RetrogeneDB ID:

retro_pabe_3259

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:8:56443652..56444374(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL7L1
Ensembl ID:ENSPPYG00000016619
Aliases:None
Description:60S ribosomal protein L7-like 1 [Source:RefSeq peptide;Acc:NP_001124607]


Retrocopy-Parental alignment summary:






>retro_pabe_3259
AAAGAAAAAATCCTTTTTGTTCCAGAAAGTCTCCTGAAAAAGAGGAAAGCTTATCAAGCCCTCAAAGCCACCCAGGCAAA
GCAGGCACTTTTGGCAAAGAAGGAGCAGAGGAAAGGAAAAGGGCTCAGGTTTAAGTGACTGGAATCATTCCTACATGATT
CCTGGCAGCAGAAATGTGACAAAGTATGTCTCAGATGACCAGAAGTGAAACCTCATGCCTTAGAATTGCCAGATAAACAT
TCCTTGGCCTTTGTTGTACGCATCAAAAGGATTGATGGCGTGATTTTACTGGTGCAGAGAACCACTTCAAGACGCCGCCT
AAAGAAAATGTTTAGTGGTGTCTTAGTAGAAGTCATCCCCCAGAACCTAAAAATGCTGCATATAGTGGAACCTTATGTGA
CTGGGGATTTCCAAATCTGAAATCTGTCTGGGAACTCATTTTGAAACGTGGACAAACCAAGGTCAAGAATAAGATCATTC
TTCTGACAGACAACACAGTGATTTAGGAGCACCTGGGGAAGTTTGGCATCATTTCCTTGGAAGACCTCATTCATGAAATT
GCCTTCCCAGGGAAGCATTTCCAAGAGATCTCATGGTCCTTGCACCCTTTCCACCTCTCAGTGGCCCGTCATGCTACCAA
AAATAGAGTGGGCTTCCTCAAGGAGATGGGCACACCTGGCTATCGGGGTGAACGCATCAATCAGCTCATCTGCTAGCTGA
AC

ORF - retro_pabe_3259 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.54 %
Parental protein coverage: 95.63 %
Number of stop codons detected: 4
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalQRKIPLVPENLLKKRKAYQALKATQAKQALLAKKEQRKGKGLRFKRLESFLHDSWRQKRDMVRLRRLEMK
..KI..VPE.LLKKRKAYQALKATQAKQALLAKKEQRKGKGLRFK.LESFLHDSW.QK.D.V.LR..E.K
RetrocopyKEKILFVPESLLKKRKAYQALKATQAKQALLAKKEQRKGKGLRFK*LESFLHDSWQQKCDKVCLR*PEVK
ParentalPHALELPDKHSLAFVVRIERIDGVSLLVQRTIARLRLKKIFSGVFVKVTPQNLKMLRIVEPYVT-WGFPN
PHALELPDKHSLAFVVRI.RIDGV.LLVQRT..R.RLKK.FSGV.V.V.PQNLKML.IVEPYVT.WGFPN
RetrocopyPHALELPDKHSLAFVVRIKRIDGVILLVQRTTSRRRLKKMFSGVLVEVIPQNLKMLHIVEPYVT<WGFPN
ParentalLKSVRELILKRGQAKVKNKTIPLTDNTVIEEHLGKFGVICLEDLIHEIAFPGKHFQEISWFLRPFHLSVA
LKSV.ELILKRGQ.KVKNK.I.LTDNTVI.EHLGKFG.I.LEDLIHEIAFPGKHFQEISW.L.PFHLSVA
RetrocopyLKSVWELILKRGQTKVKNKIILLTDNTVI*EHLGKFGIISLEDLIHEIAFPGKHFQEISWSLHPFHLSVA
ParentalRHATKNRVGFLKEMGTPGYRGERINQLIRQLN
RHATKNRVGFLKEMGTPGYRGERINQLI..LN
RetrocopyRHATKNRVGFLKEMGTPGYRGERINQLIC*LN

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 86 .53 RPM
SRP007412_cerebellum 0 .00 RPM 71 .74 RPM
SRP007412_heart 0 .00 RPM 35 .79 RPM
SRP007412_kidney 0 .00 RPM 77 .63 RPM
SRP007412_liver 0 .03 RPM 51 .56 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_3259 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_3259 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_3259 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3957
Pan troglodytes retro_ptro_2686
Gorilla gorilla retro_ggor_2659

Parental genes homology:
Parental genes homology involve 26 parental genes, and 137 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
Gorilla gorilla ENSGGOG0000000995815 retrocopies
Macaca mulatta ENSMMUG000000213131 retrocopy
Monodelphis domestica ENSMODG000000190281 retrocopy
Mustela putorius furoENSMPUG000000132961 retrocopy
Mus musculus ENSMUSG000000638884 retrocopies
Otolemur garnettii ENSOGAG000000126713 retrocopies
Pongo abelii ENSPPYG00000016619 21 retrocopies
Pongo abelii ENSPPYG0000001867150 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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