RetrogeneDB ID:

retro_ptro_465

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:10:125862911..125863507(+)
Located in intron of:ENSPTRG00000003046
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SAR1A
Ensembl ID:ENSPTRG00000002584
Aliases:None
Description:SAR1 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:10534]


Retrocopy-Parental alignment summary:






>retro_ptro_465
ATGTCTTTCATCTGTGAGTGGATCTACAATGGCTTCTACAGTGTGCTCCAGTTTCTAGGACTCTACAAGAAATCTAGTAA
ACTTGTTCTCTTGGGTTGGGACAATGTGGATGAAACCATTCTTCCTCATATGCTCAAAGATGGCGGATTGGGCCAACAGG
CTCCAACACGACCTCTGACATCAGCAGAGCTGACAACTGCTAGCCTGGCTTTTACAACTTTTGATCTTCTGGGGCATGAG
CAAACACGTTGGATTTGGAACAGTGATATCCCAGCAATAAATGGGATTGCCTTTCTGGGGTACTGTGCAGATTGTCCTCA
GATCCTGGAATCCAAAGTGGAGCTCAATGCTTCAATGACTGATGAAAGAATATCCCATGTGCCAGTCCTTATCTTGATTA
GCAAAAATTGGACAGAACAGGCACAATCAGTGAAGAAAAACTCTGTCTGCCATTTGGTCTTTATGGACAGACCACAGGAA
AGGGAACTCGTGACCCTGAAGGAGCCAAATGCCTTTTCCAAGGAATCGTTCACATTCAGTGTGTACAACAACAGGGCTAT
GGCAAGGGCTTCTGCTGGTTTGCCCAGTATATTGAC

ORF - retro_ptro_465 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 64.36 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMSFIFEWIYNGFSSVLQFLGLYKKSGKLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEELTIAGMT
MSFI.EWIYNGF.SVLQFLGLYKKS.KLV.LG.DN...T.L.HMLKD..LGQ..PT...TS.ELT.A...
RetrocopyMSFICEWIYNGFYSVLQFLGLYKKSSKLVLLGWDNVDETILPHMLKDGGLGQQAPTRPLTSAELTTASLA
ParentalFTTFDLGGHEQARRVWKNYLPAINGIVFLVDCADHSRLVESKVELNALMTDETISNVP-ILILGN-KIDR
FTTFDL.GHEQ.R..W....PAINGI.FL..CAD.....ESKVELNA.MTDE.IS.VP........K.DR
RetrocopyFTTFDLLGHEQTRWIWNSDIPAINGIAFLGYCADCPQILESKVELNASMTDERISHVPVLILISK<KLDR
ParentalTDAISEEKLREIFGLYGQTTGKGN-VTLKELNARPMEVFMCSV-LKRQGYGEGFRWLSQYID
T..ISEEKL...FGLYGQTTGKG..VTLKE.NA...E.F..SV....QGYG.GF.W..QYID
RetrocopyTGTISEEKLCLPFGLYGQTTGKGT>VTLKEPNAFSKESFTFSV<VQQQGYGKGFCWFAQYID

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 52 .44 RPM
SRP007412_cerebellum 0 .00 RPM 60 .94 RPM
SRP007412_heart 0 .00 RPM 51 .88 RPM
SRP007412_kidney 0 .00 RPM 72 .52 RPM
SRP007412_liver 0 .00 RPM 64 .45 RPM
SRP007412_testis 0 .00 RPM 52 .80 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_465 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_465 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_465 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_639
Pongo abelii retro_pabe_565
Callithrix jacchus retro_cjac_1006

Parental genes homology:
Parental genes homology involve 12 parental genes, and 40 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000163535 retrocopies
Homo sapiens ENSG000000793324 retrocopies
Gorilla gorilla ENSGGOG000000248793 retrocopies
Myotis lucifugus ENSMLUG000000066262 retrocopies
Nomascus leucogenys ENSNLEG000000112434 retrocopies
Otolemur garnettii ENSOGAG000000050403 retrocopies
Pongo abelii ENSPPYG000000023744 retrocopies
Pan troglodytes ENSPTRG00000002584 4 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000127802 retrocopies
Tupaia belangeri ENSTBEG000000086575 retrocopies
Tarsius syrichta ENSTSYG000000059552 retrocopies
Vicugna pacos ENSVPAG000000026312 retrocopies



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