RetrogeneDB ID: | retro_btau_413 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 11:78917476..78918182(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RNFT1 | ||
| Ensembl ID: | ENSBTAG00000009747 | ||
| Aliases: | None | ||
| Description: | RING finger and transmembrane domain-containing protein 1 [Source:RefSeq peptide;Acc:NP_001069875] |
Retrocopy-Parental alignment summary:
>retro_btau_413
TTTTCCCAAGATGAAAATGCTCAGACTCGGTGTGCTTGGTTCCTCGTTTTCTGAGCAGGGTCTTCTGTTTTCCTCTGTTA
TCTCTCTCATTCTCAGTGACTTTATTACCGTTAACTTTTGTAAATCCTTTGGATCTTTTGAGCTTGTGGGAGATACTTTG
AATGGTTTGAATTGCTGATTTCATTCCAAAATTTCCCTTCATGGGTTTCAAATGCCTTCTTTTATTGGTGCCTCCTTTCA
TCATGCCTTTCAAATCCAAGGGTTATTGATGCTTTGAGAAGAATTCTGTCAGTATTAACAGATGCTTGTTCCCATGCCAG
TTTGTTTGCTTATTGGCTGTGGGGAGTTTAGTAATGTAACTCCGTGGAGTCTTGAAATCTTGGTGGTTTTACTTGACCTC
ACTGAAAACTTTTGAGTTTTTTTCTTTTGGATATCTGAGCTTTCAGACAGATTTTGCAGATATTTTCTGCATAATAAAGT
TCTAGAGTTACTGCTAGCAAAAGACAATATTTAGATGTGGAAACTATTTGTTCACCATGTAAAGGAGAATTTAAAAAATG
TATTCTCATGTATGTCAGAATATGCTTTGTGAAGAGGCTACACTTCATGGTTTAACAAATAGAAAACATGCATGCAATGC
AGAATTTTGAATTCAGACCATGTAAGCCAATGGAAGGATGGAACTGCTTCATCAAACTTTCAAATA
ORF - retro_btau_413 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 54.07 % |
| Parental protein coverage: | 55.43 % |
| Number of stop codons detected: | 10 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | FLRERCSKIQCAWLLVFLAGSSVLLYYTFHSQSLYYS-LIFLNPTLDYSSFWEVLWVVGITDFILKFLFM |
| F.........CAW.LVF.AGSSV.L.Y..HSQ.LYY..L.F.NP.LD..S.WE.L..V.I.DFI.KF.FM | |
| Retrocopy | FSQDENAQTRCAWFLVF*AGSSVFLCYLSHSQ*LYYR<LTFVNP-LDLLSLWEIL*MV*IADFIPKFPFM |
| Parental | GLKCLILLVPSLIMP-FKSKGYWYMLLEELCQYYRTFVPIPVWFRYLISYGEFGNVTRWSLGILLALLYL |
| G.KCL.LLVP..IMP.F...G...ML.EE.CQY....VP.PV....LI..GEF.NVT.WSL.IL..LL.L | |
| Retrocopy | GFKCLLLLVPPFIMP<FQIQGL-LML*EEFCQY*QMLVPMPVCL--LIGCGEFSNVTPWSLEILVVLLDL |
| Parental | IL-KLLDFFG-HLRTFRQVLRIFVTRPSYGVPASKRQCSDVDDICSICQAEFQKPILL-ICQHIFCEEC- |
| ...KLL.FF......FRQ.L.IF....S..V.ASKRQ..DV..ICS.C..EF.K.IL...CQ...CEE.. | |
| Retrocopy | TE<KLLSFFLLDI*AFRQILQIFSA**SSRVTASKRQYLDVETICSPCKGEFKKCILM<VCQNMLCEEA< |
| Parental | ITLWFNREKTCPLCRTVISDHINKWKDGATSSHLQI |
| .T.WFN..KTC..CR...SDH...WKDG..SS..QI | |
| Retrocopy | YTSWFNK*KTCMQCRILNSDHVSQWKDGTASSNFQI |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(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 | 110 .74 RPM |
| ERP005899_muscle | 0 .00 RPM | 40 .49 RPM |
| SRP017611_brain | 0 .00 RPM | 9 .46 RPM |
| SRP017611_kidney | 0 .00 RPM | 55 .24 RPM |
| SRP017611_liver | 0 .00 RPM | 56 .48 RPM |
| SRP030211_testis | 0 .01 RPM | 50 .69 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_413 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_413 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_413 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000009747 | 2 retrocopies |
retro_btau_1229, retro_btau_413 ,
|
| Cavia porcellus | ENSCPOG00000014736 | 1 retrocopy | |
| Sus scrofa | ENSSSCG00000017671 | 2 retrocopies |