RetrogeneDB ID: | retro_btau_1640 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 8:24520013..24520584(-) | ||
| Located in intron of: | ENSBTAG00000043972 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RDM1 | ||
| Ensembl ID: | ENSBTAG00000000030 | ||
| Aliases: | LOC513486, RDM1 | ||
| Description: | RAD52 motif-containing protein 1 [Source:RefSeq peptide;Acc:NP_001179280] |
Retrocopy-Parental alignment summary:
>retro_btau_1640
CATTCTCTGTTCACAGTCTTCTCCCAGTTCGGCCTTCTGTATTCGGTCCGAGTCTTCCCAAACGCAGCAGTGGCCGGCCC
TGGATTTTATGCCGTCATCAAGTTTTATTCAGCGAGGGATGCTCACAGAGCCCAAAAGGCATGCAACCAGAAGCAGCTTT
TCCAGAAATCTCCAGTGAAGATTTCGTCTTGGCACCCAACATAAGGTGGTTCAACACAACGCCCTTGCCCTAAACAGCTC
CAGATGCCAAGAATTGGCAAATTACTACTTTGGTTTCAATGGATGGTCAAAAAGGATCATCAAGCTTCAGGATCTTTCTG
ACCCTGAAGAAGAAAGGGAAAATGAAGATATTGTGGCACCTCTTCAGAGGCAAAGCCTGAAGTTCTTCTGTGCTTTAGAG
GTGGTGTTGCCATCCTACGAGTGCAGAAGTCCAGGAGTTGGCATGGCTGAGGAACCTTTGGATAACTTGAAAGAAGGGCC
ATTATCACTCCTTATGAAAAGGAAGAAAACCCAGAAGCTTGCTATTCAGAAGGCTAAGACAGATGGATTCCAGAAACTGC
AGATTGTGGTT
ORF - retro_btau_1640 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 95.81 % |
| Parental protein coverage: | 66.67 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | HSLFTVFSQFGLLYSVRVFPNAAVAGPGFYAVIKFYSARDAYRAQKACNQKQLFQKSPVKI-RLGTQHKA |
| HSLFTVFSQFGLLYSVRVFPNAAVAGPGFYAVIKFYSARDA.RAQKACNQKQLFQKSPVKI.RLGTQHK. | |
| Retrocopy | HSLFTVFSQFGLLYSVRVFPNAAVAGPGFYAVIKFYSARDAHRAQKACNQKQLFQKSPVKI>RLGTQHKV |
| Parental | VQHNALALNSSRCQELANYYFGFNGWSKRIIKLQDLSDPEEETENEDMVAPLQRQSLKFFCALEVVLPSY |
| VQHNALALNSSRCQELANYYFGFNGWSKRIIKLQDLSDPEEE.ENED.VAPLQRQSLKFFCALEVVLPSY | |
| Retrocopy | VQHNALALNSSRCQELANYYFGFNGWSKRIIKLQDLSDPEEERENEDIVAPLQRQSLKFFCALEVVLPSY |
| Parental | ECRSPGVGMAEEPLDNLEEGPLSLLMKRKKTQKLAIQKAMTDAFQKLQIVV |
| ECRSPGVGMAEEPLDNL.EGPLSLLMKRKKTQKLAIQKA.TD.FQKLQIVV | |
| Retrocopy | ECRSPGVGMAEEPLDNLKEGPLSLLMKRKKTQKLAIQKAKTDGFQKLQIVV |
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 .07 RPM |
| ERP005899_muscle | 0 .00 RPM | 2 .01 RPM |
| SRP017611_brain | 0 .09 RPM | 2 .92 RPM |
| SRP017611_kidney | 0 .00 RPM | 0 .41 RPM |
| SRP017611_liver | 0 .00 RPM | 0 .08 RPM |
| SRP030211_testis | 0 .02 RPM | 3 .86 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_1640 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_1640 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_1640 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 | ENSBTAG00000000030 | 1 retrocopy |
retro_btau_1640 ,
|
| Oryctolagus cuniculus | ENSOCUG00000022704 | 1 retrocopy | |
| Tursiops truncatus | ENSTTRG00000006200 | 1 retrocopy |