RetrogeneDB ID: | retro_ecab_44 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | X:52050454..52051270(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSECAG00000001902 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | OTUD6B | ||
| Ensembl ID: | ENSECAG00000018205 | ||
| Aliases: | None | ||
| Description: | OTU domain containing 6B [Source:HGNC Symbol;Acc:24281] |
Retrocopy-Parental alignment summary:
>retro_ecab_44
ATGGAAGATTCACAGCGGATGGTACGACGCCACTACCGCGAAAAGAAAGAGCTGCAGGCCCGCATCCAGAGCATGAAGAA
CTCTGTCCCCAAGAGCGACAAGGAGAGAAGAAAGCAGTTGCTCCTCGACGTCGCCCGCCTCAAGGCCGAGATGGAGCAGA
AGCACCAGCAGGAGCTGGAGAAGTTCCAAGAGAGTTTTCCCGATGACAGCAACCTCGATTCTGTCACTGAAGATCTTGCC
AAGATGGATCTCGAGAACCAGCCTCCCCGCCTCGCAAAGGCACAAAGAAGGCGCGAACGAAGGGCGGCCGAGGAGGCAGC
GCGCCTGGAGAGGATCGCTGAGGTGGAGGCGGAGCGTCAGGCCGGCTTCCGCCACGACGACGAGGAAGAGAAGCTCTCCG
CCATCCTGGAGGCCAGAAATCTGGAGATGAAGGAAATCCCAGCCGACGGCCACTGCATGTACCGCGCCATCCAAGACCAG
CTGGTGTTCCCGGTGACCGTGGAGAGCCTGCGGCGTCGCACCGCCAACTACCTGAGGAAGCACGTCGACGACTTCCTGCC
CTTCTTCAGCGACTCCGAAACCGGCGACACCTGCAGCCGCGACAGCTTCTTGAGTTACTGCGACGACATCGTGCACAGCG
CGTTGTGGGGAGGCCAGCTCGAGCTGAGGGCCCTGTCGCACGTCCTGCAGACCCCCATCGAGGTGATCCAGGCCTACTCT
CCCGTCCTCGTCATCGGGGAGGAGTACGCCAAGAAGCCGCTCACCCTCGTCTACCTGCGCTACTCCTGCAGCCTCGGGGA
GCACTACAACTCGGTG
ORF - retro_ecab_44 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 57.76 % |
| Parental protein coverage: | 54.27 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | LDEEQQLVRRHRKEKKELQAKIQGMKNAVPKNDKKRRKQLTEDISKLEAEMEQKHREELEQLKLT-SKES |
| ....Q..VRRH..EKKELQA.IQ.MKN.VPK.DK.RRKQL..D...L.AEMEQKH..ELE.........S | |
| Retrocopy | MEDSQRMVRRHYREKKELQARIQSMKNSVPKSDKERRKQLLLDVARLKAEMEQKHQQELEKFQESFPDDS |
| Parental | KIDSVADNISNLVLENQPPRISKARKRRDKKAALEKEREERIAEAEIENLTGARH-VESEKLAQILAARQ |
| ..DSV........LENQPPR..KA..RR...AA.E..R.ERIAE.E.E...G.RH..E.EKL..IL.AR. | |
| Retrocopy | NLDSVTEDLAKMDLENQPPRLAKAQRRRERRAAEEAARLERIAEVEAERQAGFRHDDEEEKLSAILEARN |
| Parental | LEIKQIPSDGHCMYRAIEDQL |
| LE.K.IP.DGHCMYRAI.DQL | |
| Retrocopy | LEMKEIPADGHCMYRAIQDQL |
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 | 4 .01 RPM |
| SRP021940_cerebellum | 0 .00 RPM | 2 .65 RPM |
| SRP021940_embryo | 0 .03 RPM | 7 .01 RPM |
| SRP021940_placental_villous | 0 .00 RPM | 1 .78 RPM |
| SRP021940_synovial_membrane | 0 .00 RPM | 2 .61 RPM |
| SRP021940_testis | 6 .33 RPM | 2 .62 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_44 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_44 was not experimentally validated.