RetrogeneDB ID: | retro_btau_1336 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 4:116235288..116235510(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | BT.49569 | ||
| Ensembl ID: | ENSBTAG00000011893 | ||
| Aliases: | None | ||
| Description: | Haloacid dehalogenase-like hydrolase domain-containing protein 2 [Source:UniProtKB/Swiss-Prot;Acc:Q3ZCH9] |
Retrocopy-Parental alignment summary:
>retro_btau_1336
ATGGAGGCATTGCGGGGCACTGGCTGTGAACCTGAGGAGACCGTTATGATTGGAGATGACTGCGGAGATGATGTTGGTGG
GGCTCAGAATGCTGGCATGCGGGACATCTTAGTCAAGACAGGGAAATATCGAGCACCAGACGAAGACAAAATTAACCCAG
CTCCTTACTTAACCTGTGAGAGCTTCCCACATGCCATGGACCACATTCTGGAGCATTTGCTG
ORF - retro_btau_1336 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 91.89 % |
| Parental protein coverage: | 57.81 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | LEALRGTGCEPEETVMIGDDCRDDVGGAQNAGMRGILVKTGKYRAADEDKINPAPYLTCESFPHAVDHIL |
| .EALRGTGCEPEETVMIGDDC.DDVGGAQNAGMR.ILVKTGKYRA.DEDKINPAPYLTCESFPHA.DHIL | |
| Retrocopy | MEALRGTGCEPEETVMIGDDCGDDVGGAQNAGMRDILVKTGKYRAPDEDKINPAPYLTCESFPHAMDHIL |
| Parental | QHLL |
| .HLL | |
| Retrocopy | EHLL |
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 | 9 .59 RPM |
| ERP005899_muscle | 0 .00 RPM | 14 .57 RPM |
| SRP017611_brain | 0 .00 RPM | 24 .53 RPM |
| SRP017611_kidney | 0 .00 RPM | 16 .71 RPM |
| SRP017611_liver | 0 .00 RPM | 8 .23 RPM |
| SRP030211_testis | 0 .01 RPM | 37 .46 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_1336 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_1336 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_1336 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000011893 | 1 retrocopy |
retro_btau_1336 ,
|
| Choloepus hoffmanni | ENSCHOG00000009397 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000010999 | 1 retrocopy | |
| Ictidomys tridecemlineatus | ENSSTOG00000008527 | 1 retrocopy |