RetrogeneDB ID: | retro_ecab_363 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 16:45992158..45992627(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CENPP | ||
| Ensembl ID: | ENSECAG00000019351 | ||
| Aliases: | None | ||
| Description: | centromere protein P [Source:HGNC Symbol;Acc:32933] |
Retrocopy-Parental alignment summary:
>retro_ecab_363
CAAAAATCATTTCAAGAAATATATCAATCAGATTCTGAAGGATGGGAGTCTTCAAAAGATCTGAGAGGTCAGCTTGGACA
TTTAGAATCAGAACTTTCATTTCTAAATACACTTACTGGCATCAACGTAAGAAATTACTCCAAGAGGACAGAGGTTTTAG
CAAGCACTGAGATGACGGAGAAAAGTACAATGAAAGTTCTACAAAGACAGATTATCAGGAAATTGCCACATGGCTACATT
TCAACTGGGATTTCAGATTCTGGGAATCCAGAATGAGGAGAGTTCGTCTTTCATTACTAGTGACCTCAATATGATAATGG
AGCTCACAGAATACTCAGAATTAAGTAAATACGTTTTGTGTCTAAAGCAGAAGAAAGAAGCTATTTTTTCATGGTTTTCA
GAAGCTTACACTTTTTTGAGGAGTGGTGTGAATAAATGTAAGCACATACTTAAACATTTAGAGGTAAAA
ORF - retro_ecab_363 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 53.46 % |
| Parental protein coverage: | 60.31 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | RKSFQEIYQSDSEGWESSKDLRSHLGHLESEILFLSTLTGIKIRNYSKKTKDLTSTEMTEKSIKKVLQRH |
| .KSFQEIYQSDSEGWESSKDLR..LGHLESE..FL.TLTGI..RNYSK.T..L.STEMTEKS..KVLQR. | |
| Retrocopy | QKSFQEIYQSDSEGWESSKDLRGQLGHLESELSFLNTLTGINVRNYSKRTEVLASTEMTEKSTMKVLQRQ |
| Parental | RLSGNCH-MITFQLEFQ-ILEIQNKKSLSSVITDLNIIMEPTEYSELSEFVSRAEERRDLFM--FFRSLR |
| ......H....F...F..IL.IQN..S.S....DLN.IME.TEYSELS..V.............F..... | |
| Retrocopy | IIRKLPH<WLHFNWDFR<ILGIQNEESSSFITSDLNMIMELTEYSELSKYVLCLKQKKEAIFSWFSEAYT |
| Parental | FFVEWCEYRKRTFKHFKEK |
| F........K...KH...K | |
| Retrocopy | FLRSGVNKCKHILKHLEVK |
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 | 0 .89 RPM |
| SRP021940_cerebellum | 0 .00 RPM | 1 .30 RPM |
| SRP021940_embryo | 0 .03 RPM | 6 .90 RPM |
| SRP021940_placental_villous | 0 .00 RPM | 3 .80 RPM |
| SRP021940_synovial_membrane | 0 .00 RPM | 2 .75 RPM |
| SRP021940_testis | 0 .00 RPM | 76 .80 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_363 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_363 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_363 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 | |
|---|---|---|---|
| Equus caballus | ENSECAG00000019351 | 1 retrocopy |
retro_ecab_363 ,
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