RetrogeneDB ID:

retro_ptro_2198

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:5:144092596..144093213(+)
Located in intron of:ENSPTRG00000017363
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL7L1
Ensembl ID:ENSPTRG00000018175
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ptro_2198
CAGAAGAAAGGAAAAGGGCTCAGGTTTAAATGACTGGAATCATTCCTACATGATTCCTGGTGGCAGAAACGCGACAAGGT
GCGTCTCAGACGACTAGAAGTGAAACCTCATGCCTTGGAATTGCCAGATAAACATTCCTTGGCCTTTGTTGTACGCATCG
AAAGGATTGATGGCGTGAGTTTACTGGTGCAGAGAACCATTGCAAGACTTCGCCTAAAGAAAATTTTCAGTGGTGTCTTT
GTAAAAGTTACCCCCAGAATCTAAAAATGCTGCGTATAGTGGAACCTTATGTGACCTGGGGATTTCCAAATCTGAAGTCT
GTCCGAGAACTCATTTTGAAATGTGGACAAGCCAATGTCAAGAATAAGACCATCCCTCTGACAGACAACACAGTGATTGA
GGAGCACCTGGGGAAGTTTGGCGTCATTTGCTTGGAAGACCTCATTCATGAAATTGCCTTCCCAGGGAAGCATTTCCAGG
AGATCTCATGGTTCTTGCGCCCTTTCCACCTCTCAGTGGCCCGTCATGCTACCAAAAATAGAGTGGGCTTCCTCAAGGAG
ATGGGCACACCTGGCTATCGGGGTGAACGCATCAATCAGCTCATCCGTCAGCTGAAC

ORF - retro_ptro_2198 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 97.1 %
Parental protein coverage: 83.74 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalQKKGKGLRFKRLESFLHDSWRQKRDKVRLRRLEVKPHALELPDKHSLAFVVRIERIDGVSLLVQRTIARL
QKKGKGLRFK.LESFLHDSW.QKRDKVRLRRLEVKPHALELPDKHSLAFVVRIERIDGVSLLVQRTIARL
RetrocopyQKKGKGLRFK*LESFLHDSWWQKRDKVRLRRLEVKPHALELPDKHSLAFVVRIERIDGVSLLVQRTIARL
ParentalRLKKIFSGVFVKVTP-QNLKMLRIVEPYVTWGFPNLKSVRELILKRGQAKVKNKTIPLTDNTVIEEHLGK
RLKKIFSGVFVKVTP.QNLKMLRIVEPYVTWGFPNLKSVRELILK.GQA.VKNKTIPLTDNTVIEEHLGK
RetrocopyRLKKIFSGVFVKVTP<QNLKMLRIVEPYVTWGFPNLKSVRELILKCGQANVKNKTIPLTDNTVIEEHLGK
ParentalFGVICLEDLIHEIAFPGKHFQEISWFLHPFHLSVARHATKNRVGFLKEMGTPGYRGERINQLIRQLN
FGVICLEDLIHEIAFPGKHFQEISWFL.PFHLSVARHATKNRVGFLKEMGTPGYRGERINQLIRQLN
RetrocopyFGVICLEDLIHEIAFPGKHFQEISWFLRPFHLSVARHATKNRVGFLKEMGTPGYRGERINQLIRQLN

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 .18 RPM 15 .94 RPM
SRP007412_cerebellum 0 .61 RPM 11 .15 RPM
SRP007412_heart 0 .55 RPM 6 .56 RPM
SRP007412_kidney 0 .76 RPM 10 .80 RPM
SRP007412_liver 0 .65 RPM 6 .84 RPM
SRP007412_testis 0 .42 RPM 2 .42 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_2198 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_2198 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_2198 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3250

Parental genes homology:
Parental genes homology involve 25 parental genes, and 116 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000127912 retrocopies
Bos taurus ENSBTAG000000184782 retrocopies
Canis familiaris ENSCAFG000000017284 retrocopies
Choloepus hoffmanni ENSCHOG000000003064 retrocopies
Cavia porcellus ENSCPOG000000211892 retrocopies
Dasypus novemcinctus ENSDNOG000000134851 retrocopy
Equus caballus ENSECAG000000031131 retrocopy
Erinaceus europaeus ENSEEUG000000104311 retrocopy
Echinops telfairi ENSETEG000000024193 retrocopies
Felis catus ENSFCAG000000097071 retrocopy
Homo sapiens ENSG0000014622322 retrocopies
Monodelphis domestica ENSMODG000000190281 retrocopy
Mustela putorius furoENSMPUG000000132961 retrocopy
Mus musculus ENSMUSG000000638884 retrocopies
Nomascus leucogenys ENSNLEG0000000464921 retrocopies
Otolemur garnettii ENSOGAG000000126713 retrocopies
Pan troglodytes ENSPTRG00000018175 23 retrocopies
Pteropus vampyrus ENSPVAG000000086963 retrocopies
Rattus norvegicus ENSRNOG000000162691 retrocopy
Sorex araneus ENSSARG000000052862 retrocopies
Sarcophilus harrisii ENSSHAG000000112191 retrocopy
Sus scrofa ENSSSCG000000264723 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000098412 retrocopies
Tursiops truncatus ENSTTRG000000069716 retrocopies
Vicugna pacos ENSVPAG000000088942 retrocopies



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