RetrogeneDB ID:

retro_btau_299

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:1:67446807..67447725(-)
Located in intron of:ENSBTAG00000011138
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:BT.39594
Ensembl ID:ENSBTAG00000047031
Aliases:None
Description:WD repeat-containing protein 5 [Source:RefSeq peptide;Acc:NP_001098945]


Retrocopy-Parental alignment summary:






>retro_btau_299
AAGCCAGTGTCTGAAAAACCAAACTACGCTCTGAAATTCACTCTGGAGGGACATACGGAAGCAGTATCATCAGTTAAGTT
TAGTCCTAATGGAGAATGGCTAGCAAGTTCTTCTGCTGATAAAGTAATTATAATTTGGGGAGCCTATGATGGAAAATATG
AGAAAACACTTAAAGGACACAATCTTGAAATATCAGATGTTGCCTGGTCATCAGATTCCAGTCGTCTTGTTTCTGCCTCA
GATGATAAAACTCTAAAAATTTGGGATGTGAGGTCTGGAAAATGTTTGAAAACACTTAAAGGGCACAGTAATTACGTTTT
TTGCTGTAATTTCAATCCACCGTCCAACCTCATCATTTCAGGATCTTTTGATGAAAGCGTGAAAATATGGGAGGTGAAAA
CAGGCAAGTGCCTTAAGACTTTGTCTGCTCATTCTGACCCAGTTTCTGCTGTTCATTTTAATTGTAGTGGGTCATTGATA
GTATCAGGTAGCTATGATGGTGTCTGTCGAATCTGGGATGCTGCATCAGGTCAGTGTTTAAAAGCACTTGTTGATGATGA
TAACCCTCCTGTCTCTTTTGTAAAATTTTCTCCAAACGGTAAATATATTCTCATTGCAACTTTGGACAATACTCTTAAAC
TGTGGGATTACAGCAGAGGCAGATGCCTGAAAACATATACTGGTCATAAGAATGAGAAGTACTGTGTATTTGCCAGTTTT
TCAGTTACTGGTGGAAAATGGATTGTCTCTGGTTCAGAGGATAACCTGGTATACATTTGGAATCTTCAAACTAAAGAGAT
TGTACAGAAATTGCAAGGTCATACAGATGTGGTAATCTCAGCAGCTTGTCATCCTACAGAAAACATCATTGCGTCAGCAG
CATTAGGAAATGACAAAACAGTTAAACTGTGGACAAGT

ORF - retro_btau_299 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.91 %
Parental protein coverage: 99.35 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalQPTPVKPNYALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWGAYDGKFEKTISGHKLGISDVAWS
.P...KPNYALKFTL.GHT.AVSSVKFSPNGEWLASSSADK.I.IWGAYDGK.EKT..GH.L.ISDVAWS
RetrocopyKPVSEKPNYALKFTLEGHTEAVSSVKFSPNGEWLASSSADKVIIIWGAYDGKYEKTLKGHNLEISDVAWS
ParentalSDSNLLVSASDDKTLKIWDVSSGKCLKTLKGHSNYVFCCNFNPQSNLIVSGSFDESVRIWDVKTGKCLKT
SDS..LVSASDDKTLKIWDV.SGKCLKTLKGHSNYVFCCNFNP.SNLI.SGSFDESV.IW.VKTGKCLKT
RetrocopySDSSRLVSASDDKTLKIWDVRSGKCLKTLKGHSNYVFCCNFNPPSNLIISGSFDESVKIWEVKTGKCLKT
ParentalLPAHSDPVSAVHFNRDGSLIVSSSYDGLCRIWDTASGQCLKTLIDDDNPPVSFVKFSPNGKYILAATLDN
L.AHSDPVSAVHFN..GSLIVS.SYDG.CRIWD.ASGQCLK.L.DDDNPPVSFVKFSPNGKYIL.ATLDN
RetrocopyLSAHSDPVSAVHFNCSGSLIVSGSYDGVCRIWDAASGQCLKALVDDDNPPVSFVKFSPNGKYILIATLDN
ParentalTLKLWDYSKGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNLQTKEIVQKLQGHTDVVIS
TLKLWDYS.G.CLKTYTGHKNEKYC.FA.FSVTGGKWIVSGSEDNLVYIWNLQTKEIVQKLQGHTDVVIS
RetrocopyTLKLWDYSRGRCLKTYTGHKNEKYCVFASFSVTGGKWIVSGSEDNLVYIWNLQTKEIVQKLQGHTDVVIS
ParentalTACHPTENIIASAALENDKTIKLWKS
.ACHPTENIIASAAL.NDKT.KLW.S
RetrocopyAACHPTENIIASAALGNDKTVKLWTS

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 5 .26 RPM 3 .03 RPM
ERP005899_muscle 2 .01 RPM 16 .58 RPM
SRP017611_brain 4 .98 RPM 12 .70 RPM
SRP017611_kidney 5 .04 RPM 16 .24 RPM
SRP017611_liver 2 .79 RPM 13 .67 RPM
SRP030211_testis 4 .74 RPM 61 .59 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_299 retrocopy.

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_299 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_299 has 10 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_11
Pan troglodytes retro_ptro_18
Gorilla gorilla retro_ggor_171
Macaca mulatta retro_mmul_190
Callithrix jacchus retro_cjac_1
Mus musculus retro_mmus_132
Rattus norvegicus retro_rnor_258
Sus scrofa retro_sscr_1
Canis familiaris retro_cfam_128
Equus caballus retro_ecab_82
Parental genes homology:
Parental genes homology involve 27 parental genes, and 29 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000111791 retrocopy
retro_amel_29,
Bos taurus ENSBTAG000000045711 retrocopy
retro_btau_1341,
Bos taurus ENSBTAG00000047031 1 retrocopy
retro_btau_299 ,
Canis familiaris ENSCAFG000000198301 retrocopy
retro_cfam_128,
Callithrix jacchus ENSCJAG000000101231 retrocopy
retro_cjac_1,
Cavia porcellus ENSCPOG000000147901 retrocopy
retro_cpor_12,
Dipodomys ordii ENSDORG000000150101 retrocopy
retro_dord_7,
Equus caballus ENSECAG000000173891 retrocopy
retro_ecab_82,
Echinops telfairi ENSETEG000000157311 retrocopy
retro_etel_15,
Felis catus ENSFCAG000000057121 retrocopy
retro_fcat_119,
Homo sapiens ENSG000001963631 retrocopy
retro_hsap_11,
Gorilla gorilla ENSGGOG000000049972 retrocopies
retro_ggor_171, retro_ggor_2023,
Loxodonta africana ENSLAFG000000111921 retrocopy
retro_lafr_55,
Microcebus murinus ENSMICG000000080851 retrocopy
retro_mmur_34,
Myotis lucifugus ENSMLUG000000022361 retrocopy
retro_mluc_11,
Macaca mulatta ENSMMUG000000141591 retrocopy
retro_mmul_190,
Mustela putorius furoENSMPUG000000121841 retrocopy
retro_mputfur_2,
Mus musculus ENSMUSG000000269171 retrocopy
retro_mmus_132,
Nomascus leucogenys ENSNLEG000000134721 retrocopy
retro_nleu_63,
Otolemur garnettii ENSOGAG000000089601 retrocopy
retro_ogar_86,
Procavia capensis ENSPCAG000000134761 retrocopy
retro_pcap_43,
Pan troglodytes ENSPTRG000000236532 retrocopies
retro_ptro_18, retro_ptro_1975,
Pteropus vampyrus ENSPVAG000000016661 retrocopy
retro_pvam_112,
Rattus norvegicus ENSRNOG000000082121 retrocopy
retro_rnor_258,
Sus scrofa ENSSSCG000000249121 retrocopy
retro_sscr_1,
Ictidomys tridecemlineatus ENSSTOG000000158991 retrocopy
retro_itri_117,
Drosophila melanogaster FBgn00400661 retrocopy
retro_dmel_69,




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