RetrogeneDB ID:

retro_pabe_1488

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:17:25419239..25419728(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SH3GL1
Ensembl ID:ENSPPYG00000009405
Aliases:None
Description:SH3-domain GRB2-like 1 [Source:HGNC Symbol;Acc:10830]


Retrocopy-Parental alignment summary:






>retro_pabe_1488
CTGAGTGAGTGCCTGATCCGCCACCAGGAGGAGCTGGGCAACGAGTCCAACTTCAGTGATGCACTGCTCGATGCCAGTGA
GTCCATGAAGCACCTGGCAGAGGTGAAGTACTCCCTGGACATAGAGGTCAAGCAGAACTTCATTGACCTCCTCCAGAACC
TGTGTGAGAAAGACCTGAAGGGGATCCCGCACCACCTGCAGAAGCTGGACGGCCGCCGCCTGGACTTAGAATAAAAGAAG
TGGCAGGGCAAGAGCCCCGATGAGGAGCTGTGCCAGGCACTGGAGAAGTTTGAGGACTCCAAGGAGGTGGAAGAAACCAG
CATGCACAACCTCCTGGACACCAACATTGAGCAGGTGAGTCAACTCCCAGCCCTGGTAGAGGCGCAGCTGGACTACCATT
GGCAGGCTTTGCAGATCCTGGACGAGCTGACAGAGAAGCTCAAGCACAGGATGCGGAAATCTTCCTCACATCAAATATTT
GAAAAGAAA

ORF - retro_pabe_1488 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.56 %
Parental protein coverage: 53.11 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalVAEVLARTIEYL--QPNPGDALLDAGESMKRLAEVKDSLDIEVKQNFIDPLQNLCEKDLKEIQHHLKKLE
..E.L.R..E.L....N..DALLDA.ESMK.LAEVK.SLDIEVKQNFID.LQNLCEKDLK.I.HHL.KL.
RetrocopyLSECLIRHQEELGNESNFSDALLDASESMKHLAEVKYSLDIEVKQNFIDLLQNLCEKDLKGIPHHLQKLD
ParentalGRRLDFDYKKKRQGKIPDEELRQALEKFEESKEVAETSMHNLLETDIEQVSQLSALVDAQLDYHRQAVQI
GRRLD...KK..QGK.PDEEL.QALEKFE.SKEV.ETSMHNLL.T.IEQVSQL.ALV.AQLDYH.QA.QI
RetrocopyGRRLDLE*KKW-QGKSPDEELCQALEKFEDSKEVEETSMHNLLDTNIEQVSQLPALVEAQLDYHWQALQI
ParentalLDELAEKLKRRMREASSRPKREYK
LDEL.EKLK.RMR..SS....E.K
RetrocopyLDELTEKLKHRMRKSSSHQIFEKK

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 1 .16 RPM 28 .53 RPM
SRP007412_cerebellum 2 .07 RPM 17 .15 RPM
SRP007412_heart 0 .36 RPM 5 .06 RPM
SRP007412_kidney 0 .76 RPM 29 .07 RPM
SRP007412_liver 0 .24 RPM 21 .42 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_1488 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_1488 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_1488 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 6 parental genes, and 16 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG000001419853 retrocopies
Gorilla gorilla ENSGGOG000000081983 retrocopies
Macaca mulatta ENSMMUG000000002731 retrocopy
Monodelphis domestica ENSMODG000000009311 retrocopy
Nomascus leucogenys ENSNLEG000000031222 retrocopies
Pongo abelii ENSPPYG00000009405 6 retrocopies



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