RetrogeneDB ID:

retro_btau_1461

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:6:83391261..83391990(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:GNB2L1
Ensembl ID:ENSBTAG00000019648
Aliases:GNB2L1, RACK1
Description:Guanine nucleotide-binding protein subunit beta-2-like 1 [Source:UniProtKB/Swiss-Prot;Acc:P63243]


Retrocopy-Parental alignment summary:






>retro_btau_1461
CTGGTAATCTCCTCAGATGGCCAATTTGCCGTCTCAGGCTCTGGGGATGGAACTCTTTACCTCTGGGATCTCACAATGGG
CACCAAGACGCACCACACCAAAGATGTGCTGAGTGTGGCCTTTTCTGACAACTGGCAAATTGCCTCTGGCTCCTGAGACA
AAACCATCAAACTATGGAATATTTCAGGTGTATGTAAATATACTTTCCAGAATGAGAGTCAATCAGAGTGAGTGTCTTGT
GTCAGTTTCTTGCCCAACAACAGCAATCCCATCATTCTTTCCTGTGGCTGGGACAAACTGGTCAAGGTATGGAACTTTGC
AAACTGTAAGCTGAAGCCCAGCTACATCGGCCACACAGGCTCCCTGAACATTGTGACCATCTCTCCAGATGGATCTTTCT
GCGCTTCTGGAGGCAAGGATGGATAGGCCATGTTGTGAGATCTGAATGAAGGCAAGCACCTTTATACACTAGATGGTGAG
AACATCATCAGCACCCTGTGCTTCAGTACCAACCACTATTGGCTCTGTGCTGCCATGGGCCCTAGCATTAAAATCTGGGA
CTTGGAGGCAAAATCACTATAGATGAACTGAAGCAAGACATTATTGGTACCAGCAGCAAGACAGAGCCTTCCCAGTGTAT
CTCTCTGGCTTGGGTCTGCTGATGGCCAGATACTGTTTGTTGGCTACATGTACAGCCAAGTGTGCATGTGGCAGGTAACC
ATTGGCACC

ORF - retro_btau_1461 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.0 %
Parental protein coverage: 78.23 %
Number of stop codons detected: 4
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalVVISSDGQFALSGSWDGTLRLWDLTTGTTTRRFVGHTKDVLSVAFSSDNRQIVSGSRDKTIKLWNTLGVC
.VISSDGQFA.SGS.DGTL.LWDLT.GT.T.....HTKDVLSVAFS.DN.QI.SGS.DKTIKLWN..GVC
RetrocopyLVISSDGQFAVSGSGDGTLYLWDLTMGTKTH----HTKDVLSVAFS-DNWQIASGS*DKTIKLWNISGVC
ParentalKYTVQDESHSEWVSCVRFSPNSSNPIIVSCGWDKLVKVWNLANCKLKTNHIGHTGYLNTVTVSPDGSLCA
KYT.Q.ES.SE.VSCV.F.PN.SNPII.SCGWDKLVKVWN.ANCKLK...IGHTG.LN.VT.SPDGS.CA
RetrocopyKYTFQNESQSE*VSCVSFLPNNSNPIILSCGWDKLVKVWNFANCKLKPSYIGHTGSLNIVTISPDGSFCA
ParentalSGGKDGQAMLWDLNEGKHLYTLDGGDIINALCFSPNRYWLCAATGPSIKIWDLE-GKIIVDELKQEVIST
SGGKDG.AML.DLNEGKHLYTLDG..II..LCFS.N.YWLCAA.GPSIKIWDLE.GKI..DELKQ..I.T
RetrocopySGGKDG*AML*DLNEGKHLYTLDGENIISTLCFSTNHYWLCAAMGPSIKIWDLE<GKITIDELKQDIIGT
ParentalSSKAEPPQCTSLAW-SADGQTLFAGYTDNLVRVWQVTIGT
SSK.EP.QC.SLAW.SADGQ.LF.GY....V..WQVTIGT
RetrocopySSKTEPSQCISLAW>SADGQILFVGYMYSQVCMWQVTIGT

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 264 .38 RPM
ERP005899_muscle 0 .00 RPM 2370 .76 RPM
SRP017611_brain 0 .00 RPM 144 .30 RPM
SRP017611_kidney 0 .00 RPM 485 .14 RPM
SRP017611_liver 0 .00 RPM 356 .17 RPM
SRP030211_testis 0 .00 RPM 232 .30 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_1461 retrocopy.

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_1461 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_1461 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 25 parental genes, and 34 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000120081 retrocopy
retro_acar_185,
Ailuropoda melanoleuca ENSAMEG000000000041 retrocopy
retro_amel_1627,
Bos taurus ENSBTAG00000019648 1 retrocopy
retro_btau_1461 ,
Canis familiaris ENSCAFG000000248181 retrocopy
retro_cfam_1824,
Callithrix jacchus ENSCJAG000000187521 retrocopy
retro_cjac_2876,
Cavia porcellus ENSCPOG000000087241 retrocopy
retro_cpor_687,
Dipodomys ordii ENSDORG000000107351 retrocopy
retro_dord_117,
Erinaceus europaeus ENSEEUG000000087291 retrocopy
retro_eeur_368,
Echinops telfairi ENSETEG000000160243 retrocopies
retro_etel_1135, retro_etel_114, retro_etel_2086,
Homo sapiens ENSG000002046281 retrocopy
retro_hsap_3226,
Gorilla gorilla ENSGGOG000000253671 retrocopy
retro_ggor_2194,
Macropus eugenii ENSMEUG000000110553 retrocopies
retro_meug_1095, retro_meug_1109, retro_meug_1532,
Myotis lucifugus ENSMLUG000000155071 retrocopy
retro_mluc_811,
Macaca mulatta ENSMMUG000000036041 retrocopy
retro_mmul_1956,
Monodelphis domestica ENSMODG000000040911 retrocopy
retro_mdom_1426,
Mustela putorius furoENSMPUG000000011482 retrocopies
retro_mputfur_1103, retro_mputfur_1111,
Mus musculus ENSMUSG000000203721 retrocopy
retro_mmus_3282,
Nomascus leucogenys ENSNLEG000000026041 retrocopy
retro_nleu_729,
Ornithorhynchus anatinus ENSOANG000000026001 retrocopy
retro_oana_127,
Otolemur garnettii ENSOGAG000000149242 retrocopies
retro_ogar_1257, retro_ogar_1591,
Pongo abelii ENSPPYG000000199391 retrocopy
retro_pabe_149,
Pan troglodytes ENSPTRG000000227341 retrocopy
retro_ptro_2178,
Rattus norvegicus ENSRNOG000000023903 retrocopies
retro_rnor_1831, retro_rnor_2130, retro_rnor_895,
Ictidomys tridecemlineatus ENSSTOG000000070631 retrocopy
retro_itri_1752,
Tupaia belangeri ENSTBEG000000146612 retrocopies
retro_tbel_3897, retro_tbel_3899,


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