RetrogeneDB ID:

retro_pabe_3685

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:X:111687779..111688304(+)
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:ENSPPYG00000020818
Aliases:None
Description:high mobility group box 3 [Source:HGNC Symbol;Acc:5004]


Retrocopy-Parental alignment summary:






>retro_pabe_3685
GGTGACCACAAGAAACCAAAGGGCAAGATGTCTGCTTATGCCTTCTTTGCGCAGACATGCAGAGAAGAACATAAGAAGAA
AAACCCAGAGGTCCCTGTCAATTTTGTAGAATTTTCCAAGAAGTGCTCTGAGAAGCGGAAGACCATGTCTGGGAAAGAGA
AGAGCAAATTTGATGAAATGGCAAAGGTGGATAAAGTACACTATGATCAGGAAATGAAGGATAATGGACCAGTTGAGGGA
GGCAAGAAGAAGGACCCTAATGCCCTCAAAAGGCCACTGTCTGGATTCTTCCTGTTCTGTTCAGAATTCCACCCCAAGAT
CAAATCCACAAATCCTGGCATCTCTATTGGAGACATGGCAAAAAAGCTGGGTGAGATGTGGATTAACTAAAGTGACAAGG
AAAAGCAGCCTTACATCACTAAGGCAGCAAACCTGAAGGAGAAGTATGAGAAGGATGTTGCTGACTATAAGTCTAAAGGA
AAGTTTGATAGTGCAAACGGTCCCACTAAAATTGCCTGGAAAAAG

ORF - retro_pabe_3685 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.23 %
Parental protein coverage: 88.44 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalGDPKKPKGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRYDR
GD.KKPKGKMSAYAFF.QTCREEHKKKNPEVPVNF.EFSKKCSE..KTMSGKEKSKFDEMAK.DKV.YD.
RetrocopyGDHKKPKGKMSAYAFFAQTCREEHKKKNPEVPVNFVEFSKKCSEKRKTMSGKEKSKFDEMAKVDKVHYDQ
ParentalEMKDYGPAKGGKKKKDPNAPKRPPSGFFLFCSEFRPKIKSTNPGISIGDVAKKLGEMWNNLNDSEKQPYI
EMKD.GP..GGKKK.DPNA.KRP.SGFFLFCSEF.PKIKSTNPGISIGD.AKKLGEMW.N..D.EKQPYI
RetrocopyEMKDNGPVEGGKKK-DPNALKRPLSGFFLFCSEFHPKIKSTNPGISIGDMAKKLGEMWIN*SDKEKQPYI
ParentalTKAAKLKEKYEKDVADYKSKGKFDGAKGPAKVARKK
TKAA.LKEKYEKDVADYKSKGKFD.A.GP.K.A.KK
RetrocopyTKAANLKEKYEKDVADYKSKGKFDSANGPTKIAWKK

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 17 .91 RPM
SRP007412_cerebellum 0 .00 RPM 11 .19 RPM
SRP007412_heart 0 .00 RPM 11 .08 RPM
SRP007412_kidney 0 .00 RPM 14 .02 RPM
SRP007412_liver 0 .00 RPM 78 .59 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_3685 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_3685 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_3685 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_4739
Pan troglodytes retro_ptro_3154
Gorilla gorilla retro_ggor_2944
Macaca mulatta retro_mmul_2526

Parental genes homology:
Parental genes homology involve 27 parental genes, and 230 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000051502 retrocopies
Choloepus hoffmanni ENSCHOG000000050052 retrocopies
Callithrix jacchus ENSCJAG000000039369 retrocopies
Dipodomys ordii ENSDORG000000108264 retrocopies
Echinops telfairi ENSETEG000000156894 retrocopies
Homo sapiens ENSG000000299938 retrocopies
Gorilla gorilla ENSGGOG0000002716416 retrocopies
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
Pongo abelii ENSPPYG0000000554635 retrocopies
Pongo abelii ENSPPYG000000152043 retrocopies
Pongo abelii ENSPPYG00000020818 22 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



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