RetrogeneDB ID:

retro_pabe_3724

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:X:12741179..12741688(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MRPL35
Ensembl ID:ENSPPYG00000012214
Aliases:None
Description:mitochondrial ribosomal protein L35 [Source:HGNC Symbol;Acc:14489]


Retrocopy-Parental alignment summary:






>retro_pabe_3724
ATGGCTGCCTCTGCCTTTGCTGGTGTGATGAGAGCAGCTTCAGGAATCTATGGCTCCTGAATATTTTTGCATCTCCAGCC
CACCAAAACTGTGCCAGAAATGCCTCTCTTATTTCTGCATTGTCTACTGGACGTTTTAGTCATATTCGGACACCATTTGT
TTCCTCCACTCCCAGGCTTATCACATCTGTCAGAAACCTGACATGTGGGCATACTGCAGTGATCCCCAAGAGAGTGGCCC
CCTTGCTTCCAAGTGTCCTGAAGCTGCCAGTCAGAACTGTAATATACGTCAGTACACAAAAATGCAAGAGAAAGACTGTG
AAAGCTGTCATCTATAGGTTTCTTCGACTTCATTCTGGCCTTTGGGTGAGGAGAAACGCTGGTTATAAGAAAAAATTCTG
GAAAAAGACACCTGCAAGAAAAAAGTGATTGAGGGAATTTGTGTTCTGCAATAAAACCCAGAGTAAACTCTTAGATAAAA
TGACAATGTCCTTCTGGAAGAGGTGAAAC

ORF - retro_pabe_3724 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.7 %
Parental protein coverage: 81.73 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMAASAFAGAVRAASGI-LRPLNILASSTYRNCVKNASLISALSTGRFSHIQTPVVSSTPRLPTSERNLTC
MAASAFAG..RAASGI.L..LNI.AS....NC..NASLISALSTGRFSHI.TP.VSSTPRL.TS.RNLTC
RetrocopyMAASAFAGVMRAASGI<LWLLNIFASPAHQNCARNASLISALSTGRFSHIRTPFVSSTPRLITSVRNLTC
ParentalGHTSVILNRVAPVLPSVLKLPVRSLTYFSARKGKRKTVKAVIYRFLRLHCGLWVRRKAGYKKKLWKKTPA
GHT.VI..RVAP.LPSVLKLPVR...Y.S..K.KRKTVKAVIYRFLRLH.GLWVRR.AGYKKK.WKKTPA
RetrocopyGHTAVIPKRVAPLLPSVLKLPVRTVIYVSTQKCKRKTVKAVIYRFLRLHSGLWVRRNAGYKKKFWKKTPA
ParentalRKKRLREFVFCNKTQSKLLDKMTTSFWKRRN
RKK.LREFVFCNKTQSKLLDKMT.SFWKR.N
RetrocopyRKK*LREFVFCNKTQSKLLDKMTMSFWKR*N

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 .06 RPM 14 .93 RPM
SRP007412_cerebellum 0 .00 RPM 10 .34 RPM
SRP007412_heart 0 .00 RPM 12 .34 RPM
SRP007412_kidney 0 .00 RPM 11 .57 RPM
SRP007412_liver 0 .00 RPM 10 .40 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_3724 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_3724 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_3724 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_4784
Pan troglodytes retro_ptro_3185
Gorilla gorilla retro_ggor_2979

Parental genes homology:
Parental genes homology involve 10 parental genes, and 27 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000194671 retrocopy
Dasypus novemcinctus ENSDNOG000000083291 retrocopy
Macropus eugenii ENSMEUG000000047731 retrocopy
Mus musculus ENSMUSG000000529621 retrocopy
Nomascus leucogenys ENSNLEG000000027564 retrocopies
Otolemur garnettii ENSOGAG000000040481 retrocopy
Pongo abelii ENSPPYG00000012214 5 retrocopies
Rattus norvegicus ENSRNOG000000085461 retrocopy
Tupaia belangeri ENSTBEG0000001536610 retrocopies
Tarsius syrichta ENSTSYG000000077132 retrocopies



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