RetrogeneDB ID:

retro_pabe_303

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:1:139866919..139868086(+)
Located in intron of:ENSPPYG00000001176
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
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_303
GTTGAAGCAGATCGCCCAGGAAAGCTCTTCATTGGTGGGCTTAATACGGAGACAAATGAGAAAGCTCTTGAAACAGTATT
TGGCAAATATGGACGAATAGTGGAAGTACTCTTAATAAAAGACCGTGAAACCAACAAATCAAGAGGATTTGCTTTTGTCA
CCTTTGAAAGCCCAGCAGACGCTAAGGATGCAGCCAGAGACATGAATGGAAAGTCATTAGATGGAAAAGCCATCAAGGTG
GAACAAGCCACCAAACCATCATTTGAAAGAGGTAGACATGGACCGCCCCCACCTCCAAGAAGTAGAGGTCCTCCAAGAGG
TTTTGGAGCTGGAAGAGGAGGAAGTGGAGGAACCAGGGGACCTCCTTCACGAGGACACATGGATGACGGTGGATATTCCA
TGAATTTTAACATGAGTTCTTCCAGGGGACCACTCCCAGTAAAAAGAGGACCACCACCAAGAAGTGGGGGTCCTTCTCCT
AAGAGATCTGCACCTTCAGGACTAGTTCGCAGCAGCAGTGGAATGGGAGGAAGAGCTCCTCTATCACGTGGAAGAGATAG
TTACGGAGGTCCACCTCGAAGGGAACCGCTCCCCTCTCGTAGAGATGTTTATTTGTCCCCAAGAGATGATGGGTATTCTA
CTAAAGACAGCTATTCAAGCAGAGATTACCCAAATTCTCGTGATACAAGAGATTATGCACCACCACCACGAGATTATACT
TACCGTGATTATGGTCATTCCAGTTCACGTGATGACTATCCATCAAGAGGCTATGGCGATAGAGATGGATATGGTCGTGA
TCGTGACTATTCAGATCATCCAAGTGGAGGTTCCTACAGAGATTCATATGAGAGTTACGGTAACTCACGTAGTGCTCCAC
CTACACGAGGGCCCCCGCCATCTTATGGTGGAAGCAGTCGCTATGATGATTATAGCAGCTCACGTGATGGATATGGTGGA
AGTCGAGACAGTTACTCAAGCAGCCGAAGTGATCTCTACTCAAGTGGTTGTGATAGGGTTGGCAGACAAGAAAGAGGGCT
TCCCCCTTCTGTAGAAAGGGGGTACCCTTCTTCACGTGATTCCTACAGCAGTTCAAGCCGCGGAGCACCAAGAGGTGCTG
GCGCTGGAGGAAGCCGATCTGATAGAGGGGAAGGCAGAAGCAGGTAC

ORF - retro_pabe_303 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.87 %
Parental protein coverage: 99.74 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalVEADRPGKLFIGGLNTETNEKALEAVFGKYGRIVEVLLMKDRETNKSRGFAFVTFESPADAKDAARDMNG
VEADRPGKLFIGGLNTETNEKALE.VFGKYGRIVEVLL.KDRETNKSRGFAFVTFESPADAKDAARDMNG
RetrocopyVEADRPGKLFIGGLNTETNEKALETVFGKYGRIVEVLLIKDRETNKSRGFAFVTFESPADAKDAARDMNG
ParentalKSLDGKAIKVEQATKPSFESGRRGPPPPPRSRGPPRGLRGGRGGSGGTRGPPSRGGHMDDGGYSMNFNMS
KSLDGKAIKVEQATKPSFE.GR.GPPPPPRSRGPPRG...GRGGSGGTRGPPSRG.HMDDGGYSMNFNMS
RetrocopyKSLDGKAIKVEQATKPSFERGRHGPPPPPRSRGPPRGFGAGRGGSGGTRGPPSRG-HMDDGGYSMNFNMS
ParentalSSRGPLPVKRGPPPRSGGPPPKRSAPSGPVRSSSGMGGRAPVSRGRDSYGGPPRREPLPSRRDVYLSPRD
SSRGPLPVKRGPPPRSGGP.PKRSAPSG.VRSSSGMGGRAP.SRGRDSYGGPPRREPLPSRRDVYLSPRD
RetrocopySSRGPLPVKRGPPPRSGGPSPKRSAPSGLVRSSSGMGGRAPLSRGRDSYGGPPRREPLPSRRDVYLSPRD
ParentalDGYSTKDSYSSRDYPSSRDTRDYAPPPRDYTYRDYGHSSSRDDYPSRGYSDRDGYGRDRDYSDHPSGGSY
DGYSTKDSYSSRDYP.SRDTRDYAPPPRDYTYRDYGHSSSRDDYPSRGY.DRDGYGRDRDYSDHPSGGSY
RetrocopyDGYSTKDSYSSRDYPNSRDTRDYAPPPRDYTYRDYGHSSSRDDYPSRGYGDRDGYGRDRDYSDHPSGGSY
ParentalRDSYESYGNSRSAPPTRGPPPSYGGSSRYDDYSSSRDGYGGSRDSYSSSRSDLYSSGRDRVGRQERGLPP
RDSYESYGNSRSAPPTRGPPPSYGGSSRYDDYSSSRDGYGGSRDSYSSSRSDLYSSG.DRVGRQERGLPP
RetrocopyRDSYESYGNSRSAPPTRGPPPSYGGSSRYDDYSSSRDGYGGSRDSYSSSRSDLYSSGCDRVGRQERGLPP
ParentalSMERGYPPPRDSYSSSSRGAPRGGGRGGSRSDRGGGRSRY
S.ERGYP..RDSYSSSSRGAPRG.G.GGSRSDRG.GRSRY
RetrocopySVERGYPSSRDSYSSSSRGAPRGAGAGGSRSDRGEGRSRY

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 3 .10 RPM 25 .27 RPM
SRP007412_cerebellum 6 .44 RPM 34 .53 RPM
SRP007412_heart 4 .40 RPM 28 .21 RPM
SRP007412_kidney 2 .65 RPM 34 .37 RPM
SRP007412_liver 3 .27 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_303 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_303 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_303 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_23
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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