RetrogeneDB ID: | retro_btau_1190 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 29:18522323..18522888(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSBTAG00000009268 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | DNAL1 | ||
| Ensembl ID: | ENSBTAG00000015930 | ||
| Aliases: | None | ||
| Description: | Dynein light chain 1, axonemal [Source:UniProtKB/Swiss-Prot;Acc:Q2KID4] |
Retrocopy-Parental alignment summary:
>retro_btau_1190
ATGGCAGAAGCAACAACAATCAAAGGAGCACTAGCCAGAGGGGAAGAGAAAACCGGCCAGAAGCCATCTGAAGCCAGAGC
GATAAGGCTGTATGCCCAGATTCCCCCTGTAGAGAAGATGGACGCATCATTGTCCACACTTTCTAACTGTGAGAAGCTTT
CACTGACTACAAACTGCATTGAAAAAACTGCAAACCTGAATGACTTAAAAACCTTAAGAATATTGTCTTTAGGAAGAAAC
AACACAAACAACTTAAATGAACTGGAAGTAGTAGGGGACACATTAGAAGAACTGTGGATCCCCTACAATTTTACTGAGAA
GTTGAAAGGGACCCATGTAATGAAGAAACTGAAGATTCTCTACATGTCTAATAACCTGGTGAAAGATGGCTGAATTTGTG
AAGCTGGCAGAACTGCCATGCCTAGAAGACCTGGTGTTTGTAGGCAATCTCTTGGAAGAGAAACATTCTGCTGAGAACTG
GATTGAAGAGGCAACCAAGACAATGCCCAAACTGAAAAAGCTAGATGGTACCCCAGTAGTTAAAGAAGATGAGGAAGAAG
ATAAC
ORF - retro_btau_1190 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 86.46 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | MAKATTIKEALARWEEKTSQKPSEAREIKLYAQIPPIEKMDASLSTLSNCEKLSLSTNCIEKIANLNGLK |
| MA.ATTIK.ALAR.EEKT.QKPSEAR.I.LYAQIPP.EKMDASLSTLSNCEKLSL.TNCIEK.ANLN.LK | |
| Retrocopy | MAEATTIKGALARGEEKTGQKPSEARAIRLYAQIPPVEKMDASLSTLSNCEKLSLTTNCIEKTANLNDLK |
| Parental | NLRILSLGRNNIKNLNGLEAVGDTLEELWISYNFIEKLKGIHVMKKLKILYMSNNLVKD-W-AEFVKLAE |
| .LRILSLGRNN..NLN.LE.VGDTLEELWI.YNF.EKLKG.HVMKKLKILYMSNNLVKD.W.AEFVKLAE | |
| Retrocopy | TLRILSLGRNNTNNLNELEVVGDTLEELWIPYNFTEKLKGTHVMKKLKILYMSNNLVKD<W<AEFVKLAE |
| Parental | LPCLEDLVFVGNPLEEKHSAEGNWVEEATKRVPKLKKLDGTPVIKEDEEEDN |
| LPCLEDLVFVGN.LEEKHSAE.NW.EEATK..PKLKKLDGTPV.KEDEEEDN | |
| Retrocopy | LPCLEDLVFVGNLLEEKHSAE-NWIEEATKTMPKLKKLDGTPVVKEDEEEDN |
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 | 2 .23 RPM |
| ERP005899_muscle | 0 .00 RPM | 1 .48 RPM |
| SRP017611_brain | 0 .00 RPM | 13 .70 RPM |
| SRP017611_kidney | 0 .00 RPM | 12 .33 RPM |
| SRP017611_liver | 0 .00 RPM | 1 .96 RPM |
| SRP030211_testis | 0 .00 RPM | 12 .75 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_1190 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_1190 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_1190 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 | ENSBTAG00000015930 | 1 retrocopy |
retro_btau_1190 ,
|
| Cavia porcellus | ENSCPOG00000010655 | 1 retrocopy | |
| Drosophila melanogaster | FBgn0033408 | 1 retrocopy |