RetrogeneDB ID:

retro_pabe_297

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:1:136162552..136163058(+)
Located in intron of:ENSPPYG00000001153
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:HMGB2
Ensembl ID:ENSPPYG00000015204
Aliases:None
Description:high mobility group box 2 [Source:HGNC Symbol;Acc:5000]


Retrocopy-Parental alignment summary:






>retro_pabe_297
ATGGCTAAAGGTGATCCCAAGAAACCAGAGGGAAAGGTGTCTGCTTATTCCTTCTTTGTGCAGACATGCAGAGAAGAACA
TAAGAAAAACCCAGAGGTCTCTTGTCAGTTTTGCAGAATTTTCCAAGAAGTGCTCTGAGAGGTGGAAGACAGTGTCTGGC
AAAGAGAATCCTAAATGTGATGAAATGACAAAGGCAGATAAAGTATGCTATGCTTGGAAGATGAATGATTGTGAACCAGT
TAAGCGAGGCAAGAAGAAGGACCTTCATGTCTCCAAAAGGCCACCGTCTGTATTCTTCCTGCATTGTTCAGAATTTCACC
CCAAGATCAAATCCACAAACCCTGGCATCTTTATTAGAGATGTAGCAAAAAAGCTGGGTGAGATGTTGGATAACAAGTGT
CAGTGAAAAGCAGCCTTGCATCACTAAGGCAGTGAAGCTGAGGGAGGAATACGAGAAGGATGTTGCTGACTTTAAGTCTA
ACGGCAAGTCTGGTGCAAAGGGTCCT

ORF - retro_pabe_297 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 59.89 %
Parental protein coverage: 83.33 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMGKGDPNKPRGKMSSYAFFVQTCREEHKKKHPDSS-VNFAEFSKKCSERWKTMSAKEKSKFEDMAKSDKA
M.KGDP.KP.GK.S.Y.FFVQTCREEHKK..P..S.V.FAEFSKKCSERWKT.S.KE..K...M.K.DK.
RetrocopyMAKGDPKKPEGKVSAYSFFVQTCREEHKK-NPEVS>VSFAEFSKKCSERWKTVSGKENPKCDEMTKADKV
ParentalRYDREMKNYVPPKGDKKGKKKDPNAPKRPPSAFFLFCSEHRPKIKSEHPGLSIGDTAKKLGEM-WSEQSA
.Y...M....P....K.GKKKD....KRPPS.FFL.CSE..PKIKS..PG..I.D.AKKLGEM.W...S.
RetrocopyCYAWKMNDCEPV---KRGKKKDLHVSKRPPSVFFLHCSEFHPKIKSTNPGIFIRDVAKKLGEM>WI-TSV
ParentalKDKQPYEQKAAKLKEKYEKDIAAYRAKGKSEAGKKGP
..KQP...KA.KL.E.YEKD.A.....GKS..G.KGP
RetrocopySEKQPCITKAVKLREEYEKDVADFKSNGKS--GAKGP

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 .17 RPM 11 .67 RPM
SRP007412_cerebellum 0 .61 RPM 12 .40 RPM
SRP007412_heart 0 .27 RPM 15 .08 RPM
SRP007412_kidney 0 .00 RPM 17 .40 RPM
SRP007412_liver 0 .09 RPM 22 .95 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_297 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_297 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_297 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_422
Gorilla gorilla retro_ggor_414
Macaca mulatta retro_mmul_514

Parental genes homology:
Parental genes homology involve 26 parental genes, and 147 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000151011 retrocopy
Callithrix jacchus ENSCJAG000000051122 retrocopies
Cavia porcellus ENSCPOG000000035524 retrocopies
Dasypus novemcinctus ENSDNOG000000194404 retrocopies
Erinaceus europaeus ENSEEUG000000122388 retrocopies
Echinops telfairi ENSETEG000000103793 retrocopies
Echinops telfairi ENSETEG000000163791 retrocopy
Felis catus ENSFCAG000000042182 retrocopies
Homo sapiens ENSG000001641041 retrocopy
Gorilla gorilla ENSGGOG000000158821 retrocopy
Loxodonta africana ENSLAFG000000104173 retrocopies
Macropus eugenii ENSMEUG000000022563 retrocopies
Myotis lucifugus ENSMLUG000000263034 retrocopies
Monodelphis domestica ENSMODG000000035273 retrocopies
Mustela putorius furoENSMPUG000000019199 retrocopies
Mus musculus ENSMUSG0000005471723 retrocopies
Nomascus leucogenys ENSNLEG000000066623 retrocopies
Oryctolagus cuniculus ENSOCUG000000000741 retrocopy
Otolemur garnettii ENSOGAG000000171493 retrocopies
Pongo abelii ENSPPYG0000000554635 retrocopies
Pongo abelii ENSPPYG00000015204 3 retrocopies
retro_pabe_297 , retro_pabe_3005, retro_pabe_3380,
Pongo abelii ENSPPYG0000002081822 retrocopies
Pan troglodytes ENSPTRG000000165973 retrocopies
Rattus norvegicus ENSRNOG000000131672 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000239802 retrocopies
Tursiops truncatus ENSTTRG000000156501 retrocopy



Copyright © RetrogeneDB 2014-2017