RetrogeneDB ID: | retro_btau_921 | ||
Retrocopylocation | Organism: | Cow (Bos taurus) | |
| Coordinates: | 20:54745198..54745718(-) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | MARCKSL1 | ||
| Ensembl ID: | ENSBTAG00000046862 | ||
| Aliases: | None | ||
| Description: | MARCKS-related protein [Source:RefSeq peptide;Acc:NP_001069640] |
Retrocopy-Parental alignment summary:
>retro_btau_921
ATGGGCAGCCAGAGCTCCAAGGCTCCCTGGAGTGACCTGACTACCAAGGAGGCAGAAGATGCTTCCCCCTCCACAATTGA
CAGAAAGGGGAATGGCCCCCCATGAAAAGCAATGGAGACTTATCCCCTCAAAGGTGAAGGGGAGTCAACCTTCAAAAATG
GAACACAGGAGGTAGCAGGGGCCACTGGTGATGCCATAGAGCCAGGATCCCCTAGGCAGAGAGCTGAGGCCAAGGCGGGA
AGGGGTGCCCCCATGGAGACCCTCAAGAAGAGGAAGATATTCTCTTTCAAAAAACCTTCCAAATTGAGTAGCCTGTCCTC
AAGAGAAATCAGAAGGAGGGTGGGGGTGATTCGTCTGCCTCCTCACCCGCAGAGGCAGAGCAGGAGCAGGGGGAGATGGT
TCCCTGCAGCAATGAAGCACTGCCAAGGAAGGGAAGGCCGTTGCCACTCCTTAGAGCCAGGAGCACCAGGCCAAAGGGGC
ACGCTATCTCCAAGGGAGGAGCACAGAAGAGGCAGGACCA
ATGGGCAGCCAGAGCTCCAAGGCTCCCTGGAGTGACCTGACTACCAAGGAGGCAGAAGATGCTTCCCCCTCCACAATTGA
CAGAAAGGGGAATGGCCCCCCATGAAAAGCAATGGAGACTTATCCCCTCAAAGGTGAAGGGGAGTCAACCTTCAAAAATG
GAACACAGGAGGTAGCAGGGGCCACTGGTGATGCCATAGAGCCAGGATCCCCTAGGCAGAGAGCTGAGGCCAAGGCGGGA
AGGGGTGCCCCCATGGAGACCCTCAAGAAGAGGAAGATATTCTCTTTCAAAAAACCTTCCAAATTGAGTAGCCTGTCCTC
AAGAGAAATCAGAAGGAGGGTGGGGGTGATTCGTCTGCCTCCTCACCCGCAGAGGCAGAGCAGGAGCAGGGGGAGATGGT
TCCCTGCAGCAATGAAGCACTGCCAAGGAAGGGAAGGCCGTTGCCACTCCTTAGAGCCAGGAGCACCAGGCCAAAGGGGC
ACGCTATCTCCAAGGGAGGAGCACAGAAGAGGCAGGACCA
ORF - retro_btau_921 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 60.89 % |
| Parental protein coverage: | 88.38 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | MGSQSSKAPRGDVTAEEAGGAAIERAPGEENGHVKSNGDLSP-KGEGESPPVNGTEEAAGATGDAIEPAP |
| MGSQSSKAP..D.T..EA..A.........NG.........P.KGEGES...NGT.E.AGATGDAIEP.. | |
| Retrocopy | MGSQSSKAPWSDLTTKEAEDASPSTIDRKGNGPP*KAMETYPLKGEGESTFKNGTQEVAGATGDAIEPGS |
| Parental | PSQGAEAK-GEVPPKETPKKKKKFSFKKPFKLSGLS-FKRNRKEGGGDSSASSPTEEEQEQGEISACGEE |
| P.Q.AEAK.G...P.ET.KK.K.FSFKKP.KLS.LS..KRN.KEGGGDSSASSP.E.EQEQGE...C..E | |
| Retrocopy | PRQRAEAKAGRGAPMETLKKRKIFSFKKPSKLSSLS<LKRNQKEGGGDSSASSPAEAEQEQGEMVPCSNE |
| Parental | -GTAQEGKAAATPESQEPQAKGAEASAAAKGGDTEEAGP |
| ..TA.EGKA.ATP.SQE.QAKGA.......G..TEEAGP | |
| Retrocopy | <STAKEGKAVATP*SQEHQAKGAR---YLQGRSTEEAGP |
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 | 0 .50 RPM |
| ERP005899_muscle | 0 .00 RPM | 7 .28 RPM |
| SRP017611_brain | 0 .00 RPM | 58 .01 RPM |
| SRP017611_kidney | 0 .00 RPM | 2 .19 RPM |
| SRP017611_liver | 0 .00 RPM | 1 .74 RPM |
| SRP030211_testis | 0 .00 RPM | 14 .75 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_921 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_921 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_921 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000046862 | 2 retrocopies |
retro_btau_494, retro_btau_921 ,
|