RetrogeneDB ID: | retro_ecab_356 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 16:12288741..12289088(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | HINT1 | ||
| Ensembl ID: | ENSECAG00000023180 | ||
| Aliases: | None | ||
| Description: | histidine triad nucleotide binding protein 1 [Source:HGNC Symbol;Acc:4912] |
Retrocopy-Parental alignment summary:
>retro_ecab_356
AGGCTCAGGCCACCCAACCAGATAACAACACGATCTTCAGGAAGAATACCTGCAAGGAAATCTCGGCCAAAAGTCATTTT
TGAGGATGACTGACATCTTGCTTTCCATGATATTTTCCTTCAAGCACCAACACATTTTGTGGTGACATCTAAGAAACAGG
TTTCTCGGATTTCTGTAGCAGAGGTGATGATAAAAGTCTTCTTGGACATTTAATGATTGTTGGTAGGAAATGTGCTGCTG
CTCTGGGCCTGAAGAAGGGTTGTGGAATGGCGGTGAAGGAAGGTTCCAGTAAGGGACAGGCTGGCTGTCACTTTCATCCC
CGTGTTCCTAGAAGTCAGCAGATGAAT
ORF - retro_ecab_356 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 64.1 % |
| Parental protein coverage: | 93.55 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | RLRPLGLVGTRSSGRSFAKESQPKIIFEDDQCLAFHDISPQAPTHFLVIPKKHISQISVAE-DDDESLLG |
| RLRP.....TRSSGR..A..S.PK.IFEDD..LAFHDI..QAPTHF.V..KK..S.ISVAE..DD.SLLG | |
| Retrocopy | RLRPPNQITTRSSGRIPARKSRPKVIFEDD*HLAFHDIFLQAPTHFVVTSKKQVSRISVAE<GDDKSLLG |
| Parental | HLMIVGKKCAADLGLKKGYRMVVNEGSDGGQSVYHVHLHVLGGRQMN |
| HLMIVG.KCAA.LGLKKG..M.V.EGS..GQ...H.H..V....QMN | |
| Retrocopy | HLMIVGRKCAAALGLKKGCGMAVKEGSSKGQAGCHFHPRVPRSQQMN |
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 | 32 .70 RPM |
| SRP021940_cerebellum | 0 .00 RPM | 77 .48 RPM |
| SRP021940_embryo | 0 .00 RPM | 43 .24 RPM |
| SRP021940_placental_villous | 0 .00 RPM | 44 .50 RPM |
| SRP021940_synovial_membrane | 0 .00 RPM | 36 .04 RPM |
| SRP021940_testis | 0 .00 RPM | 47 .25 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_356 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_356 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_356 has 1 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Sus scrofa | retro_sscr_371 |