RetrogeneDB ID: | retro_btau_1227 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 3:65200053..65200398(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSBTAG00000011537 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CISD3 | ||
| Ensembl ID: | ENSBTAG00000046569 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_btau_1227
CCGGCGGCCTGGACGGTGAACCAGAGACGGGGGCATCACCTCCTGGCTGGCCCAATGGTTCCCCAAAACCCCAGCCAAGT
CCGTGGTGGCCCTAAAAACACCCATCAAGGTGGAGCTGGTGGCTGGGAAAACCTACAAGTGGTGTGTGTGTGGCCACAGC
AAAAAGTAGTCCTCTGTGATGGCTCCCACTTCTTCAAATGCCCTGGACTATCCCCACTGAAGTTCAAGGCCCAGGAGACC
TGCATGGTGGCACGCTGTACCTGCAAGGCCACCCAGAAGCCCCCATACTGCGATGGTACCCACAAGAGTGAACTGGTGCA
AAAGGCAGAACTGGGCTCTCCACTC
ORF - retro_btau_1227 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 82.05 % |
| Parental protein coverage: | 85.19 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | PPPLTLNQRRD-ITSWLARWFPKTPAKSVVALKTPIKVELVAGKTYRWCVCGRSK-KQPFCDGSHFFKRT |
| P...T.NQRR..ITSWLA.WFPKTPAKSVVALKTPIKVELVAGKTY.WCVCG.SK.K...CDGSHFFK.. | |
| Retrocopy | PAAWTVNQRRG>ITSWLAQWFPKTPAKSVVALKTPIKVELVAGKTYKWCVCGHSK<KVVLCDGSHFFKCP |
| Parental | GLSPLKFKAQETRTVALCTCKATQKPPYCDGTHRSEQVQKAELGSSL |
| GLSPLKFKAQET..VA.CTCKATQKPPYCDGTH.SE.VQKAELGS.L | |
| Retrocopy | GLSPLKFKAQETCMVARCTCKATQKPPYCDGTHKSELVQKAELGSPL |
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 | 1 .23 RPM |
| ERP005899_muscle | 0 .00 RPM | 17 .47 RPM |
| SRP017611_brain | 0 .00 RPM | 5 .02 RPM |
| SRP017611_kidney | 0 .00 RPM | 6 .28 RPM |
| SRP017611_liver | 0 .00 RPM | 2 .64 RPM |
| SRP030211_testis | 0 .00 RPM | 8 .85 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_1227 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_1227 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_1227 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000046569 | 1 retrocopy |
retro_btau_1227 ,
|
| Mus musculus | ENSMUSG00000078695 | 1 retrocopy |