RetrogeneDB ID: | retro_btau_1229 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 3:66769029..66769748(+) | ||
| 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_1229
TGGGCCTCTAAATAATTTTCAAACCAGGCTTTTCTAAGAAAAATGTGCTCAAAATCCAGTAAGCTTAGTTACTGGTATTC
TTAGCAGGATTTTCCATTCTCTTTCATTCTTGGTCTCTTTATTACAACTTAATCTTTTTAAAATCCTATTTTGGATCATT
TGAACTTCTCAGAAGTACTTTGGATTATTGGAATTACAGACTTCATTTTGAAATTGCTTTTCATGGCTCAAAAAGTCTTA
TTATAGTGGTGCCTTCTTTCATCATGCTTTTTAAAGTCAAGGGTTCCTGGGATATGCTCTTAGAAGAATTAAGTCAGTTT
TACTGAATTTTATCCCCTACCAGTTTTGGTTTTATTACCTTATTTGCCTCAGGGAGTTTAACAGTATAATTAAATAGGTT
CTTTAGATATTAGTTGCTTTATTCTACCTCATTTTAAAGCTTTTGGATTTTTTGGAAATCTAAGAACTTTCAGATAGGTT
TGTGAATATTTTTTACACAACCAAGTTATGGAGTGACTTATTCAGATGTGGGTGATATTTGTTCAATATGTGAAGCTGAA
TTTCAGAAAAGTATTCTTCCCTTCTGTCAGCATATATTTTTTGAAGAGTGCATTACCTTATGGTTTTACAAAAAGAATGT
ATGTCCACTGCACAAGACTGTGATTTTAGACCATAGTCCCAAATGGAAAGATGGGGCTGTCTCATCACACCTTCAAATA
ORF - retro_btau_1229 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 62.11 % |
| Parental protein coverage: | 57.74 % |
| Number of stop codons detected: | 7 |
| Number of frameshifts detected: | 6 |
Retrocopy - Parental Gene Alignment:
| Parental | YANKSIVNQVFLRERCSK-IQCAWLLVFLAGSSVLLYYTFHSQSLYYSLIFL-NPTLDYSSFWEVLWVVG |
| .A.K...NQ.FLR..CSK.IQ.A.LLVFLAG.S.L....FHS.SLYY.LIFL.NP.LD...F.EVLW..G | |
| Retrocopy | WASK*FSNQAFLRKMCSK<IQ*A*LLVFLAGFSIL----FHSWSLYYNLIFL>NPILDHLNFSEVLWIIG |
| Parental | ITDFILKFLFM-GLKCLILLVPSLIMPFKSKGYWYMLLEELCQYY-RTFVPIPVWFRYLISYGEFGNVTR |
| ITDFILK.LFM.G.K.LI..VPS.IM.FK.KG.W.MLLEEL.Q.Y...F.P...WF.YLI...EF..... | |
| Retrocopy | ITDFILKLLFM<GSKSLIIVVPSFIMLFKVKGSWDMLLEELSQFY<LNFIPYQFWFYYLICLREFNSIIK |
| Parental | WSLGILLALLYLILKLLD-FFGHLRTFRQV-LRIFVTRPSYGVPASKRQCSDVDDICSICQAEFQKPILL |
| ..L.IL.AL.YLILKLLD.FFG.LRTFR.V.L.IF.T.PSYGV..S.....D...IC....AEFQK.IL. | |
| Retrocopy | *VL*ILVALFYLILKLLD<FFGNLRTFR*V<L*IFFTQPSYGVTYS--DVGDICSIC---EAEFQKSILP |
| Parental | ICQHIFCEECITLWFNREKTCPLCRTVISDHINKWKDGATSSHLQI |
| .CQHIF.EECITLWF.....CPL..TVI.DH..KWKDGA.SSHLQI | |
| Retrocopy | FCQHIFFEECITLWFYKKNVCPLHKTVILDHSPKWKDGAVSSHLQI |
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 .30 RPM | 55 .24 RPM |
| SRP017611_liver | 0 .00 RPM | 56 .48 RPM |
| SRP030211_testis | 0 .00 RPM | 50 .69 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_1229 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_1229 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_1229 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 |