RetrogeneDB ID: | retro_fcat_1701 | ||
Retrocopy location | Organism: | Cat (Felis catus) | |
| Coordinates: | E2:6483537..6484051(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | STX12 | ||
| Ensembl ID: | ENSFCAG00000029657 | ||
| Aliases: | None | ||
| Description: | syntaxin 12 [Source:HGNC Symbol;Acc:11430] |
Retrocopy-Parental alignment summary:
>retro_fcat_1701
AAAGGACGCCAACTGAATGACTTCTCTGCAGCCTTAAAGGATTTCCAGGCTGGGTGGAGAGGAGGGTCTGCAAAGGAAAA
GGAGAAGATCGCCAGGGCGAGAGCCGCATGTCTCCCTGCAGAGGGGAGGCCACGAAAGAGCAGCGCCTGTCCTTTGATGG
CCACGACGAGTGGGACCAGATGCAGAACCAGGGGGATGACGTGGCCACCTCGGAGCAGGAACTGGAACTGATTAAAGAGA
GGGAAAGGGCAATTCGGCAGCTGCAGGCTCACACTTTGGACGTCCGTCAGAGGTTTAAAGATTTGCCCGTGATGATCCGT
GACCAAGGAGACCCCACTGACAGCACGGAAGCCGACGGAGAAGGCCCAGAGGTGCGTGCAGACAGAGCCACGCCGGTCAG
TTTCCGCAAGCAGCTTACGATCAGAAAAGAAAATCTCGCAAGAACGTCTGTGTTCTGGTGCTCGTCCTGTTGGTTATCAC
TGTTCCCTTGGTACTTAGTATCTGACAGATTTAT
ORF - retro_fcat_1701 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 61.71 % |
| Parental protein coverage: | 62.41 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | KERLMNDFSAALNNFQAVQRRVSEKEKESIARARAGSRLSAEERQRE-EQLVSFDGHEEWNQMQSQEDEV |
| K.R..NDFSAAL..FQA..R..S.KEKE.IARARA...L.AE.R.R..EQ..SFDGH.EW.QMQ.Q.D.V | |
| Retrocopy | KGRQLNDFSAALKDFQAGWRGGSAKEKEKIARARAAC-LPAEGRPRK<EQRLSFDGHDEWDQMQNQGDDV |
| Parental | AITEQDLELIKERETAIRQLEADILDVNQIFKDLAMMIHDQGDLIDSIEANVESSEVHVERATDQLQR-A |
| A..EQ.LELIKERE.AIRQL.A..LDV.Q.FKDL..MI.DQGD..DS.EA..E..EV...RAT....R.. | |
| Retrocopy | ATSEQELELIKERERAIRQLQAHTLDVRQRFKDLPVMIRDQGDPTDSTEADGEGPEVRADRATPVSFR<Q |
| Parental | AYYQKK--SRKKICILVLVLSVIIVILVLIIWQIY |
| A.Y..K..SRK..C.LVLVL.VI.V.LVL.I.QIY | |
| Retrocopy | AAYDQKRKSRKNVCVLVLVLLVITVPLVLSI*QIY |
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 .11 RPM | 144 .50 RPM |
| SRP017611_kidney | 0 .00 RPM | 47 .72 RPM |
| SRP017611_liver | 0 .30 RPM | 12 .03 RPM |
Felis catus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_fcat_1701 retrocopy.
Felis catus was not studied using FANTOM5 data.
retro_fcat_1701 was not experimentally validated.
Retrocopy orthology:
Felis catus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Felis catus | ENSFCAG00000002292 | 1 retrocopy | |
| Felis catus | ENSFCAG00000029657 | 1 retrocopy |
retro_fcat_1701 ,
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