC
CAGCTGCTGGATGCTCCAGCCATTGTTCCAGGGCCCAGCTCAGAGGTGGGGACCATCCTGCATAACTGCATCCACATCTA
GAGGCTGGCAGACCCCATGACCCCAGTGGAGACCATCTTGCAGTGCTGCAACCTGGAGGAGATTTCCAACTATTACCTTC
TCTCTGGGTACCAGACTACTGAGCACTTTCTGACGGCAGTGGCCCACCATTTGGGGAAGAAGAGAGACTTACACAGTCAG
GAGCAGGCAGCCAAAACTGTCCTAGCTGACTGGGTGAGCGGGAAGATCAGCTTCTGTAGACCACCACCACCCACTCACAC
TCTGCCTGCCCATCTCAGTGCTGAGAATTAAGGAAATGACCAAGGTCTTTGACATCGAGGATACCGAGCAGGTCAATGAA
GACACCATGGAATGCTTGGCCACTGGAGAATCTGATGAACTGTTGGGTGACACAGACCCACTCAAAATGGAGATCAAGTT
GCTCCATTCTCCAATGATGGAAATAGCAGATGCCATTGAAGATAAAGCTACTGTGTATAAGATTGGAGATCTCACTGGTT
ATTGCACCAATCCGAATCATCATCAGATGGGGTGGGCTAAACTCAATGTAGACCACCACCCTAAAAAAACAGTAAGGTGG
ATGTGTGCCCAGTGGACTGCTGCCCAGTACTGCAGAGGATCATGGAGATGGACCCCCTACAACAGGGCCAGGCTCTGGCA
TCCTCCCTGAAGAGTAAGAATTTACAGAAATGTGCAGATAAAATCCCCAGGGAGCTGTCTGATTCCATGATGTCTGCCCT
CCACCTCTCTGGCAATGCTGATGGCAGTGTTGGTAAC

Alignment

ORF - retro_ggor_1296 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.23 %
• Parental protein coverage: 62.37 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ASKSLLKSKACFGAESLMRVLGNYCRLGEVRTHIRVGVVGLPNVGKSSLINSLKRSRACSVGAVPGITKF
          A.K........FGAE.LMRVLGNYC.LGEVRTHI...VVGLPN.GKSSLI.SLK.S.ACSVGA.PG.TKF
Retrocopy AFKARTQHQVSFGAENLMRVLGNYCCLGEVRTHIHMDVVGLPNIGKSSLIKSLKHSHACSVGAIPGVTKF

Parental  MQEVYLDKFIRLLDAPGIVPGPNSEVGTILRNCVHVQKLADPVSPVETILQRCNLEEISNYYGVSGFQTT
          MQEVYLDKFI.LLDAP.IVPGP.SEVGTIL.NC.H...LADP..PVETILQ.CNLEEISNYY..SG.QTT
Retrocopy MQEVYLDKFIQLLDAPAIVPGPSSEVGTILHNCIHI*RLADPMTPVETILQCCNLEEISNYYLLSGYQTT

Parental  EHFLTAVAHRLGKKKKGGLYSQEQAAKAVLADWVSGKISFYI-PP-PATHTLPTHLSAEIVKEMTEVFDI
          EHFLTAVAH.LGKK....L.SQEQAAK.VLADWVSGKISF...PP.P.T..LP...S....KEMT.VFDI
Retrocopy EHFLTAVAHHLGKKRD--LHSQEQAAKTVLADWVSGKISFCRPPP>PLTLCLP--ISVLRIKEMTKVFDI

Parental  EDTEQANEDTMECLATGESDELLGDTDPLEMEIKLLHSPMTKIADAIENKTTVYKIGDLTGYCTNLNRHQ
          EDTEQ.NEDTMECLATGESDELLGDTDPL.MEIKLLHSPM..IADAIE.K.TVYKIGDLTGYCTN.N.HQ
Retrocopy EDTEQVNEDTMECLATGESDELLGDTDPLKMEIKLLHSPMMEIADAIEDKATVYKIGDLTGYCTNPNHHQ

Parental  MGWAKRNVDHRPK-SNSMVDVCSVDRRSVLQRIMETDPLQQGQALASALKNKKKMQKRADKIASKLSDSM
          MGWAK.NVDH.PK..NS.VDVC.VD...VLQRIME.DPLQQGQALAS.LK..K..QK.ADKI...LSDSM
Retrocopy MGWAKLNVDHHPK<KNSKVDVCPVDCCPVLQRIMEMDPLQQGQALASSLKS-KNLQKCADKIPRELSDSM

Parental  MSALDLSGNADDGVGD
          MSAL.LSGNAD..VG.
Retrocopy MSALHLSGNADGSVGN

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	0.38 RPM	4.36 RPM
SRP007412_cerebellum	0.16 RPM	4.73 RPM
SRP007412_heart	0.06 RPM	2.10 RPM
SRP007412_kidney	0.20 RPM	5.56 RPM
SRP007412_liver	0.08 RPM	4.62 RPM
SRP007412_testis	0.41 RPM	4.25 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_1296 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1296 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3327
Pongo abelii	retro_pabe_2742
Macaca mulatta	retro_mmul_2084
Callithrix jacchus	retro_cjac_1853

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000252	2 retrocopies	retro_cjac_1591, retro_cjac_1853,
Homo sapiens	ENSG00000130119	1 retrocopy	retro_hsap_3327,
Gorilla gorilla	ENSGGOG00000007550	1 retrocopy	retro_ggor_1296 ,
Microcebus murinus	ENSMICG00000010144	1 retrocopy	retro_mmur_662,
Macaca mulatta	ENSMMUG00000008231	1 retrocopy	retro_mmul_2084,
Nomascus leucogenys	ENSNLEG00000016233	1 retrocopy	retro_nleu_1672,
Oryzias latipes	ENSORLG00000014117	1 retrocopy	retro_olat_29,
Pongo abelii	ENSPPYG00000020383	1 retrocopy	retro_pabe_2742,