RetrogeneDB ID:

retro_pabe_169

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:4:122046183..122047293(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSPPYG00000015017
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:TRAM1
Ensembl ID:ENSPPYG00000018660
Aliases:None
Description:translocating chain-associated membrane protein 1 [Source:RefSeq peptide;Acc:NP_001126237]


Retrocopy-Parental alignment summary:






>retro_pabe_169
ATGGGGCTCCGTAAGAAGAGCACCAAGAACCCCCCCGTTCTGAGCCAGGAATTCATCCTGCAGAATCATGCGGACATCGT
CTCCTGCGTGGGGATGTTCTTCCTGCTGGGGCTTGTGTTCGAGGGAACAGCAGAAGCATCCATCGTGTTTCTCACTCTTC
AGCACAGTGTTGCTGTCCCTGCAGCAGAGGAACAAGCCACGGGATCAAAGTCCCTCTATTATTATGGTGTCAAAGATTTG
GCCACGGTTTTCTTCTACATGCTGGTGGCAATCATTATTCACGCCACAATTCAGGAGTATGTGTTGGATAAAATTAACAA
GAGAATGCAGTTCACCAAAGCGAAACAAAACAAGTTTAACGAATCTGGTCAGTTTAGTGTGTTCTACTTTTTTTCTTGTA
TTTGGGGCACATTCATTTTAATCTCTGAAAACTGCCTGTCAGACCCAACTCTCATATGGAAGGCTCGTCCCCATAGCATG
ATGACATTTCAAATGAAGTTTTTCTACATATCCCAGTTGGCTTACTGGTTTCATGCTTTTCCTGAACTCTACTTCCAGAA
AACCAAAAAACAAGACATCCCTCGTCAACTTGTCTACATTGGTCTTCACCTCTTCCACATTACTGGAGCTTATCTCTTGT
ACTTAAATCATTTGGGACTTCTTCTTTTGGTACTGCATTATTTTGTTGAGTTACTTTCCCACATGTGCGGCCTGTTTTAC
TTTAGTGATGAAAAGTACCAGAAAGGCTTATCTCTGTGGGCCATTGTGTTTATCTTGGGTAGACTTGTGACTTTAATTGT
TTCCGTACTCACTGTTGGGTTTCACCTGGCTGGATCGCAGAATCGGAATCCTGATGCCCTTACTGGAAATGTAAATGTGT
TGGCAGCTAAAATTGCTGTTCTGTCATCCAGTTGCACGATCCAAGCCTACGTAACATGGAACTTAATTACTCTCTGGCTT
CAGAGGTGGGTAGAAGATTCTAATATTCAGGCCTCATGTATGAAGAAGAAAAGGTCGAGATCTTCTAAAAAAAGAACAGA
AAACGGAGTGGGAGTGGAAACTTCAAATAGAGTAGACTGTCCGCCAAAGAGGAAAGAGAAATCTTCATAA

ORF - retro_pabe_169 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.12 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAIRKKSTKSPPVLSHEFVLQNHADIVSCVAMVFLLGLMFEIRAKASIIFVTLQYNVTLPATEEQATESA
M..RKKSTK.PPVLS.EF.LQNHADIVSCV.M.FLLGL.FE..A.ASI.F.TLQ..V..PA.EEQAT.S.
RetrocopyMGLRKKSTKNPPVLSQEFILQNHADIVSCVGMFFLLGLVFEGTAEASIVFLTLQHSVAVPAAEEQATGSK
ParentalSLYYYGIKDLATVFFYMLVAIIIHAVIQEYMLDKINRRMHFSKTKHSKFNESGQLSAFYLFACVWGTFIL
SLYYYG.KDLATVFFYMLVAIIIHA.IQEY.LDKIN.RM.F.K.K..KFNESGQ.S.FY.F.C.WGTFIL
RetrocopySLYYYGVKDLATVFFYMLVAIIIHATIQEYVLDKINKRMQFTKAKQNKFNESGQFSVFYFFSCIWGTFIL
ParentalISENYISDPTILWRAYPHNLMTFQMKFFYISQLAYWLHAFPELYFQKTKKEDIPRQLVYIGLYLFHIAGA
ISEN..SDPT..W.A.PH..MTFQMKFFYISQLAYW.HAFPELYFQKTKK.DIPRQLVYIGL.LFHI.GA
RetrocopyISENCLSDPTLIWKARPHSMMTFQMKFFYISQLAYWFHAFPELYFQKTKKQDIPRQLVYIGLHLFHITGA
ParentalYLLNLNHLGLVLLVLHYFVEFLFHISRLFYFSNEKYQKGFSLWAVLFVLGRLLTLILSVLTVGFGLARAE
YLL.LNHLGL.LLVLHYFVE.L.H...LFYFS.EKYQKG.SLWA..F.LGRL.TLI.SVLTVGF.LA...
RetrocopyYLLYLNHLGLLLLVLHYFVELLSHMCGLFYFSDEKYQKGLSLWAIVFILGRLVTLIVSVLTVGFHLAGSQ
ParentalNQKLDFSTGNFNVLAVRIAVLASICITQAFMMWKFINFQLRRWREHSAFQAPAVKKKPTVTKGRSSKKGT
N...D..TGN.NVLA..IAVL.S.C..QA...W..I...L.RW.E.S..QA...KKK......RSSKK.T
RetrocopyNRNPDALTGNVNVLAAKIAVLSSSCTIQAYVTWNLITLWLQRWVEDSNIQASCMKKK----RSRSSKKRT
ParentalENGVNGTLTSNVADSPRNKKEKSS
ENGV.G..TSN..D.P...KEKSS
RetrocopyENGV-GVETSNRVDCPPKRKEKSS

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(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 .82 RPM 9 .07 RPM
SRP007412_cerebellum 4 .13 RPM 12 .89 RPM
SRP007412_heart 1 .38 RPM 18 .72 RPM
SRP007412_kidney 1 .43 RPM 47 .80 RPM
SRP007412_liver 0 .03 RPM 61 .30 RPM

ChIP-Seq - click to see more details

Pongo abelii was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_pabe_169 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_169 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_169 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Callithrix jacchus retro_cjac_168
Parental genes homology:
Parental genes homology involve 25 parental genes, and 26 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000063251 retrocopy
retro_amel_78,
Bos taurus ENSBTAG000000075621 retrocopy
retro_btau_24,
Canis familiaris ENSCAFG000000078661 retrocopy
retro_cfam_15,
Callithrix jacchus ENSCJAG000000078931 retrocopy
retro_cjac_168,
Dasypus novemcinctus ENSDNOG000000092962 retrocopies
retro_dnov_27, retro_dnov_906,
Dipodomys ordii ENSDORG000000019011 retrocopy
retro_dord_27,
Equus caballus ENSECAG000000183781 retrocopy
retro_ecab_506,
Echinops telfairi ENSETEG000000184471 retrocopy
retro_etel_674,
Felis catus ENSFCAG000000287751 retrocopy
retro_fcat_136,
Homo sapiens ENSG000000671671 retrocopy
retro_hsap_51,
Loxodonta africana ENSLAFG000000116251 retrocopy
retro_lafr_9,
Macaca mulatta ENSMMUG000000015161 retrocopy
retro_mmul_235,
Monodelphis domestica ENSMODG000000073161 retrocopy
retro_mdom_308,
Mustela putorius furoENSMPUG000000106161 retrocopy
retro_mputfur_558,
Mus musculus ENSMUSG000000259351 retrocopy
retro_mmus_117,
Nomascus leucogenys ENSNLEG000000113761 retrocopy
retro_nleu_73,
Oryctolagus cuniculus ENSOCUG000000087341 retrocopy
retro_ocun_52,
Otolemur garnettii ENSOGAG000000063791 retrocopy
retro_ogar_2932,
Pongo abelii ENSPPYG00000018660 1 retrocopy
retro_pabe_169 ,
Pan troglodytes ENSPTRG000000203341 retrocopy
retro_ptro_2081,
Rattus norvegicus ENSRNOG000000078921 retrocopy
retro_rnor_287,
Sus scrofa ENSSSCG000000061931 retrocopy
retro_sscr_980,
Ictidomys tridecemlineatus ENSSTOG000000055371 retrocopy
retro_itri_38,
Tarsius syrichta ENSTSYG000000138871 retrocopy
retro_tsyr_24,
Tursiops truncatus ENSTTRG000000003281 retrocopy
retro_ttru_24,


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