RetrogeneDB ID: | retro_ecab_79 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | X:85217250..85217682(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSECAG00000003478 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | NCBP2 | ||
| Ensembl ID: | ENSECAG00000016153 | ||
| Aliases: | None | ||
| Description: | nuclear cap binding protein subunit 2, 20kDa [Source:HGNC Symbol;Acc:7659] |
Retrocopy-Parental alignment summary:
>retro_ecab_79
GAGCTGAGCGAGCATGGGGACCAGCAGTTTGGTGGCGGCAACGAAGAGCATGAAAGATTACTGAAGGAAAGCTCGACACT
GTATGTGGGAAATCTATCTTTTTATACAACTGAAGAGCATGTACTTGAACTCTTCAGTAGATGCGGTGATGTCAAGAATG
TATTTATGGGCCTGGGTAAAGTCAAGAAAGCGGCATGTAATTTCTGTTTTGTAGAATACCATAAGAGAGCTGATGCCGAA
AATGCCTTGTGGTTCCTAAATGGGACCCGCCTAGATGACCGTATCATCCGCGTAGATTGGGATATAGGCTTTAGAGAGCG
CAGACGGTATGGCCGGTATGGCCGTGGCCGATTTCGAGGCCAGGTAAGAGAGGGGCTTCGTTTTGACTTTGATGCTGGTA
GAGGAGGCTTTGGAAAGCAGACTCAGGCCCGT
ORF - retro_ecab_79 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 66.9 % |
| Parental protein coverage: | 89.1 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | ELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCF |
| ELS...DQ.F.G.NEE.E.LLK.S.TLYVGNLSFYTTEE...ELFS..GD.K...MGL.K.KK.AC.FCF | |
| Retrocopy | ELSEHGDQQFGGGNEEHERLLKESSTLYVGNLSFYTTEEHVLELFSRCGDVKNVFMGLGKVKKAACNFCF |
| Parental | VEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQYGR---GRSGGQVRDEYRQDYDAGRGGYGKL |
| VEY..RADAENA....NGTRLDDRIIR.DWD.GF.E.R.YGR...GR..GQVR...R.D.DAGRGG.GK. | |
| Retrocopy | VEYHKRADAENALWFLNGTRLDDRIIRVDWDIGFRERRRYGRYGRGRFRGQVREGLRFDFDAGRGGFGKQ |
| Parental | AQ |
| .Q | |
| Retrocopy | TQ |
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 .06 RPM | 13 .93 RPM |
| SRP021940_cerebellum | 0 .00 RPM | 18 .33 RPM |
| SRP021940_embryo | 0 .03 RPM | 18 .77 RPM |
| SRP021940_placental_villous | 0 .05 RPM | 13 .76 RPM |
| SRP021940_synovial_membrane | 0 .00 RPM | 11 .20 RPM |
| SRP021940_testis | 8 .06 RPM | 18 .29 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_79 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_79 was not experimentally validated.