RetrogeneDB ID:

retro_pabe_2782

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:5:134448021..134448492(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SNRNP27
Ensembl ID:ENSPPYG00000012332
Aliases:None
Description:small nuclear ribonucleoprotein 27kDa (U4/U6.U5) [Source:HGNC Symbol;Acc:30240]


Retrocopy-Parental alignment summary:






>retro_pabe_2782
ATGGGTCGCAGTCGCAGCCGCTCCCCACGGAGGGAAGGTAGGCGTTCCCGGTCCACATCCCGTGAGAGAGAACGCAGGCG
CCGAGAAAGGTCCAGGTCTCCGGAGAGAGATGGGAGAAGGAACCGCTCGCGATCCCCGCACCTAAGACGCTCCCGATCTC
CAAGACGACATAAATCCACATCTCCTTCCCCTTCTCAACCGAATGAAAGAAGAGATGAGGAAAAGAAAGAAACAAAGAGC
AAAGAATGGCAGATTACTGAGGAAGACTTAGAGGGCAAAACAGAGGAAGAAATAGAAATGATGAAGTTAATGGAATTTGC
CTCCTTTGACTCCACAAAAGGTAAGAAGGTGGATTGCTCTGTAAATGCCTATGCCATAAATGTCTCTCAGAAGAGGAAGT
ACAGGCAGTACATGAATCGAAAAGGTGGATTCCACAGACCTTTGGATTTCATTGCATGAGAATTGAAATGT

ORF - retro_pabe_2782 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.12 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMGRSRSRSPRRERRRSRSTSRERERRRRERSRSRERDRRRSRSRSPHRRRSRSPRRHRSTSPSPSRLKER
MGRSRSRSPRRE.RRSRSTSRERERRRRERSRS.ERD.RR.RSRSPH.RRSRSPRRH.STSPSPS...ER
RetrocopyMGRSRSRSPRREGRRSRSTSRERERRRRERSRSPERDGRRNRSRSPHLRRSRSPRRHKSTSPSPSQPNER
ParentalRDEEKKETKETKSKERQITEEDLEGKTEEEIEMMKLMGFASFDSTKGKKVDGSVNAYAINVSQKRKYRQY
RDEEKKETK...SKE.QITEEDLEGKTEEEIEMMKLM.FASFDSTKGKKVD.SVNAYAINVSQKRKYRQY
RetrocopyRDEEKKETK---SKEWQITEEDLEGKTEEEIEMMKLMEFASFDSTKGKKVDCSVNAYAINVSQKRKYRQY
ParentalMNRK-WIQQTFGFHCMRLKC
MNRK........F....LKC
RetrocopyMNRKGGFHRPLDFIA*ELKC

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 5 .42 RPM
SRP007412_cerebellum 0 .00 RPM 8 .15 RPM
SRP007412_heart 0 .00 RPM 5 .63 RPM
SRP007412_kidney 0 .00 RPM 5 .70 RPM
SRP007412_liver 0 .00 RPM 5 .45 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_2782 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_2782 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_2782 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3387
Pan troglodytes retro_ptro_2300

Parental genes homology:
Parental genes homology involve 9 parental genes, and 14 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000377464 retrocopies
Choloepus hoffmanni ENSCHOG000000030421 retrocopy
Echinops telfairi ENSETEG000000173441 retrocopy
Homo sapiens ENSG000001243801 retrocopy
Mus musculus ENSMUSG000000011582 retrocopies
Oryctolagus cuniculus ENSOCUG000000229671 retrocopy
Pongo abelii ENSPPYG00000012332 2 retrocopies
retro_pabe_1990, retro_pabe_2782 ,
Pan troglodytes ENSPTRG000000120221 retrocopy
Sus scrofa ENSSSCG000000256741 retrocopy



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