RetrogeneDB ID:

retro_btau_1678

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:9:73936387..73937167(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SPIN1
Ensembl ID:ENSBTAG00000003044
Aliases:None
Description:spindlin-1 [Source:RefSeq peptide;Acc:NP_001179750]


Retrocopy-Parental alignment summary:






>retro_btau_1678
ATGAAGACTTCATTAAGGAAGATAGCTGACCAGTGGTCCAGAGCTGATGCAGCTATCACTGGTGTATCTGCTAGCATAAT
GAAGAAAAGGACGACTCACGCAAAACATCGGAGCAGTGTGGGACCCAGCTCACTTGTTTCTCAGCCGGAACAGAGCATCA
TAGGCTGCAGGATTCGCCATGGGTGGAAAGAAGGTAACAGCCCTGTCACCCAGTGGAAAGGAACCATTCTGGACCAGGTG
CCTGTAAATCCTTCTTTGTGTCTTATAAAATACGATGGATTTGACTGTGTCTATGGACTAGAACTTAATAAAGATGAAAG
AATTTCTGCACTTGAAGTCCTCCCTGATAGAGTTGCAACCTCTCAAACCTGTGATGCACACCTAGCAGACATGATGAGTA
GCAAAGCAGTGAAGCACCTGTTTGAAACGGAGGATGGCTCTAAAGATGAGTGGAGGGGAATGACCCTGGCACGCGTCCCT
GTAATGAACACGGGTTTTTACATCACTTATGAAGAAGATCCTGTCTTATATATGTACCAGCTCTTAGATGATTATAAAGA
AGGTGACCTTCGCATTATGCCTTATTCTATTGATTCACTTCCAGTATAAAGGGAACGAGGAGAAGTGGTAGACTTCTTGG
TGGGCAAACGAGTGGACTACGCCAAACAAGATGGCTCTGAAAGGAATGGCATGATCATCCATCAAGTAAAGGTCAAACCG
TCCATCTGCTTCATCAAATTTGATGATGATTTCTATATTTATGTCTACGATTTGGTGAAA

ORF - retro_btau_1678 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.85 %
Parental protein coverage: 99.24 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMKTPFGKTPGQRSRADAGHAGVSASMMKKRTSHKKHRSSVGPSKPVSQPRRNIVGCRIQHGWKEGNGPVT
MKT...K...Q.SRADA...GVSAS.MKKRT.H.KHRSSVGPS..VSQP...I.GCRI.HGWKEGN.PVT
RetrocopyMKTSLRKIADQWSRADAAITGVSASIMKKRTTHAKHRSSVGPSSLVSQPEQSIIGCRIRHGWKEGNSPVT
ParentalQWKGTVLDQVPVNPSLYLIKYDGFDCVYGLELNKDERVSALEVLPDRVATSRISDAHLADTMIGKAVEHM
QWKGT.LDQVPVNPSL.LIKYDGFDCVYGLELNKDER.SALEVLPDRVATS...DAHLAD.M..KAV.H.
RetrocopyQWKGTILDQVPVNPSLCLIKYDGFDCVYGLELNKDERISALEVLPDRVATSQTCDAHLADMMSSKAVKHL
ParentalFETEDGSKDEWRGMVLARAPIMNTWFYITYEKDPVLYMYQLLDDYKEGDLRIMPDSNDSPPAEREPGEVV
FETEDGSKDEWRGM.LAR.P.MNT.FYITYE.DPVLYMYQLLDDYKEGDLRIMP.S.DS.P..RE.GEVV
RetrocopyFETEDGSKDEWRGMTLARVPVMNTGFYITYEEDPVLYMYQLLDDYKEGDLRIMPYSIDSLPV*RERGEVV
ParentalDSLVGKQVEYAKEDGSKRTGMVIHQVEAKPSVYFIKFDDDFHIYVYDLVK
D.LVGK.V.YAK.DGS.R.GM.IHQV..KPS..FIKFDDDF.IYVYDLVK
RetrocopyDFLVGKRVDYAKQDGSERNGMIIHQVKVKPSICFIKFDDDFYIYVYDLVK

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 .07 RPM 60 .13 RPM
ERP005899_muscle 0 .00 RPM 55 .38 RPM
SRP017611_brain 0 .00 RPM 105 .20 RPM
SRP017611_kidney 0 .18 RPM 78 .36 RPM
SRP017611_liver 0 .15 RPM 21 .82 RPM
SRP030211_testis 0 .10 RPM 44 .95 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_1678 retrocopy.

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_1678 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_1678 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 23 parental genes, and 49 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000033014 retrocopies
retro_amel_1831, retro_amel_1879, retro_amel_38, retro_amel_41,
Bos taurus ENSBTAG00000003044 4 retrocopies
retro_btau_1678 , retro_btau_1841, retro_btau_187, retro_btau_553,
Canis familiaris ENSCAFG000000022083 retrocopies
retro_cfam_153, retro_cfam_2095, retro_cfam_59,
Choloepus hoffmanni ENSCHOG000000069832 retrocopies
retro_chof_1343, retro_chof_1852,
Callithrix jacchus ENSCJAG000000174521 retrocopy
retro_cjac_227,
Cavia porcellus ENSCPOG000000007431 retrocopy
retro_cpor_123,
Echinops telfairi ENSETEG000000137191 retrocopy
retro_etel_28,
Felis catus ENSFCAG000000071972 retrocopies
retro_fcat_32, retro_fcat_70,
Homo sapiens ENSG000001067231 retrocopy
retro_hsap_64,
Loxodonta africana ENSLAFG000000274972 retrocopies
retro_lafr_18, retro_lafr_58,
Microcebus murinus ENSMICG000000145101 retrocopy
retro_mmur_8,
Myotis lucifugus ENSMLUG000000085162 retrocopies
retro_mluc_132, retro_mluc_1626,
Mustela putorius furoENSMPUG000000085851 retrocopy
retro_mputfur_139,
Mus musculus ENSMUSG000000213953 retrocopies
retro_mmus_112, retro_mmus_16, retro_mmus_3351,
Oryctolagus cuniculus ENSOCUG000000118801 retrocopy
retro_ocun_63,
Otolemur garnettii ENSOGAG000000021662 retrocopies
retro_ogar_2327, retro_ogar_9,
Procavia capensis ENSPCAG000000158001 retrocopy
retro_pcap_14,
Pongo abelii ENSPPYG000000193551 retrocopy
retro_pabe_33,
Pan troglodytes ENSPTRG000000210882 retrocopies
retro_ptro_116, retro_ptro_95,
Pteropus vampyrus ENSPVAG000000133913 retrocopies
retro_pvam_2, retro_pvam_22, retro_pvam_858,
Rattus norvegicus ENSRNOG000000111194 retrocopies
retro_rnor_1483, retro_rnor_1531, retro_rnor_281, retro_rnor_2818,
Ictidomys tridecemlineatus ENSSTOG000000291071 retrocopy
retro_itri_136,
Tursiops truncatus ENSTTRG000000056026 retrocopies
retro_ttru_1061, retro_ttru_13, retro_ttru_1452, retro_ttru_1506, retro_ttru_1669, retro_ttru_1698,


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