RetrogeneDB ID:

retro_ptro_1937

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:3:154397308..154397682(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SNRPC
Ensembl ID:ENSPTRG00000018070
Aliases:None
Description:small nuclear ribonucleoprotein polypeptide C [Source:HGNC Symbol;Acc:11157]


Retrocopy-Parental alignment summary:






>retro_ptro_1937
AAGTTTTGTTGTGACTTCTGCAATACATACCTCACCCATGACTCTCCATCTGTGAGAACCTACCATTGCAGTGGAAGGAA
ACACAAAGAGAATGTGAAAGACTACTACCAGAAATGGATAGAAGAGCAGGCTCGGAGCCTGGCTGACAGAACAAAGACTG
CATCTCAACAAGGAAGAACACCTCCTACTCTGTTCTCTGTTCCTCCTCCTGCAGGAGCGATGATCCAACCTCCCCCCAGT
CTCTTCCTGTTCCTCACCAGGTATGATGCCAGCACCCCAGCTGGGGGGCCCTCCCATGATGCCAATGATGGCCCCCCCTC
CTCTCCTGGATGATGCCAATGGGATGTGCTCCTGGAATGAGGCTGCCCATTGGA

ORF - retro_ptro_1937 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.65 %
Parental protein coverage: 69.06 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalRFYCDYCDTYLTHDSPSVRKTHCSGRKHKENVKDYYQKWMEEQAQSLIDKTTAAFQQGKIPPTPFSAPPP
.F.CD.C.TYLTHDSPSVR..HCSGRKHKENVKDYYQKW.EEQA.SL.D.T..A.QQG..PPT.FS.PPP
RetrocopyKFCCDFCNTYLTHDSPSVRTYHCSGRKHKENVKDYYQKWIEEQARSLADRTKTASQQGRTPPTLFSVPPP
ParentalAGAMIPP-PPSLPGPPRPGMMPAPHMGGPPMMPMMGPPP-PGMMPVGPAPGMRPPMG
AGAMI.P.PP.......PGMMPAP..GGPPMMPMM.PPP...MMP.G.APGMR.P.G
RetrocopyAGAMIQP>PP-VSSCSSPGMMPAPQLGGPPMMPMMAPPP>SWMMPMGCAPGMRLPIG

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 .13 RPM 20 .54 RPM
SRP007412_cerebellum 0 .04 RPM 17 .03 RPM
SRP007412_heart 0 .03 RPM 33 .17 RPM
SRP007412_kidney 0 .08 RPM 31 .38 RPM
SRP007412_liver 0 .10 RPM 22 .49 RPM
SRP007412_testis 0 .11 RPM 69 .13 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_1937 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_1937 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_1937 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2865
Gorilla gorilla retro_ggor_1981
Pongo abelii retro_pabe_2367
Macaca mulatta retro_mmul_1465

Parental genes homology:
Parental genes homology involve 20 parental genes, and 108 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000009637 retrocopies
Canis familiaris ENSCAFG000000012313 retrocopies
Callithrix jacchus ENSCJAG0000001532116 retrocopies
Cavia porcellus ENSCPOG000000085633 retrocopies
Felis catus ENSFCAG0000000587612 retrocopies
Gorilla gorilla ENSGGOG000000124997 retrocopies
Myotis lucifugus ENSMLUG000000024888 retrocopies
Macaca mulatta ENSMMUG000000008699 retrocopies
Monodelphis domestica ENSMODG000000139041 retrocopy
Mustela putorius furoENSMPUG000000032107 retrocopies
Nomascus leucogenys ENSNLEG000000083922 retrocopies
Oryctolagus cuniculus ENSOCUG000000266683 retrocopies
Otolemur garnettii ENSOGAG000000087559 retrocopies
Procavia capensis ENSPCAG000000168851 retrocopy
Pongo abelii ENSPPYG000000299023 retrocopies
Pan troglodytes ENSPTRG00000018070 6 retrocopies
Pteropus vampyrus ENSPVAG000000155971 retrocopy
Sarcophilus harrisii ENSSHAG000000009451 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000137863 retrocopies
Tarsius syrichta ENSTSYG000000112166 retrocopies



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