RetrogeneDB ID: | retro_btau_390 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 11:14689853..14690257(+) | ||
| Located in intron of: | ENSBTAG00000009246 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TMEM33 | ||
| Ensembl ID: | ENSBTAG00000043958 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_btau_390
GCTTTGCTGGCAAGTGCTCTGGCCAGTGCTCTGAGGCTGTACCAAAGATGACTTCGCTTCCAGTTAAGCAGAGCATTTCT
GGCCTGAGCTTTGTTAGGGGACTGCTGGCACTACCTGTTATATTCATTCATCTTTGTCAACTCTTCCAGTTACAATGAAT
ATTCTCCCAGTCTTGTTATTTTCTTGGCTTCATGCTGCCACATACTGGAAAAAGGCACTTAGTGCAAAGGGTTCAAATAG
TTTATCTCTACTGGGACCTCTCGTCCATAAATTAAACACTAATCAACAGAATATTCTGAAATTCAATACTTATCATTAAA
TAATCTTGATGGCTGCTACAGTTTTTATGCTTTTTTAGTGGCCAAGAAAGTTTGCTCCAGCTTTTTATATACTATAGATT
CCTC
ORF - retro_btau_390 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 66.42 % |
| Parental protein coverage: | 54.88 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | ALLANALTSALRLHQRLPHFQLSRAFLAQALLEDSCHYLL-YSLIFVNSYPVTMSIFPVLLFSLLHAATY |
| ALLA.AL.SALRL.QR...FQLSRAFLA.ALL.D.C...L.Y........PVTM.I.PVLLFS.LHAATY | |
| Retrocopy | ALLASALASALRLYQR*LRFQLSRAFLA*ALLGD-CWHYL>YIHSSLSTLPVTMNILPVLLFSWLHAATY |
| Parental | TKKILDAKDSNSLPLLRSLLDKLSANQQNILKFIACNEIFLMPATVFML-FSGQGSLFQPFIYYRFL |
| .KK.L.AK.SNSL.LL..L..KL..NQQNILKF.....I.LM.ATVFML.FSGQ.SL.Q.FIYYRFL | |
| Retrocopy | WKKALSAKGSNSLSLLGPLVHKLNTNQQNILKFNTYH*IILMAATVFML>FSGQESLLQLFIYYRFL |
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 | 6 .85 RPM |
| ERP005899_muscle | 0 .05 RPM | 18 .90 RPM |
| SRP017611_brain | 0 .09 RPM | 18 .68 RPM |
| SRP017611_kidney | 0 .71 RPM | 32 .84 RPM |
| SRP017611_liver | 0 .00 RPM | 16 .31 RPM |
| SRP030211_testis | 0 .26 RPM | 4 .62 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_390 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_390 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_390 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000043958 | 1 retrocopy |
retro_btau_390 ,
|
| Choloepus hoffmanni | ENSCHOG00000007675 | 1 retrocopy | |
| Tursiops truncatus | ENSTTRG00000003870 | 1 retrocopy |