RetrogeneDB ID: retro_ggor_2996

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: X:41969679..41970084(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SHISA5
• Ensembl ID: ENSGGOG00000028207
• Aliases: None
• Description: None

Sequence

>retro_ggor_2996
GGGTTCAGAGCGACTGTGGCCGTCGGCCTGACCATCTTTGTGCTGTCTGTTGTCACTATCATCATCTGCTTCACCTGCTC
CTGCTGCTCCCTCTACAAGATGTGCCACTGACCACGTGCAGTTGTGACCACTACCACGCCCACCACTGTGGTGCATGCCC
CTTACCCTCAGCCTCCAAGTGTGCCACCTAGCTACCCTGGACTACCAGGGCTACCACCCCATGCCCCCCCCCCCCAGCCA
GGAATGCCAGCAGCACCCTACCCAGTGCAGTACCCATCACCTTACCCGGCCCAGCCCATGGGCCTGCCGGCCTACTTCGA
GACCCTGGCTGGAGGAGCAGCCACACCCTACCCCACCAGCCAGCCTCCTTCCAACCCAGACTACATGGATGCCCCGAAGG
CGGCC

Alignment

ORF - retro_ggor_2996 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.26 %
• Parental protein coverage: 56.25 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GFGATLAVGLTIFVLSVVTIIICFTCSCCCLYKTCRRPRPVVTTTTSTTVVHAPYPQPPSVPPSYPGPSY
          GF.AT.AVGLTIFVLSVVTIIICFTCSCC.LYK.C..PR.VVTTTT.TTVVHAPYPQPPSVPPSYPG...
Retrocopy GFRATVAVGLTIFVLSVVTIIICFTCSCCSLYKMCH*PRAVVTTTTPTTVVHAPYPQPPSVPPSYPGLPG

Parental  QGYHTMPPQPGMPAAPYPMQYPPPYPAQPMGPPAYHETLAEGAAAPYPASQPPYNPAYMDAPKAA
          ...H.....PGMPAAPYP.QYP.PYPAQPMG.PAY.ETLA.GAA.PYP.SQPP.NP.YMDAPKAA
Retrocopy LPPHXXXXXPGMPAAPYPVQYPSPYPAQPMGLPAYFETLAGGAATPYPTSQPPSNPDYMDAPKAA

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	131.20 RPM
SRP007412_cerebellum	0.00 RPM	68.28 RPM
SRP007412_heart	0.03 RPM	35.21 RPM
SRP007412_kidney	0.00 RPM	67.79 RPM
SRP007412_liver	0.00 RPM	32.95 RPM
SRP007412_testis	0.00 RPM	35.95 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_2996 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2996 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4812
Macaca mulatta	retro_mmul_2565
Callithrix jacchus	retro_cjac_4152

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002915	2 retrocopies	retro_cjac_4077, retro_cjac_4152,
Homo sapiens	ENSG00000164054	2 retrocopies	retro_hsap_4706, retro_hsap_4812,
Gorilla gorilla	ENSGGOG00000028207	2 retrocopies	retro_ggor_2996 , retro_ggor_86,
Macaca mulatta	ENSMMUG00000010062	1 retrocopy	retro_mmul_2565,
Nomascus leucogenys	ENSNLEG00000006485	1 retrocopy	retro_nleu_1984,
Pongo abelii	ENSPPYG00000013902	3 retrocopies	retro_pabe_2120, retro_pabe_3653, retro_pabe_3739,
Pan troglodytes	ENSPTRG00000014888	1 retrocopy	retro_ptro_3128,