RetrogeneDB ID:

retro_pabe_699

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:11:59031856..59032155(+)
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:ENSPPYG00000011426
Aliases:None
Description:high mobility group nucleosome binding domain 1 [Source:HGNC Symbol;Acc:4984]


Retrocopy-Parental alignment summary:






>retro_pabe_699
CCCAAGAGGAAGTGCAATTGCGCCGAAGGGGCAGCCAAGGAAGAGCCCAAGAGGGGATCGGTGTGGTTTTCAGCTAAATC
CGCTCCTGCAAAAGGGGAAATGAAGCCAAAAAGGCAGCAGGAAAGGATACATCTTCAGACAAAAAAAGTGTAAACAAAAG
GGAAAAGGGGAGCAGAGAGAAAACAGGCCAAGTGGCTAACCAAGAAACTAAAGAACATTTATCTGCAGAAAATGGAGAAA
CTAAAATCGGGGAGAGCCCAGCCTCTGATGAAGCCAGAGAGAGAGAAGCCAAGTCTGAT

ORF - retro_pabe_699 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.76 %
Parental protein coverage: 99. %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalPKRKVSSAEGAAKEEPKRRSARLSAKP-PAKVEAKPK-KAAAKDKSSDKK-VQTKGKRGAKGKQA-EVAN
PKRK...AEGAAKEEPKR.S...SAK..PAK.E.KPK.KAA.KD.SSDKK.V.TKGKRGA..KQA..VAN
RetrocopyPKRKCNCAEGAAKEEPKRGSVWFSAKSAPAKGEMKPK<KAAGKDTSSDKK>V*TKGKRGAERKQA<QVAN
ParentalQETKEDLPAENGETKTEESPASDEAGEKEAKSD
QETKE.L.AENGETK..ESPASDEA.E.EAKSD
RetrocopyQETKEHLSAENGETKIGESPASDEAREREAKSD

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 21 .67 RPM
SRP007412_cerebellum 0 .00 RPM 44 .75 RPM
SRP007412_heart 0 .00 RPM 14 .33 RPM
SRP007412_kidney 0 .00 RPM 76 .60 RPM
SRP007412_liver 0 .00 RPM 35 .83 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_699 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_699 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_699 has 0 orthologous retrocopies within eutheria group .


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 ENSPPYG00000011426 25 retrocopies
Pan troglodytes ENSPTRG0000003142622 retrocopies



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