RetrogeneDB ID:

retro_ggor_2104

Retrocopy
location
Organism:Gorilla (Gorilla gorilla)
Coordinates:4:103262224..103262670(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:HMGB3
Ensembl ID:ENSGGOG00000027164
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ggor_2104
GACCCCAAGAAACCAAAGGGCAAGATCTCTGCTTATGCCTTCTTTGGGCAGACGTGCAGAGAAGAACATAAGAAGAAAAA
CCCAGAGGTCCCTGTCAATTTTGCAGAATTTTCCACGAAGTGCTCTGAGAGGTGGAAGACAATGTCTGGGAAAGAAAAGT
CTAAATTTGATGAAACGGCCAAGGTGGATAAAGAACGCTATGATCGGAAAATGAAGGATTATGGACCAGCTAAGAGAGGC
AAGAAGGAGAAGGATCCTAATGCCCCCAAAGGCCACCATCTGGGTTCTTCCTATTCTGTTCAGAATTCCGCCCCAAGATC
AAATCCACAAACCTTGGCCTCTCTATTGGAGATGTGGCAAAAAAGCTTGGTGAGATGTAGAATAACTTAAATGACAGTGA
AAAGCAGCCTTACGTCACTAAGGCGGCAAAGCTGAAGGAGAAGTAT

ORF - retro_ggor_2104 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.67 %
Parental protein coverage: 74.5 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalDPKKPKGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRYDRE
DPKKPKGK.SAYAFF.QTCREEHKKKNPEVPVNFAEFS.KCSERWKTMSGKEKSKFDE.AK.DK.RYDR.
RetrocopyDPKKPKGKISAYAFFGQTCREEHKKKNPEVPVNFAEFSTKCSERWKTMSGKEKSKFDETAKVDKERYDRK
ParentalMKDYGPAKGGKKKKDPNAPK-RPPSGFFLFCSEFRPKIKSTNPGISIGDVAKKLGEMWNNLNDSEKQPYI
MKDYGPAK.GKK.KDPNAPK.RPPSGFFLFCSEFRPKIKSTN.G.SIGDVAKKLGEM.NNLNDSEKQPY.
RetrocopyMKDYGPAKRGKKEKDPNAPK<RPPSGFFLFCSEFRPKIKSTNLGLSIGDVAKKLGEM*NNLNDSEKQPYV
ParentalTKAAKLKEKY
TKAAKLKEKY
RetrocopyTKAAKLKEKY

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 16 .26 RPM
SRP007412_cerebellum 0 .04 RPM 6 .07 RPM
SRP007412_heart 0 .00 RPM 3 .53 RPM
SRP007412_kidney 0 .04 RPM 12 .80 RPM
SRP007412_liver 0 .00 RPM 21 .34 RPM
SRP007412_testis 0 .00 RPM 21 .34 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_2104 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ggor_2104 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3064
Pan troglodytes retro_ptro_2066
Pongo abelii retro_pabe_2538
Macaca mulatta retro_mmul_1957

Parental genes homology:
Parental genes homology involve 32 parental genes, and 224 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000051502 retrocopies
Canis familiaris ENSCAFG000000287151 retrocopy
Choloepus hoffmanni ENSCHOG000000050052 retrocopies
Callithrix jacchus ENSCJAG000000039369 retrocopies
Dipodomys ordii ENSDORG000000108264 retrocopies
Equus caballus ENSECAG000000205961 retrocopy
Echinops telfairi ENSETEG000000156894 retrocopies
Felis catus ENSFCAG000000246244 retrocopies
Homo sapiens ENSG000000299938 retrocopies
Gorilla gorilla ENSGGOG000000158821 retrocopy
Gorilla gorilla ENSGGOG0000002676423 retrocopies
Gorilla gorilla ENSGGOG00000027164 16 retrocopies
Loxodonta africana ENSLAFG000000258771 retrocopy
Myotis lucifugus ENSMLUG000000109264 retrocopies
Macaca mulatta ENSMMUG0000000463320 retrocopies
Monodelphis domestica ENSMODG000000057357 retrocopies
Mustela putorius furoENSMPUG000000116062 retrocopies
Mus musculus ENSMUSG000000152171 retrocopy
Oryctolagus cuniculus ENSOCUG000000059867 retrocopies
Otolemur garnettii ENSOGAG0000000177319 retrocopies
Procavia capensis ENSPCAG000000019451 retrocopy
Pongo abelii ENSPPYG0000002081822 retrocopies
Pan troglodytes ENSPTRG0000002237122 retrocopies
Pteropus vampyrus ENSPVAG000000002191 retrocopy
Rattus norvegicus ENSRNOG000000110964 retrocopies
Rattus norvegicus ENSRNOG000000509105 retrocopies
Sarcophilus harrisii ENSSHAG000000029162 retrocopies
Sus scrofa ENSSSCG000000127453 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000239086 retrocopies
Tupaia belangeri ENSTBEG0000000306818 retrocopies
Tursiops truncatus ENSTTRG000000002052 retrocopies
Vicugna pacos ENSVPAG000000000962 retrocopies



Copyright © RetrogeneDB 2014-2017