RetrogeneDB ID:

retro_ptro_1892

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:3:62669333..62669864(-)
Located in intron of:ENSPTRG00000015067
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL10A
Ensembl ID:ENSPTRG00000018085
Aliases:None
Description:ribosomal protein L10a [Source:HGNC Symbol;Acc:10299]


Retrocopy-Parental alignment summary:






>retro_ptro_1892
TATGACCTCCAGAAGGACAAGCGCTTCTCGGGCACCGTCAGACTTAAGTCCACTCCCCGCCCTAAGTTCTGTGTGTGTGT
CCTGGGGGACCAGCAGCACTGTGACGAGGCTAAGGCCGTGGATATCCCCCACGTGGACATCGAGGCGCTGAAAAAACTCA
ACAAGAATAAAAAACTGGTCAAGAAGCTGGCCAAGAAGTAAGATGCGTTTTTGGCCTCAGAGTCTCTGATCAAGCAGATT
CCACGAATCCTCGGCCCAGGTCTAAATAAGGCAGGAAAGTTCCCTTCCCTGCTCACACACAACGAAAACATGGTGGCCAA
AGTGGGTGAGGTGAAGTCCACAATCAAGTTCCAAATGAAGAAGGTGTTATGTCTGGCTGTAGCTGTTGGTCACGTGAAGA
TGACAGACGATGAGCTTGTGTATAACATTCACCTGGCTGTCAACTTCTTGGTGTCATTGCTCAAGAAAAACTGGCAGAAT
GTCTGGGCCTTATATATCAAGAGCACCATGAGCAAGTCCCAGCGCCTATAT

ORF - retro_ptro_1892 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 95.48 %
Parental protein coverage: 81.57 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalYDPQKDKRFSGTVRLKSTPRPKFSVCVLGDQQHCDEAKAVDIPHMDIEALKKLNKNKKLVKKLAKKYDAF
YD.QKDKRFSGTVRLKSTPRPKF.VCVLGDQQHCDEAKAVDIPH.DIEALKKLNKNKKLVKKLAKK.DAF
RetrocopyYDLQKDKRFSGTVRLKSTPRPKFCVCVLGDQQHCDEAKAVDIPHVDIEALKKLNKNKKLVKKLAKK*DAF
ParentalLASESLIKQIPRILGPGLNKAGKFPSLLTHNENMVAKVDEVKSTIKFQMKKVLCLAVAVGHVKMTDDELV
LASESLIKQIPRILGPGLNKAGKFPSLLTHNENMVAKV.EVKSTIKFQMKKVLCLAVAVGHVKMTDDELV
RetrocopyLASESLIKQIPRILGPGLNKAGKFPSLLTHNENMVAKVGEVKSTIKFQMKKVLCLAVAVGHVKMTDDELV
ParentalYNIHLAVNFLVSLLKKNWQNVRALYIKSTMGKPQRLY
YNIHLAVNFLVSLLKKNWQNV.ALYIKSTM.K.QRLY
RetrocopyYNIHLAVNFLVSLLKKNWQNVWALYIKSTMSKSQRLY

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 2 .09 RPM 141 .85 RPM
SRP007412_cerebellum 0 .29 RPM 162 .07 RPM
SRP007412_heart 0 .15 RPM 92 .39 RPM
SRP007412_kidney 0 .34 RPM 279 .14 RPM
SRP007412_liver 0 .23 RPM 160 .59 RPM
SRP007412_testis 1 .05 RPM 43 .42 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_1892 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_1892 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_1892 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2795

Parental genes homology:
Parental genes homology involve 13 parental genes, and 81 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG0000000131818 retrocopies
Echinops telfairi ENSETEG000000133252 retrocopies
Gorilla gorilla ENSGGOG0000002814010 retrocopies
Macropus eugenii ENSMEUG000000057606 retrocopies
Myotis lucifugus ENSMLUG0000000008010 retrocopies
Monodelphis domestica ENSMODG000000137662 retrocopies
Ornithorhynchus anatinus ENSOANG000000145741 retrocopy
Oryctolagus cuniculus ENSOCUG000000040652 retrocopies
Pan troglodytes ENSPTRG00000018085 13 retrocopies
Pteropus vampyrus ENSPVAG000000027639 retrocopies
Rattus norvegicus ENSRNOG000000005054 retrocopies
Sarcophilus harrisii ENSSHAG000000020471 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000233663 retrocopies



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