RetrogeneDB ID: retro_ggor_300

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 1:142360347..142361001(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRNT1
• Ensembl ID: ENSGGOG00000015286
• Aliases: None
• Description: None

Sequence

>retro_ggor_300
TTCCTACACTTTTATGGGACAATTGTAGAGCAACCTGGTGACCATGGTCCTGAAACTTTGTAAAAACTGCAGAAAATGCA
AAACGCTTGGGTGGAATATCAGGAATGAGGATTTGGGTGGAACTGAAAAAATTTTTGTTGGTAACCATGTAAATCATTTG
ATTCCCCTTATCCATGATCTTGATGTGGCTCCTTACATAGGTTTATCTGCTAATTAAAGTTTAGAAGAGTTTAATAAGGT
CAGTAAAAATGTTGAAGGTTTTTCACCAAAGTCAATGACTCTTTTTGCCTCATTATTCAAGTGATAGGACGATGTTGCAA
AAGTGGATCTGAGGTCGAAGACTGCACAAAAAAAGAAAAGTCTTGGATTATTTATGTTTAAAAATAGGAAAGATTTAATT
AAAGCAACAGATAGTTCAGAACCATTGAAACTCTATCAAGACTTCATTATAGGTTCCAGGGAACATGATGCAACTACTCA
TGTATGTGAGCTACTGAGGTACCAAGGAGAGCACTGTCTCTGAAAGGAAATGCAGCAACGGTGAATCCCATTTCCTGTAA
CTGTCATGACATCAGGAAAGTGGGGATCTCTTCAGGGAAAAAAATTGGGGCTCTATTACAACAGCTGGGAGAACAGTGGG
AAAAAAGTGGTTTC

Alignment

ORF - retro_ggor_300 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.23 %
• Parental protein coverage: 50.69 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  YFRFYGRIVDKPGDHDPETLEAI-AENAKGLAGISGERIWVELKKIL-VGNHVNHLIHLIYDLDVAPYIG
          ...FYG.IV..PGDH.PETL....AENAK.L.GISG.RIWVELKK.L.VGNHVNHLI.LI.DLDVAPYIG
Retrocopy FLHFYGTIVEQPGDHGPETL*KL<AENAKRLGGISGMRIWVELKKFL<VGNHVNHLIPLIHDLDVAPYIG

Parental  LPANASLEEFDKVSKNVDGFSPKPMTLLASLFKVQDDVTKLDLRLKIAKEEKNLGLFIVKNRKDLIKATD
          L.AN.SLEEF.KVSKNV.GFSPK.MTL.ASLFK..DDV.K.DLR.K.A...K.LGLF..KNRKDLIKATD
Retrocopy LSAN*SLEEFNKVSKNVEGFSPKSMTLFASLFK**DDVAKVDLRSKTAQKKKSLGLFMFKNRKDLIKATD

Parental  SSDPLKPYQDFIIDSREPDATTRVCELLKYQGEHCLLKEMQQWSIPPFPV-SGHDIRKVGISSGKEIGAL
          SS.PLK.YQDFII.SRE.DATT.VCELL.YQGEHCL.KEMQQ..I.PFPV...HDIRKVGISSGK.IGAL
Retrocopy SSEPLKLYQDFIIGSREHDATTHVCELLRYQGEHCL*KEMQQR*I-PFPV<NCHDIRKVGISSGKKIGAL

Parental  LQQLREQWKKSGY
          LQQL.EQW.KSG.
Retrocopy LQQLGEQWEKSGF

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	5.71 RPM
SRP007412_cerebellum	0.00 RPM	5.20 RPM
SRP007412_heart	0.00 RPM	1.38 RPM
SRP007412_kidney	0.00 RPM	8.46 RPM
SRP007412_liver	0.00 RPM	4.70 RPM
SRP007412_testis	0.00 RPM	14.19 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_300 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_300 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_246
Pongo abelii	retro_pabe_412

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015466	1 retrocopy	retro_cjac_1512,
Dasypus novemcinctus	ENSDNOG00000008837	1 retrocopy	retro_dnov_1635,
Dipodomys ordii	ENSDORG00000014035	1 retrocopy	retro_dord_414,
Echinops telfairi	ENSETEG00000018177	2 retrocopies	retro_etel_1871, retro_etel_905,
Homo sapiens	ENSG00000072756	2 retrocopies	retro_hsap_246, retro_hsap_2598,
Gorilla gorilla	ENSGGOG00000015286	1 retrocopy	retro_ggor_300 ,
Nomascus leucogenys	ENSNLEG00000003226	1 retrocopy	retro_nleu_856,
Petromyzon marinus	ENSPMAG00000002236	1 retrocopy	retro_pmar_17,
Pongo abelii	ENSPPYG00000013702	3 retrocopies	retro_pabe_1916, retro_pabe_2721, retro_pabe_412,
Pan troglodytes	ENSPTRG00000014564	1 retrocopy	retro_ptro_1522,
Rattus norvegicus	ENSRNOG00000006432	1 retrocopy	retro_rnor_512,