RetrogeneDB ID:

retro_ggor_2956

Retrocopy
location
Organism:Gorilla (Gorilla gorilla)
Coordinates:X:120827631..120828039(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSGGOG00000024644
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:H3F3A
Ensembl ID:ENSGGOG00000022526
Aliases:None
Description:H3 histone, family 3A [Source:HGNC Symbol;Acc:4764]


Retrocopy-Parental alignment summary:






>retro_ggor_2956
ATGGCTCGTACAAAGCAGACTGCCCGCAAATCAACCGGTGGTAAACCACCCAGGAAGCAACTGGCTACAAAAGCCGCTCG
CAAGAGTGCGCCCTCTATTGGAGGGGTGAAGAAACCTCATCGTTACAGGCCTGGTACTGTGGCGCTCCGTGAAATTAGAC
GTTATCAGAAGTCCACTGAACTTCTGATTCGCAAACTTCCCTTCCAGCGTCTGGTGCGAGAAATTGCTCAGGACTTTAAA
ACAGATCTGCGCTTCCAGAGCGCAGCTATCGGTGCTTTGCAGGAGGCAAGTGAGGCCTATCTGGTTGGCCTTTTTGAAGA
CACCAACCTGTGTGCTATCCATGCCAAACGTGTAACAATTATGCCGAAAGACATCCAGCTAGCACGCCGCATACGTGGAG
AACGTGCT

ORF - retro_ggor_2956 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 98.53 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQR
MARTKQTARKSTGGK.PRKQLATKAARKSAPS.GGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQR
RetrocopyMARTKQTARKSTGGKPPRKQLATKAARKSAPSIGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQR
ParentalLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
LVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
RetrocopyLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

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 .00 RPM 14 .34 RPM
SRP007412_cerebellum 0 .20 RPM 28 .45 RPM
SRP007412_heart 0 .13 RPM 13 .41 RPM
SRP007412_kidney 0 .33 RPM 62 .76 RPM
SRP007412_liver 0 .21 RPM 55 .89 RPM
SRP007412_testis 0 .52 RPM 47 .76 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_2956 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ggor_2956 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_3164
Pongo abelii retro_pabe_3697

Parental genes homology:
Parental genes homology involve 19 parental genes, and 122 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000245613 retrocopies
Canis familiaris ENSCAFG000000049162 retrocopies
Canis familiaris ENSCAFG000000161194 retrocopies
Dipodomys ordii ENSDORG000000081329 retrocopies
Erinaceus europaeus ENSEEUG000000137961 retrocopy
Felis catus ENSFCAG000000036174 retrocopies
Felis catus ENSFCAG000000304245 retrocopies
Gorilla gorilla ENSGGOG00000022526 11 retrocopies
Gorilla gorilla ENSGGOG000000229287 retrocopies
Gadus morhua ENSGMOG000000143061 retrocopy
Macaca mulatta ENSMMUG000000314839 retrocopies
Mus musculus ENSMUSG0000001655918 retrocopies
Nomascus leucogenys ENSNLEG000000015772 retrocopies
Otolemur garnettii ENSOGAG0000002431211 retrocopies
Otolemur garnettii ENSOGAG0000002593314 retrocopies
Pongo abelii ENSPPYG0000000016814 retrocopies
Pongo abelii ENSPPYG000000086361 retrocopy
Pteropus vampyrus ENSPVAG000000084592 retrocopies
Rattus norvegicus ENSRNOG000000032204 retrocopies



Copyright © RetrogeneDB 2014-2017