RetrogeneDB ID: | retro_btau_813 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 2:28309924..28310355(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SC5DL | ||
| Ensembl ID: | ENSBTAG00000019246 | ||
| Aliases: | None | ||
| Description: | lathosterol oxidase [Source:RefSeq peptide;Acc:NP_001030433] |
Retrocopy-Parental alignment summary:
>retro_btau_813
TATTCCTTCTTTGCAACACTGAGTTATTATGTTGTCTATGATCTTTCCTTAATTAAAGACAATTTTTAAAGAATCAAGTC
TATTGATAGATTATGCATTCTGTCCAGCCAATGCCATGGATCAGCATCCCCATATTTCCTCCTTTCCTGCTAGAGGTGAC
AGGTTACAGCAAATTGTATAATGGCATAGGAGAGTTTCCATATAGTTGGTTTCAACTCATTGCTGGTATCTATTTTTCTC
TTTTTCACTGACATGCTGATCTACTGGATTCACAGAGGCTTTCATCAGAGACTTGTATATATAAGCGCTTACACAAACCT
CATCACATCTGGCAGGTTCTGACTTCATTTGTAAATCATGCTTTTCACCTTCTGGATGACGTCCTTCAGAGTCTGCCTTA
CCATAGATATCCTTTTATCTTTCCTTTAAAC
ORF - retro_btau_813 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 58.9 % |
| Parental protein coverage: | 74.36 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | YFFFATLSYYFVYDHL-LMKHPQFLKNQVSREITHSVQSMPWMSIPTVLLFLLEVRGYSRLYDGIGEFPY |
| Y.FFATLS.Y.V...L......QFLKNQV...I.HSVQ.MPW.SIP....FLLEV.GYS.LY.GIGEFPY | |
| Retrocopy | YSFFATLS-YYVVYDL<FLN*RQFLKNQVY**IMHSVQPMPWISIPIFPPFLLEVTGYSKLYNGIGEFPY |
| Parental | GWFQLVASVLSFLFFTDMLIYWIHRGLHHKLVYKRLHKPHHIWKIPTPFASHAFHPLDGFLQSLPYHIYP |
| .WFQL.A.....LF..........R.......YKRLHKPHHIW...T.F..HAFH.LD..LQSLPYH.YP | |
| Retrocopy | SWFQLIAGIYFSLFH*HADLLDSQRLSSETCIYKRLHKPHHIWQVLTSFVNHAFHLLDDVLQSLPYHRYP |
| Parental | FIFPLH |
| FIFPL. | |
| Retrocopy | FIFPLN |
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 | 1244 .52 RPM |
| ERP005899_muscle | 0 .00 RPM | 38 .38 RPM |
| SRP017611_brain | 0 .00 RPM | 57 .78 RPM |
| SRP017611_kidney | 0 .00 RPM | 65 .61 RPM |
| SRP017611_liver | 0 .00 RPM | 239 .14 RPM |
| SRP030211_testis | 0 .01 RPM | 7 .70 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_813 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_813 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_813 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 10 parental genes, and 10 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000019246 | 1 retrocopy |
retro_btau_813 ,
|
| Canis familiaris | ENSCAFG00000011805 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000007436 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000013028 | 1 retrocopy | |
| Mustela putorius furo | ENSMPUG00000005754 | 1 retrocopy | |
| Ochotona princeps | ENSOPRG00000003219 | 1 retrocopy | |
| Ictidomys tridecemlineatus | ENSSTOG00000008946 | 1 retrocopy | |
| Tupaia belangeri | ENSTBEG00000000490 | 1 retrocopy | |
| Tarsius syrichta | ENSTSYG00000011139 | 1 retrocopy | |
| Tursiops truncatus | ENSTTRG00000006908 | 1 retrocopy |