RetrogeneDB ID: | retro_ocun_648 | ||
Retrocopylocation | Organism: | Rabbit (Oryctolagus cuniculus) | |
| Coordinates: | 13:55965829..55966339(-) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | TCFL5 | ||
| Ensembl ID: | ENSOCUG00000021283 | ||
| Aliases: | None | ||
| Description: | transcription factor-like 5 (basic helix-loop-helix) [Source:HGNC Symbol;Acc:11646] |
Retrocopy-Parental alignment summary:
>retro_ocun_648
CAGGCCTGGATTAAAGTGGGAGAAGCAGCGCTATGTAAACAAGAAATAAATAAGAGGAATCGGAGTAGAATGCATAATTG
GGCTTGAATATAGAACAAAGAGCCCTTGGAGAGATTCAGAATGTGGGTGAGGGCCACAAGGCCCACGGGGTACCTGGCAG
TCCTCAGAGTCCTGGCAGTCCACCCTGTGGGAGCAGGCCCAAAGCGGGCCCCAGGGTGGAAGGTCTCAGAGTCAGGAGAG
GCATAACCGAATGGAAAGAGATAGATGGCGTAGCATCCACATTTGTTGGGACGAGTTGAATCTCTAGTTCCGTTCTGCAA
CGCAGAGATGGACAACGCGACAGCTCTTCAGTGGAGCACGGCGTTCCTGAAGTACATTCAATAAAGACACGGAGATTCTC
TCACGAAGGTGTTTTGTGGTAAAATTGGCAGAAGGCTAAAGCTGACCAGACCAGACTCCCTGGTCACCTGTCCCGCAGAG
TAGCACCTTGATGGAGATCAAGTGATTGAG
CAGGCCTGGATTAAAGTGGGAGAAGCAGCGCTATGTAAACAAGAAATAAATAAGAGGAATCGGAGTAGAATGCATAATTG
GGCTTGAATATAGAACAAAGAGCCCTTGGAGAGATTCAGAATGTGGGTGAGGGCCACAAGGCCCACGGGGTACCTGGCAG
TCCTCAGAGTCCTGGCAGTCCACCCTGTGGGAGCAGGCCCAAAGCGGGCCCCAGGGTGGAAGGTCTCAGAGTCAGGAGAG
GCATAACCGAATGGAAAGAGATAGATGGCGTAGCATCCACATTTGTTGGGACGAGTTGAATCTCTAGTTCCGTTCTGCAA
CGCAGAGATGGACAACGCGACAGCTCTTCAGTGGAGCACGGCGTTCCTGAAGTACATTCAATAAAGACACGGAGATTCTC
TCACGAAGGTGTTTTGTGGTAAAATTGGCAGAAGGCTAAAGCTGACCAGACCAGACTCCCTGGTCACCTGTCCCGCAGAG
TAGCACCTTGATGGAGATCAAGTGATTGAG
ORF - retro_ocun_648 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 71.35 % |
| Parental protein coverage: | 56.86 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | QVWIKVGEEALCKQAINKRNRSRIRQ-LDASTERRALGEIQNVGE-GPAAAQA-WQSSESSQCPLGEQAQ |
| Q.WIKVGE.ALCKQ.INKRNRSR....L....E.RALGEIQNVGE.GP......WQSSES.Q..L.EQAQ | |
| Retrocopy | QAWIKVGEAALCKQEINKRNRSRMHN<LGLNIEQRALGEIQNVGE<GPQGPRGTWQSSESWQSTLWEQAQ |
| Parental | SGPQGGRSQRRERHNRMERDRRRRIRICCDELNL-LVPFCNAETDKATTLQWTTAFLKYIQERHGDALKK |
| SGPQGGRSQ..ERHNRMERDR.R.I.IC.DELNL.LVPFCNAE.D.AT.LQW.TAFLKYIQ.RHGD.L.K | |
| Retrocopy | SGPQGGRSQSQERHNRMERDRWRSIHICWDELNL<LVPFCNAEMDNATALQWSTAFLKYIQ*RHGDSLTK |
| Parental | EFESVFCGKTGRRLKLTRPDSLITCPAQGSLQGSPSME |
| ....VFCGK.GRRLKLTRPDSL.TCPA...L.G....E | |
| Retrocopy | ----VFCGKIGRRLKLTRPDSLVTCPAE*HLDGDQVIE |
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 |
|---|---|---|
| SRP017611_brain | 0 .00 RPM | 2 .10 RPM |
| SRP017611_kidney | 0 .00 RPM | 0 .20 RPM |
| SRP017611_liver | 0 .00 RPM | 0 .00 RPM |
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_648 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_648 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ocun_648 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 | |
|---|---|---|---|
| Oryctolagus cuniculus | ENSOCUG00000021283 | 1 retrocopy |
retro_ocun_648 ,
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