RetrogeneDB ID:

retro_ptro_3119

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:X:68904650..68904934(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:HMGN1
Ensembl ID:ENSPTRG00000031426
Aliases:None
Description:High mobility group nucleosome binding domain 1 [Source:UniProtKB/TrEMBL;Acc:K7DN21]


Retrocopy-Parental alignment summary:






>retro_ptro_3119
ATTCCCAAGAGGAAGGTCTGCTCCGCTGAAGGGGCCGCCAAGGAAGAGCCCAAGAGGAGATCTGCGCGATTGTCAGCTAA
ACCTCCTGCAAAAGTGGAAGTAAAGCCGAAAAAGGCTTTGCAAAGGACAAATCTTCAGACAAAAAAGTGCAAACAAAACG
GAAAAGGGGAGCAAAGGGAAGACAGGCCAAAGTGGCTAACCAACAAACTAAAGAAGATTTACCTGCAGAAAACAGGGAAA
GGAAAACTGAGGAGAGTCCAGCCTCTGATGAAGCAGGAGCCAAG

ORF - retro_ptro_3119 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.5 %
Parental protein coverage: 95. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMPKRKVSSAEGAAKEEPKRRSARLSAKPPAKVEAKPKKAA-AKDKSSDKKVQTKGKRGAKGKQAEVANQE
.PKRKV.SAEGAAKEEPKRRSARLSAKPPAKVE.KPKKA..AKDKSSDKKVQTK.KRGAKG.QA.VANQ.
RetrocopyIPKRKVCSAEGAAKEEPKRRSARLSAKPPAKVEVKPKKAL<AKDKSSDKKVQTKRKRGAKGRQAKVANQQ
ParentalTKEDLPAENGETKTEESPASDEAGEK
TKEDLPAEN.E.KTEESPASDEAG.K
RetrocopyTKEDLPAENRERKTEESPASDEAGAK

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 24 .15 RPM
SRP007412_cerebellum 0 .00 RPM 17 .57 RPM
SRP007412_heart 0 .00 RPM 17 .72 RPM
SRP007412_kidney 0 .00 RPM 44 .41 RPM
SRP007412_liver 0 .00 RPM 29 .20 RPM
SRP007412_testis 0 .00 RPM 38 .89 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_3119 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_3119 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_3119 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pongo abelii retro_pabe_3648

Parental genes homology:
Parental genes homology involve 10 parental genes, and 141 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG0000001410011 retrocopies
Bos taurus ENSBTAG0000001876812 retrocopies
Canis familiaris ENSCAFG0000001004512 retrocopies
Cavia porcellus ENSCPOG000000023367 retrocopies
Equus caballus ENSECAG000000190295 retrocopies
Homo sapiens ENSG000002055817 retrocopies
Monodelphis domestica ENSMODG000000209725 retrocopies
Otolemur garnettii ENSOGAG0000001032935 retrocopies
Pongo abelii ENSPPYG0000001142625 retrocopies
Pan troglodytes ENSPTRG00000031426 22 retrocopies



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