RetrogeneDB ID: retro_ggor_255

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 1:80378351..80378711(+)
• Located in intron of: ENSGGOG00000004987

Retrocopy information

• Ensembl ID: ENSGGOG00000027765
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SSR3
• Ensembl ID: ENSGGOG00000024038
• Aliases: None
• Description: None

Sequence

>retro_ggor_255
ATGGCTCCCAAAGGCAGCTCCAAACAGCCGTCCGAGGAGGACCTGCTCCTGCAGGATTTCAGCGGCAACCTCTCGGCCAA
GTCCTTCGCGATCTTCTTCCGGAATGCGTTCGTCGTGTCTGCCATCCCCATCTGGTTATACTGGAGAATATGGCATATGG
ATCTTATTCAGTCTGCTGTTTTCTATAGTGTGATGACCCTAGAAAGCACATATTTGGTAGCCTTTGCATACAAGAATGTT
AAATTTGTTCTCAAGCACAAAGTAGCACAGAAGAGGGAGGATACTGTTTCCAAAGAAGTGACTAGAAAACTTTCTGAAGC
TGATAATAGAAAGATGTCTCGGAAGGAGAAAGATGTAAGA

Alignment

ORF - retro_ggor_255 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.67 %
• Parental protein coverage: 60.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAPKGSSKQQSEEDLLLQDFSRNLSAKSSALFFGNAFIVSAIPIWLYWRIWHMDLIQSAVLYSVMTLVST
          MAPKGSSKQ.SEEDLLLQDFS.NLSAKS.A.FF.NAF.VSAIPIWLYWRIWHMDLIQSAV.YSVMTL.ST
Retrocopy MAPKGSSKQPSEEDLLLQDFSGNLSAKSFAIFFRNAFVVSAIPIWLYWRIWHMDLIQSAVFYSVMTLEST

Parental  YLVAFAYKNVKFVLKHKVAQKREDAVSKEVTRKLSEADNRKMSRKEKDER
          YLVAFAYKNVKFVLKHKVAQKRED.VSKEVTRKLSEADNRKMSRKEKD.R
Retrocopy YLVAFAYKNVKFVLKHKVAQKREDTVSKEVTRKLSEADNRKMSRKEKDVR

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	29.40 RPM
SRP007412_cerebellum	0.00 RPM	27.15 RPM
SRP007412_heart	0.09 RPM	20.04 RPM
SRP007412_kidney	0.12 RPM	80.43 RPM
SRP007412_liver	0.03 RPM	74.89 RPM
SRP007412_testis	0.00 RPM	140.79 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_255 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_255 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_173
Pan troglodytes	retro_ptro_163
Pongo abelii	retro_pabe_456
Macaca mulatta	retro_mmul_383

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003125	1 retrocopy	retro_amel_832,
Canis familiaris	ENSCAFG00000008870	5 retrocopies	retro_cfam_1296, retro_cfam_1370, retro_cfam_1924, retro_cfam_2029, retro_cfam_2041,
Choloepus hoffmanni	ENSCHOG00000001517	1 retrocopy	retro_chof_29,
Callithrix jacchus	ENSCJAG00000004643	4 retrocopies	retro_cjac_1059, retro_cjac_1503, retro_cjac_2369, retro_cjac_3213,
Cavia porcellus	ENSCPOG00000005898	2 retrocopies	retro_cpor_1243, retro_cpor_826,
Dasypus novemcinctus	ENSDNOG00000000752	2 retrocopies	retro_dnov_1922, retro_dnov_632,
Homo sapiens	ENSG00000114850	1 retrocopy	retro_hsap_173,
Gorilla gorilla	ENSGGOG00000024038	1 retrocopy	retro_ggor_255 ,
Myotis lucifugus	ENSMLUG00000015478	3 retrocopies	retro_mluc_1624, retro_mluc_1728, retro_mluc_2146,
Macaca mulatta	ENSMMUG00000016970	1 retrocopy	retro_mmul_383,
Otolemur garnettii	ENSOGAG00000010589	2 retrocopies	retro_ogar_2089, retro_ogar_3483,
Pongo abelii	ENSPPYG00000014233	1 retrocopy	retro_pabe_456,
Pan troglodytes	ENSPTRG00000015560	1 retrocopy	retro_ptro_163,
Tarsius syrichta	ENSTSYG00000010578	1 retrocopy	retro_tsyr_660,