RetrogeneDB ID:

retro_cfam_1106

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:23:34622134..34623312(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCAFG00000007544
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RBMX
Ensembl ID:ENSCAFG00000018962
Aliases:None
Description:RNA binding motif protein, X-linked [Source:HGNC Symbol;Acc:9910]


Retrocopy-Parental alignment summary:






>retro_cfam_1106
AAAATGGTTGAAGCAGATCGCCCAGGAAAGCTTTTCATTGGTGGCCTCAATACGGAAACAAATGAAAAAGCCCTTGAAGC
AGTATTTGGCAAATATGGACGAATAGTGGAAGTTCTATTGATGAAAGATCGTGAAACCAACAAATCAAGAGGATTTGCTT
TTGTCACCTTTGAGAGCCCAGCAGATGCTAAGGATGCAGCCAGAGACATGAATGGAAAGTCCTTAGATGGAAAAGCCATC
AAGGTAGAACAAGCCACAAAACCATCATTTGAAAGTGGTAGACGTGGACCACCTCCACCTCCAAGAAGCAGAGGCCCTCC
AAGAGGTCTTAGAGGTGGAAGAGGAGGAAGTAGAGGAACCAGGGGACCTCCTTCACGTGGAGGGCACATGGATGATGGTG
GCTATTCCATGAATTTTAACATGAGTTCTTCCAGGGGACCACTTCCAGTAAAAAGAGGACCACCACCACGAACTGGTGGT
CCTCCTCCTAAAAGATCTGCCCCTTCAGGACCAGTTCGCAGCAGCAGTAGAATGGGAGGAAGAGCTCCTGTGTCATGCGG
AAGAGATAGTTATGGAGGCCCACCTCGAAGGGAACCCCTGCCCTCTCGTAGAGATGTGTATTTGTCCCCAAGAGATGATG
GATATTCTACTAAAGACAGCTATTCAAGCAGAGATTACCCAAGTTCTCGTGATACTAGAGATTATGCACCACCACCAAGA
GATTATACTTACTGTGATTATGGTCATTCCAGTTCACGTGATGACTACCCATCAAGAGGCTATAGCGATAGAGATGGCTA
TGGTCGTGATCGTGACTATTCAGATCATCCAAGTGGAGGTTCCTACAGAAATTCATATGAGAGTTATGGTAACTCACATA
GTGCTCCACCTACACGAGGGCCCCTGCCCCATCTTATGGTGGAAGCAGTCGCTATGATGATTACAGCAGCTCACGTGACG
GATATGGTGGAAGTCCAGACAGTTACTCAAGCAGCCGAAGTGATCTCTACTCAAGTGGTCGTGATCGGGTTGGCAGACAA
GAAAGAGGGCTTCCCCCTTCTATGGAAAGGGGGTACTCTCCTCCACGTGATTCCTACAGCAGTTCAAGCCGTGGAGCACC
AAGAGGTGGTGGCCGTGGAGGAAGCCGATCTGATAGAGGGGGAGGCAGAAGCAGATAT

ORF - retro_cfam_1106 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.67 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalKMVEADRPGKLFIGGLNTETNEKALEAVFGKYGRIVEVLLMKDRETNKSRGFAFVTFESPADAKDAARDM
KMVEADRPGKLFIGGLNTETNEKALEAVFGKYGRIVEVLLMKDRETNKSRGFAFVTFESPADAKDAARDM
RetrocopyKMVEADRPGKLFIGGLNTETNEKALEAVFGKYGRIVEVLLMKDRETNKSRGFAFVTFESPADAKDAARDM
ParentalNGKSLDGKAIKVEQATKPSFESGRRGPPPPPRSRGPPRGLRGGRGGSGGTRGPPSRGGHMDDGGYSMNFN
NGKSLDGKAIKVEQATKPSFESGRRGPPPPPRSRGPPRGLRGGRGGS.GTRGPPSRGGHMDDGGYSMNFN
RetrocopyNGKSLDGKAIKVEQATKPSFESGRRGPPPPPRSRGPPRGLRGGRGGSRGTRGPPSRGGHMDDGGYSMNFN
ParentalMSSSRGPLPVKRGPPPRSGGPPPKRSAPSGPVRSSSGMGGRAPVSRGRDSYGGPPRREPLPSRRDVYLSP
MSSSRGPLPVKRGPPPR.GGPPPKRSAPSGPVRSSS.MGGRAPVS.GRDSYGGPPRREPLPSRRDVYLSP
RetrocopyMSSSRGPLPVKRGPPPRTGGPPPKRSAPSGPVRSSSRMGGRAPVSCGRDSYGGPPRREPLPSRRDVYLSP
ParentalRDDGYSTKDSYSSRDYPSSRDTRDYAPPPRDYTYRDYGHSSSRDDYPSRGYSDRDGYGRDRDYSDHPSGG
RDDGYSTKDSYSSRDYPSSRDTRDYAPPPRDYTY.DYGHSSSRDDYPSRGYSDRDGYGRDRDYSDHPSGG
RetrocopyRDDGYSTKDSYSSRDYPSSRDTRDYAPPPRDYTYCDYGHSSSRDDYPSRGYSDRDGYGRDRDYSDHPSGG
ParentalSYRDSYESYGNSRSAPPTRGP-PPSYGGSSRYDDYSSS-RDGYGGSRDSYSSSRSDLYSSGRDRVGRQER
SYR.SYESYGNS.SAPPTRGP.P....G.S...D..SS.RDGYGGS.DSYSSSRSDLYSSGRDRVGRQER
RetrocopySYRNSYESYGNSHSAPPTRGP<PAPSYGGSSRYDDYSSSRDGYGGSPDSYSSSRSDLYSSGRDRVGRQER
ParentalGLPPSMERGYPPPRDSYSSSSRGAPRGGGRGGSRSDRGGGRSRY
GLPPSMERGY.PPRDSYSSSSRGAPRGGGRGGSRSDRGGGRSRY
RetrocopyGLPPSMERGYSPPRDSYSSSSRGAPRGGGRGGSRSDRGGGRSRY

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
SRP012049_cerebellum 0 .04 RPM 44 .98 RPM
SRP017611_brain 0 .00 RPM 22 .79 RPM
SRP017611_kidney 0 .00 RPM 29 .06 RPM
SRP017611_liver 0 .00 RPM 15 .88 RPM

ChIP-Seq - click to see more details

Canis familiaris was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cfam_1106 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_1106 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_1106 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 28 parental genes, and 59 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000133081 retrocopy
retro_btau_36,
Canis familiaris ENSCAFG000000133452 retrocopies
retro_cfam_1971, retro_cfam_966,
Canis familiaris ENSCAFG000000154852 retrocopies
retro_cfam_1475, retro_cfam_259,
Canis familiaris ENSCAFG00000018962 4 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,
Homo sapiens ENSG000001472747 retrocopies
retro_hsap_23, retro_hsap_3074, retro_hsap_3587, retro_hsap_4144, retro_hsap_4846, retro_hsap_800, retro_hsap_91,
Gorilla gorilla ENSGGOG000000069441 retrocopy
retro_ggor_657,
Loxodonta africana ENSLAFG000000055683 retrocopies
retro_lafr_1188, retro_lafr_276, retro_lafr_35,
Microcebus murinus ENSMICG000000068562 retrocopies
retro_mmur_1252, retro_mmur_661,
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 ENSPPYG000000207713 retrocopies
retro_pabe_2548, retro_pabe_303, retro_pabe_766,
Rattus norvegicus ENSRNOG000000008661 retrocopy
retro_rnor_268,
Sorex araneus ENSSARG000000003971 retrocopy
retro_sara_169,
Ictidomys tridecemlineatus ENSSTOG000000062112 retrocopies
retro_itri_1205, retro_itri_1346,
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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