RetrogeneDB ID: retro_ggor_1109

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 14:54796498..54796994(-)
• Located in intron of: ENSGGOG00000015023

Retrocopy information

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

Parental gene information

• Parental gene symbol: NT5C
• Ensembl ID: ENSGGOG00000004740
• Aliases: None
• Description: None

Sequence

>retro_ggor_1109
GGCCTCCTGCGGGGCTTCAGCCGCTGCTTCTCAGGGAGCTGCATGTGACACTGCATCAGCACCTCAGCTTCCTGGTCTGG
AAGCAGTACCGCACCCTGCTGCCGGACCTGGTGGATAAAGTGGCCCATGGGTGTGAAGCCCTAGGCTTTTCCCTAGTCTT
GAAGCCCAACCCCGGAGGACCTTGCAAGAGATGAAGCACATGCAAAACACCGAGGTCGTCACACTGCACCAGCCCCTGCC
AAAGTATGACCACTGTGTGGGTGAGAAGCACTGCTGGGTAGAGCAGCACCTGGAGCCCCAGCTTGTGGAGTGAATTATCC
TGACAATGGACAAGACCGTGGTCTTTGGGGACTTGCTCACTGATGACAAGGATACCATTCGAGGCCAAGAGGAGAGGCCA
CAATAGTACCTGGTCCTGCCATGCATAGGGACGCGGCTGCTCTCCTGGAATGGTAACAGGAGGGAGATCATAGCCAGCCA
GCAGGGAGCTAGGCAG

Alignment

ORF - retro_ggor_1109 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.05 %
• Parental protein coverage: 79.72 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GLLRGFRRRFP-EEPHVPLEQRRGFLAREQYRALRPDLADKVASVYEAPGF-FLDLEPIPGALDAVREMN
          GLLRGF.R.F...E.HV.L.Q...FL...QYR.L.PDL.DKVA...EA.GF.F..LE..P.......EM.
Retrocopy GLLRGFSRCFS<RELHVTLHQHLSFLVWKQYRTLLPDLVDKVAHGCEALGF<FPSLEAQPRR--TLQEMK

Parental  DLPDTQVFICTSPLLKYHHCVGEKYRWVEQHLGPQFVERIILTRDKTVVLGDLLIDDKDTIRGQEETPSW
          ....T.V.....PL.KY.HCVGEK..WVEQHL.PQ.VE.IILT.DKTVV.GDLL.DDKDTIRGQEE.P..
Retrocopy HMQNTEVVTLHQPLPKYDHCVGEKHCWVEQHLEPQLVE*IILTMDKTVVFGDLLTDDKDTIRGQEERPQ-

Parental  EHILFTCCHNRHLVLPPTRRRLLSWSDNWRE
          ......C...R.L.....RR.........R.
Retrocopy *YLVLPCIGTRLLSWNGNRREIIASQQGARQ

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	4.60 RPM
SRP007412_cerebellum	0.00 RPM	14.03 RPM
SRP007412_heart	0.00 RPM	3.94 RPM
SRP007412_kidney	0.00 RPM	8.67 RPM
SRP007412_liver	0.00 RPM	5.57 RPM
SRP007412_testis	0.00 RPM	5.91 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_1109 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1109 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Callithrix jacchus	retro_cjac_810

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009175	1 retrocopy	retro_amel_1684,
Callithrix jacchus	ENSCJAG00000014578	1 retrocopy	retro_cjac_810,
Felis catus	ENSFCAG00000031408	2 retrocopies	retro_fcat_1016, retro_fcat_606,
Homo sapiens	ENSG00000125458	2 retrocopies	retro_hsap_1441, retro_hsap_1442,
Gorilla gorilla	ENSGGOG00000004740	2 retrocopies	retro_ggor_1061, retro_ggor_1109 ,
Microcebus murinus	ENSMICG00000017488	1 retrocopy	retro_mmur_1088,
Mustela putorius furo	ENSMPUG00000013985	1 retrocopy	retro_mputfur_1352,
Nomascus leucogenys	ENSNLEG00000000601	2 retrocopies	retro_nleu_1083, retro_nleu_1416,
Pongo abelii	ENSPPYG00000008619	1 retrocopy	retro_pabe_1195,