RetrogeneDB ID:

retro_ggor_2181

Retrocopy
location
Organism:Gorilla (Gorilla gorilla)
Coordinates:5:71417633..71417995(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:H3F3B
Ensembl ID:ENSGGOG00000022928
Aliases:None
Description:H3 histone, family 3B (H3.3B) [Source:HGNC Symbol;Acc:4765]


Retrocopy-Parental alignment summary:






>retro_ggor_2181
CCTGCAAAGCGGACTGCACGCAAATCCACCGGTGGTAAAGCACCCGGGAAGCAACTGGGTACAGAAGCCTTTTGCAAGAG
TGCGCCCTCTACTGGATGGGCGAATAAGCTTCATTGTTACAGGCCTCGTACTGAGGCACGATTCGCAAACTTCCCTTCCA
GCGTCTGGTGTGAGAAATTGCTCAGGATTTTAAAACAGATCTGTGCTTCCAGAGTGCAGCTATTGGTGCTTTACAGGAGG
CAATTAAGGCCTAACTGGTTGGCCTTTTTGAAGACACCCACCTGTGTGCTATCCATGCCAAACGTGTAACAATTATGCCA
AAAGACATCCAGCTAGCATGCCGCACACGTGGAGAACGTGCT

ORF - retro_ggor_2181 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 63.93 %
Parental protein coverage: 88.24 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalPRKQLATKAARKSAPSTG-GVKKPHRYRPGTVALREIRRYQKSTEL-LIRKLPFQRLVREIAQDFKTDLR
P.K..A.K.....AP....G........P.T........Y...TE...IRKLPFQRLV.EIAQDFKTDL.
RetrocopyPAKRTARKSTGGKAPGKQLGTEAFCKSAPSTGWANKLHCYRPRTEA<TIRKLPFQRLV*EIAQDFKTDLC
ParentalFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
FQSAAIGALQEA..A.LVGLFEDT.LCAIHAKRVTIMPKDIQLA.R.RGERA
RetrocopyFQSAAIGALQEAIKA*LVGLFEDTHLCAIHAKRVTIMPKDIQLACRTRGERA

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP007412_brain_prefrontal_cortex 0 .10 RPM 161 .99 RPM
SRP007412_cerebellum 0 .00 RPM 335 .67 RPM
SRP007412_heart 0 .00 RPM 65 .20 RPM
SRP007412_kidney 0 .04 RPM 187 .19 RPM
SRP007412_liver 0 .00 RPM 175 .20 RPM
SRP007412_testis 0 .00 RPM 607 .82 RPM
Gorilla gorilla was not studied using ChIP-Seq data.
Gorilla gorilla was not studied using EST data.
Gorilla gorilla was not studied using FANTOM5 data.
retro_ggor_2181 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ggor_2181 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3214
Pan troglodytes retro_ptro_2238
Pongo abelii retro_pabe_2662

Parental genes homology:
Parental genes homology involve 9 parental genes, and 66 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG0000000966110 retrocopies
Gorilla gorilla ENSGGOG0000002252611 retrocopies
Gorilla gorilla ENSGGOG00000022928 7 retrocopies
Loxodonta africana ENSLAFG000000216244 retrocopies
Myotis lucifugus ENSMLUG0000001544710 retrocopies
Oryctolagus cuniculus ENSOCUG000000246442 retrocopies
Pongo abelii ENSPPYG000000086361 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000242268 retrocopies
Tupaia belangeri ENSTBEG0000000617713 retrocopies



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