RetrogeneDB ID: | retro_ecab_623 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 23:46266288..46266626(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CLDN1 | ||
| Ensembl ID: | ENSECAG00000021074 | ||
| Aliases: | None | ||
| Description: | claudin 1 [Source:HGNC Symbol;Acc:2032] |
Retrocopy-Parental alignment summary:
>retro_ecab_623
GCCACCATTGCCATGAAAAGTCTAAAGTGCTTGGAGGATGCTGAGATGTAGAAGAGGTGAATGGCTATCATTGGAGTTTT
GTTTTTATTGTTGTAGATCTGGCTATTTTAGTTGCCACAGCATAGTAAGACGATAAAATTGTGCAAGAGGTTTATCAGTC
AATGACCCCAGTCAATGCCAGGGATGAATGGGTCAAGCTCTCTTTAATGTCTTGGCTACTGCTCTCACTGCCTTCTGAGA
AGTGCCCTATTTTGCTTTCCTGACTCCCCCAAAAGACCTCTTACCTAACACCACTGCCCTATCCTAAACCCATACCTTCT
AATGGAAAGTACCACATA
ORF - retro_ecab_623 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 52.54 % |
| Parental protein coverage: | 54.03 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | ATVGMKCMKCMEDDEVQKMRMAVIG-GVIFLFAGLAVLVATAWYGNRIVQEFYDPMTPVNARYEF-GHAL |
| AT..MK..KC.ED.E..K..MA.IG....F....LA.LVATA.....IVQE.Y..MTPVNAR.E..G.AL | |
| Retrocopy | ATIAMKSLKCLEDAEM*KR*MAIIG<SFVFIVVDLAILVATA**DDKIVQEVYQSMTPVNARDEW<GQAL |
| Parental | FTGWAAA-SLCLLGGGLLCCSCPRK-TTSYPTPRPYPKPAPSSGKDYV |
| F...A.A.S.CLL...L.C.....K..TSY.TP.PYPKP.PS.GK... | |
| Retrocopy | FNVLATA<SHCLLRSALFCFPDSPK<KTSYLTPLPYPKPIPSNGKYHI |
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 .18 RPM |
| SRP021940_cerebellum | 0 .00 RPM | 0 .68 RPM |
| SRP021940_embryo | 0 .03 RPM | 9 .79 RPM |
| SRP021940_placental_villous | 0 .00 RPM | 56 .39 RPM |
| SRP021940_synovial_membrane | 0 .00 RPM | 1 .18 RPM |
| SRP021940_testis | 0 .00 RPM | 0 .26 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_623 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_623 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_623 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Equus caballus | ENSECAG00000021074 | 1 retrocopy |
retro_ecab_623 ,
|
| Sus scrofa | ENSSSCG00000028484 | 1 retrocopy |