RetrogeneDB ID:

retro_pabe_2312

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:3:73562181..73563048(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CCDC137
Ensembl ID:ENSPPYG00000008741
Aliases:None
Description:coiled-coil domain containing 137 [Source:HGNC Symbol;Acc:33451]


Retrocopy-Parental alignment summary:






>retro_pabe_2312
ATGGCGCAAGCTGGACATGGAGCAGCGGTGCCCAGGGTGCCGGCGGGTCCTGGGAGTCCCCAGCGGGAGCAGCAGTGGGC
AGCAAGTGCAGCCGCTGGGGAACCAGCGCCCAGCCCCATGGTCCAGGCTTCACAGCAAAGAGGAGAAAGGGAATTGCAAG
CCCAAAACCCAGGACGAACAGGAGATCCCTTTCCGGCTCTGGGAGATTATGAGGAGCCGCCGGGAGATGAAAAATCCGAC
CGGTAACAAGAAGAGGAAGAAAGCGGCCCAGGTGGCCTTCAGAAAGACATTGGAAAAGGAAGCAAAGGGAGTGGAGCCCA
ACATTGCCGTCCCCAAGTTCAAGCAGAGGAAGGGGGAGTCCGACTAGGCCTATATCCAGCGCATGCAGCAAGAGGCCCAG
CACATGCTATTCCTCAGCAAGAGCCAGGCCACCCTGCAGCCAGAGGTCCAGACAGCTCCCAAGGAGAAGTCTGAGCTGTA
AAAAGCAAAAAAAGGGTTCCAGAAGCGACTACTAGATAAAGGCTGGCAGAAAAAGGAGGAAAAGACGGCAGACAGGCTGG
AGCAGGAGTTACTCCGAGACACGGTGAAGTTTGGTAAGGTTGTCCTGCAGGGCCCAGAGCTGACTACCAGGCCCTGGAGG
AGCCTAAGCAAGGACCAGCCTGGCAGGAGATCGCAGATGCTGAGGATGCTTCTGAGCCCCCGCGGTGTATTCCAGCCTCT
GACTGCCTCCCTGGCCTACCAGCGGATTGTGGGGGAGGAGAGAGAGTGGGCCTTGCAAGCCTACAGATGTTGAAGCAGCC
GCGGTGGCTGCATGGGGAGTGACCCCCCCCCCCACTCACTTCCAAGAAGAAGCCAGAGCCACAGCTG

ORF - retro_pabe_2312 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.11 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMARAGRGAAVSRVQAGPGSPRQAR-GRQQVQPLGKQGAAPWPGLRSKEKKKVNCKPKNQDEQEIPFRLRE
MA.AG.GAAV.RV.AGPGSP.......QQVQPLG.Q..APW..L.SKE.K..NCKPK.QDEQEIPFRL.E
RetrocopyMAQAGHGAAVPRVPAGPGSPQREQ>SGQQVQPLGNQRPAPWSRLHSKEEKG-NCKPKTQDEQEIPFRLWE
ParentalIMRSRQEMKNPISNKKRKKAAQVTFRKTLEKEAKGAEPDITIPKFKQRKGESDGAYIQRMQQEAQHVLFL
IMRSR.EMKNP..NKKRKKAAQV.FRKTLEKEAKG.EP.I..PKFKQRKGESD.AYIQRMQQEAQH.LFL
RetrocopyIMRSRREMKNPTGNKKRKKAAQVAFRKTLEKEAKGVEPNIAVPKFKQRKGESD*AYIQRMQQEAQHMLFL
ParentalSKNQATRQPEVQAAPKEKSEQKKAKKAFQKRRLDKVRRKKEEKAADRLEQELLRDTVKFGEVVLQPPELT
SK.QAT.QPEVQ.APKEKSE.......FQKR.LDK...KKEEK.ADRLEQELLRDTVKFG.VVLQ.PELT
RetrocopySKSQATLQPEVQTAPKEKSELXXXXXGFQKRLLDKGWQKKEEKTADRLEQELLRDTVKFGKVVLQGPELT
ParentalARPRRSVSKDQPGRRSQMLRMLLSPGGVSQPLTASLARQRIVGEERERAMQAYR-VLKQRRQRLHRE--R
.RP.RS.SKDQPGRRSQMLRMLLSP.GV.QPLTASLA.QRIVGEERE.A.QAYR..LKQ.R..LH.E...
RetrocopyTRPWRSLSKDQPGRRSQMLRMLLSPRGVFQPLTASLAYQRIVGEEREWALQAYR<MLKQPRW-LHGE*XX
ParentalPHLTSQKKPELQL
..LTS.KKPE.QL
RetrocopyXXLTSKKKPEPQL

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 15 .54 RPM
SRP007412_cerebellum 0 .00 RPM 11 .92 RPM
SRP007412_heart 0 .00 RPM 4 .30 RPM
SRP007412_kidney 0 .00 RPM 21 .45 RPM
SRP007412_liver 0 .00 RPM 7 .56 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_2312 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_2312 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_2312 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2661
Gorilla gorilla retro_ggor_1857
Macaca mulatta retro_mmul_1511

Parental genes homology:
Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species Parental gene accession Retrocopies number
Erinaceus europaeus ENSEEUG000000148781 retrocopy
Homo sapiens ENSG000001852981 retrocopy
Gorilla gorilla ENSGGOG000000093331 retrocopy
Macaca mulatta ENSMMUG000000088311 retrocopy
Monodelphis domestica ENSMODG000000027131 retrocopy
Mus musculus ENSMUSG000000499571 retrocopy
Nomascus leucogenys ENSNLEG000000138303 retrocopies
Pongo abelii ENSPPYG00000008741 1 retrocopy
retro_pabe_2312 ,
Pan troglodytes ENSPTRG000000097671 retrocopy
Rattus norvegicus ENSRNOG000000487121 retrocopy



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