RetrogeneDB ID:

retro_btau_1674

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:9:44152233..44152731(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RBPMS2
Ensembl ID:ENSBTAG00000011037
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_btau_1674
CCCGCTCCCTCCCACCCCAGCACCCTGAAGCCCCGCACCCTGGAGGAGGAGGTCCGGACGCAGCTTGCCAGGGGCCTCCC
TGTGGACTTTAAACCCAGAGAACTCTACCCGCCCTTCAGGGCGTTCAAGGGGTATGAAGGGTCCCTGACCAAGCTCTCAT
AGAGCAGCCTGCGGGTGTTGTGATCCGTGACAGCAGGGCTGGAGCAGAAGCCGTCAGAACGCATTGAACCGTATTCACTT
TGATCCTGGGGACCCGCAGACCCTGAGGCTAAAGTATGCCAAAGCCACTACCAAGACGGCCAAGAACAAGCTGATGGCCG
CACCAAATCCCACCAACGCCCAGCCCGCCCTAGAGCGCCCTTCAGCTTATGGGACCCCTAAGACCTGATCCCCCAATGCC
CGCATCCTCGGACGGGTAGGGCACCGTACCTTCTGCCCACCACGGAGCTGACCTCCACCGTCTCGCCTGCTGCGCTCACC
TGCCCAGCTGTCACTGCT

ORF - retro_btau_1674 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 58.05 %
Parental protein coverage: 84.24 %
Number of stop codons detected: 1
Number of frameshifts detected: 3


Retrocopy - Parental Gene Alignment:

ParentalPSSEHHLTSRGETSPTIQEVRTLFVSGLPVDIKPRELYLLFRPFKGYEGSLIKLT-SRQPVGFVIFDSRA
P...H..T....T.....EVRT....GLPVD.KPRELY..FR.FKGYEGSL.KL....QP.G.VI.DSRA
RetrocopyPAPSHPSTLKPRTLE--EEVRTQLARGLPVDFKPRELYPPFRAFKGYEGSLTKLS<IEQPAGVVIRDSRA
ParentalGAEAAK-NALNGIRFDPENPQTLRLEFAKANTKMAKNKLMATPNPTNAHPTL-GAHFIARDPYDLMGAAL
GAEA...NALN.I.FDP..PQTLRL..AKA.TK.AKNKLMA.PNPTNA.P.L..A.F...DP.DL.....
RetrocopyGAEAVR<NALNRIHFDPGDPQTLRLKYAKATTKTAKNKLMAAPNPTNAQPAL<RAPFSLWDP*DLIPQCP
ParentalIPASPEAWAPYPLYTTELTPAISHTAFTYPAATA
.P......APY.L.TTELT...S..A.T.PA.TA
RetrocopyHPRTGR--APYLLPTTELTSTVSPAALTCPAVTA

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 5 .55 RPM
ERP005899_muscle 0 .11 RPM 5 .38 RPM
SRP017611_brain 0 .00 RPM 5 .53 RPM
SRP017611_kidney 0 .06 RPM 17 .49 RPM
SRP017611_liver 0 .00 RPM 11 .63 RPM
SRP030211_testis 0 .01 RPM 6 .31 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_1674 retrocopy.

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_1674 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_1674 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 18 parental genes, and 39 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG00000011037 1 retrocopy
retro_btau_1674 ,
Bos taurus ENSBTAG000000337271 retrocopy
retro_btau_1555,
Callithrix jacchus ENSCJAG000000052002 retrocopies
retro_cjac_1775, retro_cjac_298,
Dipodomys ordii ENSDORG000000040251 retrocopy
retro_dord_438,
Homo sapiens ENSG000001668312 retrocopies
retro_hsap_2513, retro_hsap_3613,
Gorilla gorilla ENSGGOG000000089841 retrocopy
retro_ggor_2438,
Loxodonta africana ENSLAFG000000187256 retrocopies
retro_lafr_344, retro_lafr_393, retro_lafr_445, retro_lafr_481, retro_lafr_550, retro_lafr_859,
Macaca mulatta ENSMMUG000000132701 retrocopy
retro_mmul_1837,
Monodelphis domestica ENSMODG000000104871 retrocopy
retro_mdom_571,
Mus musculus ENSMUSG000000323879 retrocopies
retro_mmus_2671, retro_mmus_3408, retro_mmus_3410, retro_mmus_3429, retro_mmus_3431, retro_mmus_3437, retro_mmus_3562, retro_mmus_3588, retro_mmus_3596,
Nomascus leucogenys ENSNLEG000000125051 retrocopy
retro_nleu_2209,
Otolemur garnettii ENSOGAG000000260171 retrocopy
retro_ogar_3254,
Pongo abelii ENSPPYG000000065531 retrocopy
retro_pabe_2963,
Pan troglodytes ENSPTRG000000071652 retrocopies
retro_ptro_1458, retro_ptro_2441,
Sus scrofa ENSSSCG000000045491 retrocopy
retro_sscr_851,
Ictidomys tridecemlineatus ENSSTOG000000100552 retrocopies
retro_itri_1512, retro_itri_556,
Tarsius syrichta ENSTSYG000000089963 retrocopies
retro_tsyr_1433, retro_tsyr_171, retro_tsyr_445,
Tursiops truncatus ENSTTRG000000118403 retrocopies
retro_ttru_1046, retro_ttru_1212, retro_ttru_1790,


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