RetrogeneDB ID: | retro_ecab_829 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 5:39494118..39494538(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | DCTD | ||
| Ensembl ID: | ENSECAG00000017516 | ||
| Aliases: | None | ||
| Description: | dCMP deaminase [Source:HGNC Symbol;Acc:2710] |
Retrocopy-Parental alignment summary:
>retro_ecab_829
AAGATCAGAGCCTGAATCATGAATGCATAAAACATGATTGTAGGGACTGGGTACAACAGAATACCAAATGGGTACAGTGA
TGACCTCTTCCCTTAGAGGACAGCAGAGAGTAAGCCAGATACCAAATACCTGTACATGTGCCGTGCCAAACTGAATGTCG
TCATGAACAGAAATTCATCAAGTATAAAAGGATGTACTATACATGTCACCTTGTCCCTATGCAATGAGTGTGTTAAACTT
ATCATCCAGACAGGTATAAAAGAAGTTATTTTCATGTCTGATAAATACCGTGATAGTTATGAGACAACAGCTGTGAGGTT
CATATTTGACATGGCTGTGGTTACATTCAGGAACTTCACACTGAAGTGCAGCAAGATTGCTTTTGATTCATTTGGCAGTA
GACCAAGTCAGGAGCTTCAG
ORF - retro_ecab_829 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 65.03 % |
| Parental protein coverage: | 79.44 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | QVGACIVNAENKIVGIGYNGMPNGCSDDLLPWRRTAENKLDTKYPYVCHAELNAIMNKNSADVKGCTMYV |
| ...A.I.NA.N.IVG.GYN..PNG.SDDL.P.R.TAE.K.DTKY.Y.C.A.LN..MN.NS...KGCT..V | |
| Retrocopy | KIRA*IMNA*NMIVGTGYNRIPNGYSDDLFP*R-TAESKPDTKYLYMCRAKLNVVMNRNSSSIKGCTIHV |
| Parental | ALFPCNECAKLIIQAGIKEVIFMSDKYHDSDEATAARLLFDMAGVTFRKFTPKCSKIVIDFDSINSRPTQ |
| .L..CNEC.KLIIQ.GIKEVIFMSDKY.DS.E.TA.R..FDMA.VTFR.FT.KCSKI...FDS..SRP.Q | |
| Retrocopy | TLSLCNECVKLIIQTGIKEVIFMSDKYRDSYETTAVRFIFDMAVVTFRNFTLKCSKIA--FDSFGSRPSQ |
| Parental | KPQ |
| ..Q | |
| Retrocopy | ELQ |
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 |
|---|---|---|
| SRP021940_articular_cartilage | 0 .00 RPM | 5 .67 RPM |
| SRP021940_cerebellum | 0 .00 RPM | 0 .88 RPM |
| SRP021940_embryo | 0 .00 RPM | 7 .39 RPM |
| SRP021940_placental_villous | 0 .00 RPM | 5 .10 RPM |
| SRP021940_synovial_membrane | 0 .00 RPM | 8 .07 RPM |
| SRP021940_testis | 0 .00 RPM | 2 .24 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_829 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_829 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_829 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 5 parental genes, and 7 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Equus caballus | ENSECAG00000017516 | 3 retrocopies |
retro_ecab_829 , retro_ecab_830, retro_ecab_915,
|
| Mus musculus | ENSMUSG00000031562 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000013215 | 1 retrocopy | |
| Sarcophilus harrisii | ENSSHAG00000015218 | 1 retrocopy | |
| Tursiops truncatus | ENSTTRG00000001460 | 1 retrocopy |