RetrogeneDB ID:

retro_pabe_766

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:11:63367492..63368670(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSPPYG00000003521
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RBMX
Ensembl ID:ENSPPYG00000020771
Aliases:None
Description:RNA binding motif protein, X-linked [Source:HGNC Symbol;Acc:9910]


Retrocopy-Parental alignment summary:






>retro_pabe_766
ATGATTGAAGCAGATCGCCCGGGGAAGCTGTTCATTGGGGGCCTCAACCTCGAAACCGACGAGAAAGCCCTCGAAGCTGA
GTTTGGCAAGTATGGCCACATCGTCGAGGTGCTCCTGATGAAAGACCGAGAAACCAACAAGTCGAGGGGCTTTGCATTCG
TCACCTTTGAAAGCCCCGCAGACGCCAAGGCCGCCGCCAGAGACATGAACGGCAAGTCCCTGGATGGTAAGGCCATCAAG
GTGGCCCAGGCCACCAAACCGGCGTTCGAGAGCAGCCGGCGGGGCCCGCCGCCTCCCCGCAGCCGCGGTCGCCCGAGGTT
GCTGCGCGGAACCCGCGGGGGTGGCGGCGGCCCGCGGCGTTCCCCATCCCGGGGCGGGCCCGATGACGACGGCGGCTACG
CGGGGGATTTCGACCTGCGGCCCTCCAGGGCCTCGATGCCCATGAAGCGTGGGCCGCCGCCGCCGCGCAGGGCGGCCCAC
CCCCCAAAAGGGCCGCGCCGTCGGGCCCGGCTCGCAGCAGCGGCGGTGGAATGCGCGGGAGGGCCCTGGCCGTGCGGGGG
CGAGACGGCTACTCAGGCCCACCGCGCCGGGAGCCGCTGCCCCCGCGCCGCGACCCCTACCTGGGCCTGCGGGATGAGGG
CTACTCGTCCAGAGACGGCTACTCGAGCCGAAACTACCGCGAACCCCGGGGTTTTGCCCCCTCGCCCAGAGAGTACACCC
ACCGCGATTACGGCCACTCCAGTGTCCGGGACGACTGTCCCTTAAGAGGCTACAGCGACCGAGACGGCTACGGGGGTCGC
GACCGTGACTACGGGGATCATCTGAGCAGAGGCTCCTATCGAGAGCCCTTCGAGAGCTACGGAGACCTGCGTGGCGCCGC
CCCAGGAAGGGGGACACCGCCATCTTACGGAGGAGGAGGCCGCTACGAGGAGTACCGGGGCTGCTCACCCGATGCCTACA
GCGGCGGCCGCGACAGTTACAGCAGCAGTTATGGCCGGAGCGACCGCTACTCGAGGGGCCGAGACCGGATGGGCAGACCA
GATCGTGGGCTCTCTCTGTCCATGGAAAGGGGCTGCCCTCCCCAGCGTGATTCTTACAGCCGGTCAGGCTGCAGGGTGCC
CAGGGGCGGAGGCCGTCTAGGAGGCCGCTTGGAGAGAGGAGGAGGCCGGAGCAGATAC

ORF - retro_pabe_766 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.61 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalMVEADRPGKLFIGGLNTETNEKALEAVFGKYGRIVEVLLMKDRETNKSRGFAFVTFESPADAKDAARDMN
M.EADRPGKLFIGGLN.ET.EKALEA.FGKYG.IVEVLLMKDRETNKSRGFAFVTFESPADAK.AARDMN
RetrocopyMIEADRPGKLFIGGLNLETDEKALEAEFGKYGHIVEVLLMKDRETNKSRGFAFVTFESPADAKAAARDMN
ParentalGKSLDGKAIKVEQATKPSFESGRRGPPPPPRSRGPPRGLRGGRGGSGGTRGPPSRGGHMDDGGYSMNFNM
GKSLDGKAIKV.QATKP.FES.RRG.PPPPRSRG.PR.LRG.RGG.GG.R..PSRGG..DDGGY...F..
RetrocopyGKSLDGKAIKVAQATKPAFESSRRG-PPPPRSRGRPRLLRGTRGGGGGPRRSPSRGGPDDDGGYAGDFDL
ParentalSSSRGPLPVKRGPPP-RSG-GPPPKRSAPSGPVRSS-SGMGGRAPVSRGRDSYGGPPRREPLPSRRDVYL
..SR...P.KRGPPP.R.G.GPPPKR.APSGP.RSS..GM.GRA...RGRD.Y.GPPRREPLP.RRD.YL
RetrocopyRPSRASMPMKRGPPP>RAG>GPPPKRAAPSGPARSSGGGMRGRALAVRGRDGYSGPPRREPLPPRRDPYL
ParentalSPRDDGYSTKDSYSSRDYPSSRDTRDYAPPPRDYTYRDYGHSSSRDDYPSRGYSDRDGY-GRDRDYSDHP
..RD.GYS..D.YSSR.Y...R..R..AP.PR.YT.RDYGHSS.RDD.P.RGYSDRDGY.GRDRDY.DH.
RetrocopyGLRDEGYSSRDGYSSRNY---REPRGFAPSPREYTHRDYGHSSVRDDCPLRGYSDRDGYGGRDRDYGDHL
ParentalSGGSYRDSYESYGNSRSAPPTRGPPPSYGGSSRYDDY-SSSRDGYGGSRDSYSSS--RSDLYSSGRDRVG
S.GSYR...ESYG..R.A.P.RG.PPSYGG..RY..Y...S.D.Y.G.RDSYSSS..RSD.YS.GRDR.G
RetrocopySRGSYREPFESYGDLRGAAPGRGTPPSYGGGGRYEEYRGCSPDAYSGGRDSYSSSYGRSDRYSRGRDRMG
ParentalRQERGLPPSMERGYPPPRDSYSSSSRGAPRGGGRGGSRSDRGGGRSRY
R..RGL..SMERG.PP.RDSYS.S....PRGGGR.G.R..RGGGRSRY
RetrocopyRPDRGLSLSMERGCPPQRDSYSRSGCRVPRGGGRLGGRLERGGGRSRY

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 0 .00 RPM 25 .27 RPM
SRP007412_cerebellum 0 .00 RPM 34 .53 RPM
SRP007412_heart 0 .00 RPM 28 .21 RPM
SRP007412_kidney 0 .20 RPM 34 .37 RPM
SRP007412_liver 0 .03 RPM 19 .55 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_766 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_766 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_766 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 25 parental genes, and 46 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000133081 retrocopy
retro_btau_36,
Canis familiaris ENSCAFG000000189624 retrocopies
retro_cfam_1106, retro_cfam_1244, retro_cfam_1649, retro_cfam_1914,
Choloepus hoffmanni ENSCHOG000000123693 retrocopies
retro_chof_1240, retro_chof_2596, retro_chof_880,
Cavia porcellus ENSCPOG000000121641 retrocopy
retro_cpor_778,
Dasypus novemcinctus ENSDNOG000000171993 retrocopies
retro_dnov_1436, retro_dnov_2205, retro_dnov_696,
Dipodomys ordii ENSDORG000000154811 retrocopy
retro_dord_793,
Echinops telfairi ENSETEG000000131781 retrocopy
retro_etel_1952,
Felis catus ENSFCAG000000047791 retrocopy
retro_fcat_1903,
Gorilla gorilla ENSGGOG000000069441 retrocopy
retro_ggor_657,
Loxodonta africana ENSLAFG000000055683 retrocopies
retro_lafr_1188, retro_lafr_276, retro_lafr_35,
Myotis lucifugus ENSMLUG000000132095 retrocopies
retro_mluc_1630, retro_mluc_1746, retro_mluc_203, retro_mluc_2180, retro_mluc_80,
Monodelphis domestica ENSMODG000000140541 retrocopy
retro_mdom_1231,
Mustela putorius furoENSMPUG000000018552 retrocopies
retro_mputfur_1539, retro_mputfur_956,
Mus musculus ENSMUSG000000311342 retrocopies
retro_mmus_170, retro_mmus_187,
Oryctolagus cuniculus ENSOCUG000000072201 retrocopy
retro_ocun_3,
Otolemur garnettii ENSOGAG000000078395 retrocopies
retro_ogar_1057, retro_ogar_137, retro_ogar_1586, retro_ogar_2445, retro_ogar_2584,
Ochotona princeps ENSOPRG000000165931 retrocopy
retro_opri_372,
Pongo abelii ENSPPYG000000177281 retrocopy
retro_pabe_324,
Pongo abelii ENSPPYG000000203141 retrocopy
retro_pabe_40,
Pongo abelii ENSPPYG00000020771 3 retrocopies
retro_pabe_2548, retro_pabe_303, retro_pabe_766 ,
Rattus norvegicus ENSRNOG000000008661 retrocopy
retro_rnor_268,
Sorex araneus ENSSARG000000003971 retrocopy
retro_sara_169,
Tupaia belangeri ENSTBEG000000011541 retrocopy
retro_tbel_1919,
Tarsius syrichta ENSTSYG000000095551 retrocopy
retro_tsyr_15,
Tursiops truncatus ENSTTRG000000073221 retrocopy
retro_ttru_1450,


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