RetrogeneDB ID:

retro_btau_232

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:X:122325330..122327649(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSBTAG00000008511
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:SMEK2
Ensembl ID:ENSBTAG00000000545
Aliases:None
Description:serine/threonine-protein phosphatase 4 regulatory subunit 3B [Source:RefSeq peptide;Acc:NP_001178079]


Retrocopy-Parental alignment summary:






>retro_btau_232
ATGGCGGACGAGCAGAGCATAGTGAAAGTCTACTTCCTGAATGATGACCAACAATGGGAAATTCTAGGCAAGGGACATGT
CTCTGCTGTTTATGTGGAACGCCTTCAGGGCATCTGTCTGCTAGTTCGATCTGAACCTAACGGCATACAGATCTTAGAGT
CAAAGATAGATCCAGACACGCCCTATCAGAGACGACAAGGGACATTAATTGTTTGGTCTGAAGCTGAGAACCACGGTATG
GCGATGAGTTTCCCGGACGCAGCAAGTTGTTACGAGATATGGAAAGACATCTGCCAGGTTCAAGGTAAAGACCCATCTAC
TGATATCACACATGACCCCTTAGTTGAATCCGAAGACGAGACATTGGATGACGTAACAGATGACGTGCTTGAGCTGCCTA
ACTGCGAACTCGGTAAGCTTGACCAGATTGCTCACTTAGTTACCTCAGTTCTCACGTCACCTCTGCATAAGGAAAAGTTG
GCTCTGTTAGTGGCAAATGAGGACTTTATTAAACAATTACTGCAGTTGTTCCACACGTGTGAGGACCTAGAGGATACTGA
AGGCTTACAGAATCTGCATGACATTGTTAAAGGGATGTTATTTCTCAACCAGGCATCTCTGCTTGAGATCCTCGTTTCTG
ATAAGTATATCATGGATGTGGTGGGATGCCTTGAATATGACCCTGCCTTGGCTCAGCCAAAAAGGCATAGAGAATTCTTA
ACCCAAAAAGTGAAATTCAAGGAAGTTATACCAATAATAGACCAGGCACTTCTGCAAAAAATACATCAGACATACAGAGT
ACAGTACATTCAGGACATCCTTTTTCCTATCCCATCTATATTTGAAGAGAATTTTCTTTCTACTCTTACAAATTTTATTT
TATTAAACAAGAGTGATATAGTCAATATGCTGCAGGAAGATGATGAGTTTTTGTCTACCGTTTTTGCACAGTTAAGGGAT
AAGACCACAGATGATGATACACGACGTGAGCTGTTATTTTTTTTCAAGGAATTCTGTGCATTTTCTCAGACATTACACTC
TGCAAACAAGAATGCACTACTCAAAACACTGACACAACTGGGAATTCTTCCTGCTCTTAAAATTGCAATGGGTATAAATG
ACTTGCAAATAAAGTCAGCTGCTACTGATATATTTACTTATCTAGTAGAGTATAGTCCATCCAGGGTTCGAGAATTTATA
ATAGAAGACCAGGAAAGTGAAGGCAGCATCCTTTTCATTAATTTAGTAATTGAACAAATATTCTGTGATACTGACCCTGA
GCTAGGAAGTGCTGTTCATTTAATGGGAGTTCTTCGTGCCCTGCTTGATCCAAACAACATGGTGACAGCATCTAGTCACT
GTGAAAGAAGTGAATTTCTACGTTTCTTCTGTAAGCATTCTATGAATAACTTGATTGCACCACTTTTGTCAACTACTTCA
GCATATATACGTGACAAGGATAATATAGTTGGATCTGACGAAAACAACAAAAACTGTCTCAATAATTACCGCACAGCACA
GCTGCTTGCCTTAATTTTAGATCTGCTTTCATTTTGTGTGCAACATCATACATATTACATGAAAAAATATATTTTGAACA
AAGACTTGCTAAGAAAAGTCTTGATCTTGATAAATTCCAAGCACACTTTTCTAATCTTGTGTGCTATTCGTTTTATGAGA
AGGATGATTGGCCTTAGAGATGAACTTTTAAATCGTTATATCATCAAGGGAAATTTTTTTGAGCCAGTTGTAAATGCTCT
TCTAGAGAATGGAACTCGGTACAATATGTTGAATTCAGCTATTGTTGAGCTGTTTGACTACATAAGAATGGAAAATATCA
AATCTCTTGTTGCCCATATAGTTGAAAAGTTTTATGCAACGCTTAAGTCAATTGAATATGTTCAGACATTCAAAGGATTG
AAGGTGAAATATGAGCAAGAGAAAGAGCTGAAAAATCAATTAACGAAGAATTTATGTTCTGTCCTGTATAGTCAAGTATT
TTGCAGAGGTTCCAGTGTCTTGGAGGAGGAGGAGGAGGAGGAAACGAGTATTAATGAAAATATAAAGGAAGAAGCAGTTA
AGTCACCACCGGAAAGTGATATTGAGATTCAGAAAACAAAAGAAAATGAAGACAAGGTAGATCTTCCCTCCAAAACATCT
TGTGGTGACTTTAAATTTACTTCATGTCATTCTGCTGATGCTGCTGATGAAACAAGTAACCCAAACCGCACAAGCGTGAT
TTGCTTAGTGGATTATTCAGATGATGAAGAAGAGGAAGATGAAACACCTCCCAGCAAAAGACCACATCTTAGCCCATAA

ORF - retro_btau_232 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 62.75 %
Parental protein coverage: 65.45 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMSDTRRRVKVYTLNEVRQWDDRGTGHVSSIYVEELKGMSLLVRAESDGSLLLESKINPNTAYQKQQDTLI
M.D....VKVY.LN...QW...G.GHVS..YVE.L.G..LLVR.E..G...LESKI.P.T.YQ..Q.TLI
RetrocopyMADEQSIVKVYFLNDDQQWEILGKGHVSAVYVERLQGICLLVRSEPNGIQILESKIDPDTPYQRRQGTLI
ParentalVWSEAENYDLALSFQEKAGCDEIWEKICQVQGKDPSVEVTQDLIDESEEERFEEMPETSHLIDLPTCELN
VWSEAEN...A.SF...A.C.EIW..ICQVQGKDPS...T.D...ESE.E.......T.....LP.CEL.
RetrocopyVWSEAENHGMAMSFPDAASCYEIWKDICQVQGKDPSTDITHDPLVESEDETLDDV--TDDVLELPNCELG
ParentalKLEEIADLVTSVLSSPIRREKLALALENEGYIKKLLQLFQACENLENTEGLHHLYEIIRGILFLNKATLF
KL..IA.LVTSVL.SP...EKLAL...NE..IK.LLQLF..CE.LE.TEGL..L..I..G.LFLN.A.L.
RetrocopyKLDQIAHLVTSVLTSPLHKEKLALLVANEDFIKQLLQLFHTCEDLEDTEGLQNLHDIVKGMLFLNQASLL
ParentalEVMFSDECIMDVVGCLEYDPALAQPKRHREFLTKTAKFKEVIPITDSELRQKIHQTYRVQYIQDIILPTP
E...SD..IMDVVGCLEYDPALAQPKRHREFLT...KFKEVIPI.D..L.QKIHQTYRVQYIQDI..P.P
RetrocopyEILVSDKYIMDVVGCLEYDPALAQPKRHREFLTQKVKFKEVIPIIDQALLQKIHQTYRVQYIQDILFPIP
ParentalSVFEENFLSTLTSFIFFNKVEIVSMLQEDEKFLSEVFAQLTDEATDDDKRRELVNFFKEFCAFSQTLQPQ
S.FEENFLSTLT.FI..NK..IV.MLQED..FLS.VFAQL.D..TDDD.RREL..FFKEFCAFSQTL...
RetrocopySIFEENFLSTLTNFILLNKSDIVNMLQEDDEFLSTVFAQLRDKTTDDDTRRELLFFFKEFCAFSQTLHSA
ParentalNRDAFFKTLAKLGILPALEIVMGMDDLQVRSAATDIFSYLVEFSPSMVREFVMQEAQQSDDDILLINVVI
N..A..KTL..LGILPAL.I.MG..DLQ..SAATDIF.YLVE.SPS.VREF.....Q.S...IL.IN.VI
RetrocopyNKNALLKTLTQLGILPALKIAMGINDLQIKSAATDIFTYLVEYSPSRVREFIIED-QESEGSILFINLVI
ParentalEQMICDTDPELGGAVQLMGLLRTLIDPENMLATTNKTEKSEFLNFFYNHCMHVLTAPLLTNTSEDRREKD
EQ..CDTDPELG.AV.LMG.LR.L.DP.NM.......E.SEFL.FF..H.M..L.APLL..TS...R.KD
RetrocopyEQIFCDTDPELGSAVHLMGVLRALLDPNNMVTASSHCERSEFLRFFCKHSMNNLIAPLLSTTSAYIRDKD
ParentalNVVGSNKSSTIC
N.VGS......C
RetrocopyNIVGSDENNKNC

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 31 .58 RPM
ERP005899_muscle 0 .00 RPM 109 .75 RPM
SRP017611_brain 0 .00 RPM 51 .39 RPM
SRP017611_kidney 0 .00 RPM 86 .95 RPM
SRP017611_liver 0 .00 RPM 63 .88 RPM
SRP030211_testis 25 .32 RPM 84 .48 RPM

ChIP-Seq - click to see more details

Bos taurus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_btau_232 retrocopy.

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_232 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_232 has 7 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_4799
Pan troglodytes retro_ptro_3191
Macaca mulatta retro_mmul_238
Oryctolagus cuniculus retro_ocun_9
Sus scrofa retro_sscr_1187
Canis familiaris retro_cfam_226
Equus caballus retro_ecab_23
Parental genes homology:
Parental genes homology involve 18 parental genes, and 18 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000038431 retrocopy
retro_amel_48,
Bos taurus ENSBTAG00000000545 1 retrocopy
retro_btau_232 ,
Canis familiaris ENSCAFG000000028601 retrocopy
retro_cfam_226,
Equus caballus ENSECAG000000138191 retrocopy
retro_ecab_23,
Echinops telfairi ENSETEG000000024201 retrocopy
retro_etel_1699,
Felis catus ENSFCAG000000264571 retrocopy
retro_fcat_13,
Homo sapiens ENSG000001380411 retrocopy
retro_hsap_4799,
Loxodonta africana ENSLAFG000000178251 retrocopy
retro_lafr_791,
Myotis lucifugus ENSMLUG000000038751 retrocopy
retro_mluc_994,
Macaca mulatta ENSMMUG000000070011 retrocopy
retro_mmul_238,
Mustela putorius furoENSMPUG000000024351 retrocopy
retro_mputfur_92,
Nomascus leucogenys ENSNLEG000000093381 retrocopy
retro_nleu_1112,
Oryctolagus cuniculus ENSOCUG000000068801 retrocopy
retro_ocun_9,
Otolemur garnettii ENSOGAG000000098371 retrocopy
retro_ogar_140,
Pan troglodytes ENSPTRG000000119331 retrocopy
retro_ptro_3191,
Sus scrofa ENSSSCG000000083981 retrocopy
retro_sscr_1187,
Ictidomys tridecemlineatus ENSSTOG000000062761 retrocopy
retro_itri_63,
Tursiops truncatus ENSTTRG000000000271 retrocopy
retro_ttru_1397,


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