RetrogeneDB ID:

retro_pabe_602

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:10:66909959..66910537(-)
Located in intron of:ENSPPYG00000002393
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS3A
Ensembl ID:ENSPPYG00000025869
Aliases:None
Description:40S ribosomal protein S3a [Source:RefSeq peptide;Acc:NP_001126750]


Retrocopy-Parental alignment summary:






>retro_pabe_602
GGCAACACAAAGGGAGCCAAGAAGAAAGTGCTTGATCCATTTTCTAAGAAAGATTTGTATTACATGAAAGCATCTGCCGT
GTTCAATATAAGAAATATTGGGAAGACACTAGTCACCAGGACCCAAGGAACCATAATTGAATCTGATGGCCTCAAGGGTC
GTGTATTTGAAGTGAGTCTTGCTCATATGCAGAATGATAAAGTTGCATTTAGAAAATTCAGCTGATTACTGAAGATGTTC
AGAGGAATAATTGCCTGATGAGCTTCCATGGCATGGATCTTACCCATGACAAAATATGTTTCATGGTCAAAAAATGGCAG
ACAATGGTTGAAGCTCATGTCAATATCAAGACTACTGGTGCTTACTTGCTTTATGTGTTCTGTGTTGGTTTTACTAAAAA
GTGCAACAATCAGATACAGAAGACCTCTTATGCTTAGCACCAGTGGTTCGGCCAAATCCGGAACAAGTTGATGGAAATCA
TGACCCGAGAGGTGCAGACAAATTACTTGAAAGAAGTGGTCAATAAATTGATTCCAGACAGGATTGGAAAAGACATAGAA
AAAATTCTTGACAATCTA

ORF - retro_pabe_602 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.32 %
Parental protein coverage: 73.11 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASDGLKGRVFEVSLADLQNDEVAF
G..KGAKKKV.DPFSKKD.Y..KA.A.FNIRNIGKTLVTRTQGT.I.SDGLKGRVFEVSLA..QND.VAF
RetrocopyGNTKGAKKKVLDPFSKKDLYYMKASAVFNIRNIGKTLVTRTQGTIIESDGLKGRVFEVSLAHMQNDKVAF
ParentalRKF-KLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTMIEAHVDVKTTDGYLLRLFCVGFTKKRNNQI
RKF..LITEDVQ..NCL..FHGMDLT.DK.C.MVKKWQTM.EAHV..KTT..YLL..FCVGFTKK.NNQI
RetrocopyRKF<QLITEDVQRNNCLMSFHGMDLTHDKICFMVKKWQTMVEAHVNIKTTGAYLLYVFCVGFTKKCNNQI
ParentalRKTSYAQHQQVRQIRKKMMEIMTREVQTNDLKEVVNKLIPDSIGKDIEKACQSI
.KTSYA.HQ...QIR.K.MEIMTREVQTN.LKEVVNKLIPD.IGKDIEK.....
RetrocopyQKTSYA*HQWFGQIRNKLMEIMTREVQTNYLKEVVNKLIPDRIGKDIEKILDNL

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 71 .93 RPM
SRP007412_cerebellum 0 .00 RPM 99 .96 RPM
SRP007412_heart 0 .00 RPM 95 .16 RPM
SRP007412_kidney 0 .03 RPM 145 .71 RPM
SRP007412_liver 0 .00 RPM 124 .70 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_602 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_602 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_602 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_588

Parental genes homology:
Parental genes homology involve 14 parental genes, and 101 retrocopies.

Species Parental gene accession Retrocopies number
Cavia porcellus ENSCPOG000000155699 retrocopies
Equus caballus ENSECAG000000095736 retrocopies
Felis catus ENSFCAG000000312885 retrocopies
Loxodonta africana ENSLAFG000000176603 retrocopies
Macaca mulatta ENSMMUG000000218211 retrocopy
Monodelphis domestica ENSMODG000000009696 retrocopies
Mustela putorius furoENSMPUG000000071398 retrocopies
Mus musculus ENSMUSG000000280812 retrocopies
Procavia capensis ENSPCAG000000150406 retrocopies
Pongo abelii ENSPPYG00000025869 27 retrocopies
Pteropus vampyrus ENSPVAG0000001540624 retrocopies
Rattus norvegicus ENSRNOG000000118931 retrocopy
Sarcophilus harrisii ENSSHAG000000150882 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000242031 retrocopy



Copyright © RetrogeneDB 2014-2017