RetrogeneDB ID:

retro_pabe_3608

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:Un:66282082..66282555(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CBX3
Ensembl ID:ENSPPYG00000017714
Aliases:None
Description:Chromobox protein homolog 3 [Source:UniProtKB/Swiss-Prot;Acc:Q5R6X7]


Retrocopy-Parental alignment summary:






>retro_pabe_3608
GAAGAGGCAGAGCCTGAAGAATGTGTGGAAAAACTACTGGATCCAATTATAGCAAAAGGGAAGGTGGAGCATTTCCTGAA
GCGGAAGGGACGTCAGATGTTGACAGTACTTGGGAACCCGCAGAAAATTTAGATTGTCCAGAATTAATTGAAACATTCAT
TAATTCTCAAAAAGCTGGTAAAAAAAAAAAAAGGTACAAAAAGAAAGTCTTTATCTGACAATGAATCTAATGACAGCAAA
TCAAAGAAGAAAAGAGATGCTGCCGACAAACCAAGAGGCTTCACCAGAGATCTTGATCCTGAAAGAATAATTGGTGCCAC
AGGCAGCAGTGGAGAATGGATGTTTCTCCTGAAATGGGAATATTCACATCAGGCCGACTTGGTGCTGGCAAAAGCGGCAA
ATATGAAGTGTCTTGAAATTGTAATTTTTTTTACAAAGAGAGACTAAGTTGGCATTCTTGTCAAGATGATGAA

ORF - retro_pabe_3608 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.6 %
Parental protein coverage: 86.89 %
Number of stop codons detected: 0
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalEEAEPEEFVVEKVLDRRVVNGKVEYFLKWKG-FTDADNTWEPEENLDCPELIEAFLNSQKAG-KEKDGTK
EEAEPEE..VEK.LD.....GKVE.FLK.KG...D.D.TWEP.ENLDCPELIE.F.NSQKAG.....GTK
RetrocopyEEAEPEE-CVEKLLDPIIAKGKVEHFLKRKG<TSDVDSTWEPAENLDCPELIETFINSQKAG>XXXXGTK
ParentalRKSLSDSESDDSKSKKKRDAADKPRGFARGLDPERIIGATDSSGELMFLMKWKDSDEADLVLAKEANMKC
RKSLSD.ES.DSKSKKKRDAADKPRGF.R.LDPERIIGAT.SSGE.MFL.KW..S..ADLVLAK.ANMKC
RetrocopyRKSLSDNESNDSKSKKKRDAADKPRGFTRDLDPERIIGATGSSGEWMFLLKWEYSHQADLVLAKAANMKC
ParentalPQIV-IAFYEERLTWHSCPEDE
..IV......ERL.WHSC..DE
RetrocopyLEIV<XXXXKERLSWHSCQDDE

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 35 .05 RPM
SRP007412_cerebellum 0 .00 RPM 54 .60 RPM
SRP007412_heart 0 .00 RPM 29 .92 RPM
SRP007412_kidney 0 .00 RPM 36 .53 RPM
SRP007412_liver 0 .00 RPM 25 .25 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_3608 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_3608 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_3608 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 14 parental genes, and 65 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG0000000289711 retrocopies
Callithrix jacchus ENSCJAG000000079528 retrocopies
Dipodomys ordii ENSDORG0000000548711 retrocopies
Loxodonta africana ENSLAFG000000069073 retrocopies
Myotis lucifugus ENSMLUG000000075912 retrocopies
Mus musculus ENSMUSG000000298361 retrocopy
Otolemur garnettii ENSOGAG000000165831 retrocopy
Ochotona princeps ENSOPRG000000117139 retrocopies
Pongo abelii ENSPPYG000000045991 retrocopy
Pongo abelii ENSPPYG000000088911 retrocopy
Pongo abelii ENSPPYG00000017714 10 retrocopies
Rattus norvegicus ENSRNOG000000118142 retrocopies
Sarcophilus harrisii ENSSHAG000000179131 retrocopy
Sus scrofa ENSSSCG000000167114 retrocopies



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