RetrogeneDB ID: | retro_btau_688 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 18:13387835..13388672(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | DYNC1LI1 | ||
| Ensembl ID: | ENSBTAG00000014700 | ||
| Aliases: | None | ||
| Description: | cytoplasmic dynein 1 light intermediate chain 1 [Source:RefSeq peptide;Acc:NP_001039517] |
Retrocopy-Parental alignment summary:
>retro_btau_688
CAGTGTGATGCCATTAGTGTGTTGGAGAAAGAACATGACTACAGAGATGAGCATTTTGATTTTATTCAGTCACATATCCG
GAAGTTTTGTTTACAGTATGGTGCAGCACTTATATACGCTTCAGTAAAAGAAAATAAAAATATAGATTTAGTATATAAGT
ACATCGTCCAGAAACTCTATGGATTTCCTTATAAGATTCCTGCTGTTGTTGTGGAAAAAGATGCAGTATTTATTCCAGCA
GGGTGGGATAATGATAAGAAAATAGGAATATTACATGAAAACTTTCAAACGTTAAAAGCAGAAGATAATTTTGAAGACAT
CATAACTAAACCACCTGTCCGAAAGTTTGTGCATGAGAAAGAAATTATGGCGGAAGATGACCAAGTGTTTCCTATGAAGC
TACAGTCCCTTTTAGCAAAGCAACCACCAACTGCAGCTGGAAGGCCTGTGGATGCCTCACCAAGAGTCCCAAGAGGCTCC
CCTCGAACACCAAACAGATCTGTGTCATCCAACGTTGCTAGCGTATCACCCATCCCTGCTGGGTCAAAAAAGATCGATCC
AAACATGAAAGCTGGAGCTACAAGTGAAGGTGTCCTGGCAAATTTCTTTAACAGTTTGCTGAGTAAAAAGACTGGCTCCC
CAGGAGGCCCTGGTGTTGGTGGTGGTAGCCCTGGAGGTGGGGCTGCAGGCGGAGGCGGCGGTTTACCACCGTCTGCCAAA
AAGTCAGGCCAGAAGCCTGTCCTGTAAGACGTTCATGCGGAGCTGGACAGAATCGCACGGAAACCAGTGACGGTCTCCAC
TACCACACCTACATCTCCTGCAGAAGGAGAAGCTTCT
ORF - retro_btau_688 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 98.57 % |
| Parental protein coverage: | 53.24 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | KCDAISVLEKEHDYRDEHFDFIQSHIRKFCLQYGAALIYASVKENKNIDLVYKYIVQKLYGFPYKIPAVV |
| .CDAISVLEKEHDYRDEHFDFIQSHIRKFCLQYGAALIYASVKENKNIDLVYKYIVQKLYGFPYKIPAVV | |
| Retrocopy | QCDAISVLEKEHDYRDEHFDFIQSHIRKFCLQYGAALIYASVKENKNIDLVYKYIVQKLYGFPYKIPAVV |
| Parental | VEKDAVFIPAGWDNDKKIGILHENFQTLKAEDNFEDIITKPPVRKFVHEKEIMAEDDQVFLMKLQSLLAK |
| VEKDAVFIPAGWDNDKKIGILHENFQTLKAEDNFEDIITKPPVRKFVHEKEIMAEDDQVF.MKLQSLLAK | |
| Retrocopy | VEKDAVFIPAGWDNDKKIGILHENFQTLKAEDNFEDIITKPPVRKFVHEKEIMAEDDQVFPMKLQSLLAK |
| Parental | QPPTAAGRPVDASPRVPGGSPRTPNRSVSSNVASVSPIPAGSKKIDPNMKAGATSEGVLANFFNSLLSKK |
| QPPTAAGRPVDASPRVP.GSPRTPNRSVSSNVASVSPIPAGSKKIDPNMKAGATSEGVLANFFNSLLSKK | |
| Retrocopy | QPPTAAGRPVDASPRVPRGSPRTPNRSVSSNVASVSPIPAGSKKIDPNMKAGATSEGVLANFFNSLLSKK |
| Parental | TGSPGGPGVGGGSPGGGAAGGGGGLPPSAKKSGQKPVLSDVHAELDRIARKPVTVSTTTPTSPAEGEAS |
| TGSPGGPGVGGGSPGGGAAGGGGGLPPSAKKSGQKPVL.DVHAELDRIARKPVTVSTTTPTSPAEGEAS | |
| Retrocopy | TGSPGGPGVGGGSPGGGAAGGGGGLPPSAKKSGQKPVL*DVHAELDRIARKPVTVSTTTPTSPAEGEAS |
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 | 2 .60 RPM | 15 .43 RPM |
| ERP005899_muscle | 0 .00 RPM | 33 .47 RPM |
| SRP017611_brain | 0 .09 RPM | 33 .67 RPM |
| SRP017611_kidney | 0 .06 RPM | 32 .24 RPM |
| SRP017611_liver | 0 .38 RPM | 12 .84 RPM |
| SRP030211_testis | 1 .35 RPM | 42 .07 RPM |
Bos taurus was not studied using ChIP-Seq data.
1 EST(s) were mapped to retro_btau_688 retrocopy
| EST ID | Start | End | Identity | Match | Mis-match | Score |
|---|---|---|---|---|---|---|
| DY143863 | 13388065 | 13388207 | 100 | 142 | 0 | 142 |
Bos taurus was not studied using FANTOM5 data.
retro_btau_688 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_688 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000014700 | 1 retrocopy |
retro_btau_688 ,
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