RetrogeneDB ID: | retro_btau_1256 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 3:15032950..15033379(-) | ||
| Located in intron of: | ENSBTAG00000020356 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | GOLPH3L | ||
| Ensembl ID: | ENSBTAG00000020357 | ||
| Aliases: | None | ||
| Description: | Golgi phosphoprotein 3-like [Source:UniProtKB/Swiss-Prot;Acc:A6H7F6] |
Retrocopy-Parental alignment summary:
>retro_btau_1256
ATGACCACCTTAACTCACAGGGCCCGTCGCACTGAGGTAGGGAAGAATTCTGAAAAGAAGGTAGAAAGTGAGGAAAACAT
GAATCAAAACCGAAATCAAGACAATGAGGACACTGGAGACTCTAAGGATATCCGCCTCACCCTTATGGAAGAAGTATTGC
TCCTGGGACTAAAAGATAAAGAAGGTTACACATTTTTCTGGAACGACTGCATATCATCTGGCCCGCAAGGCGGCATCCTG
ATAGAGCCGGCCATGTGAGGTCGAATCTATCTAGAACCCCCAACCATGTGTAAGAAGCAACTACTAGACAGAAAGGTACT
GCTAAAGTCAGATAGCCCAATGGGTGATGTTTTAGTGGATGAAACTCTCAAACACATCAAAGCAACTGAACCCACAGAAA
CTGTCCAAACACGGATAGAGCTACTCACC
ORF - retro_btau_1256 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 90.91 % |
| Parental protein coverage: | 50.18 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MTTLTHRARRTEVGKNSEKKVESEENVNQDRNQDNEDIGDSKDIRLTLMEEVLLLGLKDKEGYTSFWNDC |
| MTTLTHRARRTEVGKNSEKKVESEEN.NQ.RNQDNED.GDSKDIRLTLMEEVLLLGLKDKEGYT.FWNDC | |
| Retrocopy | MTTLTHRARRTEVGKNSEKKVESEENMNQNRNQDNEDTGDSKDIRLTLMEEVLLLGLKDKEGYTFFWNDC |
| Parental | ISSGLRGGILIELAMRGRIYLEPPTMRKKRLLDRKVLLKSDSPTGDVLLDETLKHIKATEPTETVQTWIE |
| ISSG..GGILIE.AM.GRIYLEPPTM.KK.LLDRKVLLKSDSP.GDVL.DETLKHIKATEPTETVQT.IE | |
| Retrocopy | ISSGPQGGILIEPAM*GRIYLEPPTMCKKQLLDRKVLLKSDSPMGDVLVDETLKHIKATEPTETVQTRIE |
| Parental | LLT |
| LLT | |
| Retrocopy | LLT |
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 .07 RPM | 21 .34 RPM |
| ERP005899_muscle | 0 .16 RPM | 72 .22 RPM |
| SRP017611_brain | 0 .14 RPM | 15 .76 RPM |
| SRP017611_kidney | 0 .71 RPM | 36 .16 RPM |
| SRP017611_liver | 0 .30 RPM | 33 .75 RPM |
| SRP030211_testis | 0 .07 RPM | 19 .31 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_1256 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_1256 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_1256 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000020357 | 1 retrocopy |
retro_btau_1256 ,
|
| Choloepus hoffmanni | ENSCHOG00000013505 | 2 retrocopies | |
| Myotis lucifugus | ENSMLUG00000003484 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000047620 | 1 retrocopy |