RetrogeneDB ID: | retro_ecab_160 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 1:52902279..52902658(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSECAG00000000736 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ALG13 | ||
| Ensembl ID: | ENSECAG00000022134 | ||
| Aliases: | None | ||
| Description: | ALG13, UDP-N-acetylglucosaminyltransferase subunit [Source:HGNC Symbol;Acc:30881] |
Retrocopy-Parental alignment summary:
>retro_ecab_160
CTTGTCCTACAAATAGGTGGAGCGAAGATGGTACCTGAACCACTCAGTACTGAGTCATTAACCCTAGATCTTTACAGGTA
CAAGGATTCATTGAAAGACCTTCAGAAAGCAGATCTTGTTGTTAGTCACACAGATGCAGGAAGCCATTTGGAGACTCTGG
AAAAAAGAAAGCCACTTGTTGTGGTTATAAATGAAAAGTTGATGAACAATCATCAGCTGGAATTGGCAAAGCAGCTACAC
AAAATGGGCATCTCTTCTACTGAACCTGCAGCACTCGCCAGGGCAGTTACTGTCAGTGGACTTATCAACACTGAAATGTT
TTCTTCTTGGCCAGCCAGAAAAATTTTTTTCATTTTTGGATAAAGTTGTTGGATTACAA
ORF - retro_ecab_160 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80.0 % |
| Parental protein coverage: | 77.58 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | LVLQIGRGKVVPEPFSTESFTLDVYRYKDSLKEDLQKADLVISHAGAGSCLETLEKRKPLVVVINEKLMN |
| LVLQIG..K.VPEP.STES.TLD.YRYKDSLK.DLQKADLV.SH..AGS.LETLEKRKPLVVVINEKLMN | |
| Retrocopy | LVLQIGGAKMVPEPLSTESLTLDLYRYKDSLK-DLQKADLVVSHTDAGSHLETLEKRKPLVVVINEKLMN |
| Parental | NHQLELAKQLHK-DGHLFYCTCST-LPGLLQSMDLSTLKCFPPGQPEKFSAFLDKVVGLQ |
| NHQLELAKQLHK..GHLFY.TCST..PG.L.S.DLSTLKCF..GQPEK.....DKVVGLQ | |
| Retrocopy | NHQLELAKQLHK<NGHLFY*TCST<SPGQLLSVDLSTLKCFLLGQPEKXXXXXDKVVGLQ |
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 | 2 .89 RPM |
| SRP021940_cerebellum | 0 .00 RPM | 5 .30 RPM |
| SRP021940_embryo | 0 .00 RPM | 18 .54 RPM |
| SRP021940_placental_villous | 0 .00 RPM | 5 .77 RPM |
| SRP021940_synovial_membrane | 0 .00 RPM | 5 .00 RPM |
| SRP021940_testis | 0 .00 RPM | 34 .40 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_160 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_160 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_160 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 | ENSECAG00000022134 | 1 retrocopy |
retro_ecab_160 ,
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