RetrogeneDB ID:

retro_btau_66

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:3:88032647..88033607(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSBTAG00000004381
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:EPCAM
Ensembl ID:ENSBTAG00000006474
Aliases:EPCAM, TACSTD1
Description:epithelial cell adhesion molecule precursor [Source:RefSeq peptide;Acc:NP_001030367]


Retrocopy-Parental alignment summary:






>retro_btau_66
ATGGCCCGGGGCCCGGGCCTCGCGCTGCTGTCGCCGTGGCTCCTGATGCTGGCGGCGGTGATCGGCCACGCGGCCGCGCA
GAACCAGTGCGTGTGTCCCACCAACAAGATGACCGTGTGCGACGAGCGCGACCCGAGCGGCCGCTGCCAGTGCCGCGTGC
TCGGCTCGAACCAGGCGGTCAACTGTTCCACGCTCACGTCCAAGTGCCTGCTGCTCAAGGCGCGCATGAGCGCCTCCCAC
AGCGGCCGCGCGCTGGTGCGGCCGAGCGAGCACGCGATCGTGGACAACGACGGCCTGTACGACCCGGACTGCGACCAGCA
GGGGCGCTTCAAGGCGCGCCAGTGCAACCAGACGTCGGTGTGCTGGTGCGTGAACTCGGTGGGCGTGCGCCGCACCGACA
AGGGCGACCTGAGCCTGAAGTGCGACGAGGTGGTGCGCACCTACCACATCCTTATTGACCTGCGCCACCGCCCGGACGCC
CCAGCCTTCAACCACTCGGACCTGGACGCTGAGCTGCGGCAGCTCTTCCAGCAGCGCTATCTGCTGCAGCCCAAGTTCGT
GAGTGCTGTGCACTACGAGCACCCTACCATCCAGATCGAGCTGCGCCAGAACTCGTCGCAGAAGGTCGCCGGCGAGGTGG
ACATCGGCGACGCCGCGTACTACTTCGAGAGGGACGTCAAGGGCGAGTCGCTGTTCCTAGGCCCCCGCGACCTCAACTTG
CGCGTGGGCGGACAGCCCCTGGTCCTGGAGCAGATGCTCATCTACTACCTGGACGAGAAGCCCCCCCAGTTCTCCATGAA
GCGCCTCACCAGCGGCCTCATCGCCGTCGTCGTGGTGGTCGTGGTGGCGGTGGTCGCCGGCGCGGCCGTCCTGGTGATCA
CCAATCGCAGAAAGTCGGGAAAGTACAAGAAGGTGGAGATCAAGGAACTGGGGGAGATAAGACAGAAACCGAGCTTGTAG

ORF - retro_btau_66 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 50.16 %
Parental protein coverage: 95.86 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalLLVAAATAAVAAAQEGCVCENYKLTTNCSVNALGQCQCTSVGTQHSVICTKLATKCLVMKAEISHSKSGR
LL..AA....AAAQ..CVC...K.T........G.CQC...G....V.C..L..KCL..KA..S.S.SGR
RetrocopyLLMLAAVIGHAAAQNQCVCPTNKMTVCDERDPSGRCQCRVLGSNQAVNCSTLTSKCLLLKARMSASHSGR
ParentalR--RKPEGAIQNNDGLYDPECDDKGLFKAKQCNGTSTCWCVNTAGVRRTDK-DSEISCSEPVRTYWIIIE
...R..E.AI..NDGLYDP.CD..G.FKA.QCN.TS.CWCVN..GVRRTDK.D....C.E.VRTY.I.I.
RetrocopyALVRPSEHAIVDNDGLYDPDCDQQGRFKARQCNQTSVCWCVNSVGVRRTDKGDLSLKCDEVVRTYHILID
ParentalLKHKTREKPYDLQSLQSALKDVITNRYQLDPKYITNILYENDVITIDLVQNSSQKTQNDVDIADVAYYFE
L.H...........L...L......RY.L.PK......YE...I.I.L.QNSSQK....VDI.D.AYYFE
RetrocopyLRHRPDAPAFNHSDLDAELRQLFQQRYLLQPKFVSAVHYEHPTIQIELRQNSSQKVAGEVDIGDAAYYFE
ParentalKDVKDESLFHSKR-MDLRVNGELLDLDPGRTSIYYVDEKPPEFSMQGLQAGIIAVIVVVVVAIIAGIIVL
.DVK.ESLF...R...LRV.G..L.L......IYY.DEKPP.FSM..L..G.IAV.VVVVVA..AG..VL
RetrocopyRDVKGESLFLGPRDLNLRVGGQPLVLE--QMLIYYLDEKPPQFSMKRLTSGLIAVVVVVVVAVVAGAAVL
ParentalVVSRKKSMTKYEKAEIKEMGEMHRE
V........KY.K.EIKE.GE....
RetrocopyVITNRRKSGKYKKVEIKELGEIRQK

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
ERP005899_liver 0 .00 RPM 25 .38 RPM
ERP005899_muscle 0 .26 RPM 689 .00 RPM
SRP017611_brain 0 .09 RPM 4 .43 RPM
SRP017611_kidney 2 .02 RPM 159 .44 RPM
SRP017611_liver 0 .00 RPM 7 .40 RPM
SRP030211_testis 0 .26 RPM 97 .42 RPM

ChIP-Seq - click to see more details

Bos taurus was not studied using ChIP-Seq data.

EST - click to see more details

3 EST(s) were mapped to retro_btau_66 retrocopy
EST ID Start End Identity Match Mis-match Score
CN434363 88032638 88032888 100 250 0 250
DN638769 88032783 88033109 99.7 325 1 324
DN639026 88032888 88033109 99.6 220 1 219

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_66 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_66 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_92
Macaca mulatta retro_mmul_34
Callithrix jacchus retro_cjac_3006
Sus scrofa retro_sscr_69
Parental genes homology:
Parental genes homology involve 17 parental genes, and 19 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG00000006474 1 retrocopy
retro_btau_66 ,
Choloepus hoffmanni ENSCHOG000000138341 retrocopy
retro_chof_258,
Callithrix jacchus ENSCJAG000000006241 retrocopy
retro_cjac_3006,
Dasypus novemcinctus ENSDNOG000000117991 retrocopy
retro_dnov_345,
Erinaceus europaeus ENSEEUG000000094621 retrocopy
retro_eeur_151,
Macropus eugenii ENSMEUG000000150742 retrocopies
retro_meug_1984, retro_meug_474,
Microcebus murinus ENSMICG000000001511 retrocopy
retro_mmur_739,
Macaca mulatta ENSMMUG000000123901 retrocopy
retro_mmul_34,
Monodelphis domestica ENSMODG000000010771 retrocopy
retro_mdom_104,
Mus musculus ENSMUSG000000453941 retrocopy
retro_mmus_185,
Ochotona princeps ENSOPRG000000043011 retrocopy
retro_opri_1225,
Pelodiscus sinensis ENSPSIG000000156801 retrocopy
retro_psin_22,
Pan troglodytes ENSPTRG000000119021 retrocopy
retro_ptro_92,
Rattus norvegicus ENSRNOG000000156671 retrocopy
retro_rnor_252,
Sus scrofa ENSSSCG000000084291 retrocopy
retro_sscr_69,
Ictidomys tridecemlineatus ENSSTOG000000086311 retrocopy
retro_itri_106,
Tursiops truncatus ENSTTRG000000042352 retrocopies
retro_ttru_21, retro_ttru_394,


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