RetrogeneDB ID:

retro_ecab_91

Retrocopy
location
Organism:Horse (Equus caballus)
Coordinates:23:21876109..21876973(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSECAG00000003116
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:FAM122B
Ensembl ID:ENSECAG00000018643
Aliases:None
Description:family with sequence similarity 122B [Source:HGNC Symbol;Acc:30490]


Retrocopy-Parental alignment summary:






>retro_ecab_91
ATGGCTCAGGAGAAGATGGAGCTAGACCTGGAGCTGCCTCCGGGGACGGGCGGGAGCCCGGCGGAGGGCGGCGGCAATAG
CGGCGGCGGGGGCCTCAGGAGGTCTAACAGCGCCCCCCTGATCCACGGCCTCAGTGACACTTCGCCGGTGTTCCAGGCCG
AGGCGCCGAGCGCCAGGCGGAACAGCACGACGTTCCCGAACCGCCACGGCCTGCTGCTACCGGCCTCCCCCGTCCGCATG
CACAGCAGCCGCTTGCACCAGATCAAACAGGAGGAGGGCATGGACTTGATCAACCGAGAGACGGTCCACGAGCGCGAGGT
GCAGAACGCAATGCAGATAAGCCACTCCTGGGAGGAAAGTTTCAGCCTGAGTGACAACGATGTGGAGAAATCCGCCTCCC
CGAAGCGCATCGATTTCATTCCGGTGTCACCAGCGCCGTCACCCACCCGGGGAATTGGGAAGCAGTGTTTTTCACCATCC
TTGCAAAGTTTTGTGAGTAGCAATGGATTGCCTCCAAGTCCTATTCCCAGCCCAACGACCCGATTTTCTACCCGGAGAAG
CCAGAGTCCCATTAATTGCATTAGACCAAGTGTTCTTGGACCATTGAAAAGAAAATGTGAAATGGAAACTGAGTATCAGC
CAAAGAGATTTTTCCAGGGCATCACCACCATGCTTTCTTCTGACGTTGCACAGCTGTCAGATCCTGGTGTGTGTGTGTCT
TCAGATACCCTTGATGGAAACAGCAGCAGTGCCGGATCTTCTTGTAACTCACCAGCGAAAGTCAGCACTACCACCGACTC
TCCTGTGTCGCCTGCCCAAGCGGCCTCTCCGTTTATTCCCGTAGATGAACTTTCATCTAAGTGA

ORF - retro_ecab_91 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 65.91 %
Parental protein coverage: 94.93 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalSDGATLRRSNSAPLIHGLSDLSQVFQPYTFRTRRNSTTIMSRHNLLLSSSPNRVPSSRLHQIKREEGMDM
S.G..LRRSNSAPLIHGLSD.S.VFQ......RRNSTT...RH.LLL..SP.R..SSRLHQIK.EEGMD.
RetrocopySGGGGLRRSNSAPLIHGLSDTSPVFQAEAPSARRNSTTFPNRHGLLLPASPVRMHSSRLHQIKQEEGMDL
ParentalMNRETAHEREVQTAMQISQSWDESLSLSDSDFDKPEKLYSPKRIDFTPVSPAPSPTRGFGKQCFSPSLQM
.NRET.HEREVQ.AMQIS.SW.ES.SLSD.D....EK..SPKRIDF.PVSPAPSPTRG.GKQCFSPSLQ.
RetrocopyINRETVHEREVQNAMQISHSWEESFSLSDNDV---EKSASPKRIDFIPVSPAPSPTRGIGKQCFSPSLQS
ParentalFVSNSEAATKVPASETRLWKEGRSQSPVKCIRPSVLGPLKRKGEMETESQPKRLFQGTTNMLSPEAAQLS
FVS..........S.T......RSQSP..CIRPSVLGPLKRK.EMETE.QPKR.FQG.T.MLS...AQLS
RetrocopyFVSSNGLPPSPIPSPTTRFSTRRSQSPINCIRPSVLGPLKRKCEMETEYQPKRFFQGITTMLSSDVAQLS
ParentalDLSSC--SDILDGSSSSSGLSSDSLAKGSTTAESPVACSNSCSPFILMDDLSPK
D...C..SD.LDG.SSS.G.S..S.AK.STT..SPV......SPFI..D.LS.K
RetrocopyDPGVCVSSDTLDGNSSSAGSSCNSPAKVSTTTDSPVSPAQAASPFIPVDELSSK

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
SRP021940_articular_cartilage 7 .32 RPM 2 .77 RPM
SRP021940_cerebellum 11 .01 RPM 5 .19 RPM
SRP021940_embryo 10 .20 RPM 8 .29 RPM
SRP021940_placental_villous 7 .70 RPM 54 .75 RPM
SRP021940_synovial_membrane 8 .15 RPM 2 .99 RPM
SRP021940_testis 6 .78 RPM 1 .28 RPM
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_91 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_91 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ecab_91 has 6 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_35
Mus musculus retro_mmus_22
Rattus norvegicus retro_rnor_651
Oryctolagus cuniculus retro_ocun_205
Bos taurus retro_btau_103
Canis familiaris retro_cfam_181

Parental genes homology:
Parental genes homology involve 14 parental genes, and 14 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000013111 retrocopy
Bos taurus ENSBTAG000000018861 retrocopy
Canis familiaris ENSCAFG000000188821 retrocopy
Callithrix jacchus ENSCJAG000000043131 retrocopy
Cavia porcellus ENSCPOG000000112181 retrocopy
Equus caballus ENSECAG00000018643 1 retrocopy
retro_ecab_91 ,
Felis catus ENSFCAG000000248421 retrocopy
Myotis lucifugus ENSMLUG000000079881 retrocopy
Macaca mulatta ENSMMUG000000169481 retrocopy
Mustela putorius furoENSMPUG000000126901 retrocopy
Mus musculus ENSMUSG000000360221 retrocopy
Rattus norvegicus ENSRNOG000000501461 retrocopy
Sus scrofa ENSSSCG000000126851 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000062611 retrocopy



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