RetrogeneDB ID: | retro_ecab_383 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 16:51281085..51281958(-) | ||
| Located in intron of: | ENSECAG00000011942 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SLC25A30 | ||
| Ensembl ID: | ENSECAG00000017334 | ||
| Aliases: | None | ||
| Description: | solute carrier family 25, member 30 [Source:HGNC Symbol;Acc:27371] |
Retrocopy-Parental alignment summary:
>retro_ecab_383
ATGGCGGCCCTCAACCGGAAGCCCTTTGTGTACGGAGGGCTGGCCTCCATCCCGGCAGAATGCGGTACATTCCCAATTGA
TTTAACCAAGATGTGGCTCCAGATTCAATGGCAGACGAACGACGCCAACTTGAAAGAAATCCGGTACAGAGGCGTGTTGC
ATGCTTTCGTGACGATAGGCCGAGAGGAAGGGCTGAAAGCGCTGTAGGTCGGGATTGCCCCCGCGATGCTACGCCAGGCT
TCCTATGGCACCGTCAAGATAGGCACTTAGCAGAGCTTGAAGCGATTATTTGTCGAACGCCCAGAAGGTGAGACTCTACT
GATAAATGTGGTCTGTGGAATTCTCTCTGGAGTCCTATCCTCAGCCATTGCTAATCCAACTGATGTTTTGAAAATACGGA
TGCAAGCACAAAGCAGCAGCATTCAGGGAGGAATGATAGGCAGCTTCATTAACAATTACCAGCAAGAGGGACCGAGAGGA
CTGTGGAAGGGCGTGTCCCTTACCGCTCAGAGGGCTCCTATTGTTGTTGGCTTGGAGCTGCGGGTCTGCGACCTCGCCAA
GAAGCATCTGATCCTCTGGGGCCTGATGGGAGACCCTGTGTCTACCCACTTCCTCTCAAGCTTCACCTGAGGTCTGGCCG
GGGCCCTGGCCTCAAACCCTGTCGAAGTTGTGAGAACACCTGTGATGAATCAGAGAGTCCTTCGAGATGGCACATGCTGT
GGCTACACGGGTACCCTGGATTGCTTGTTACAGACTTGGAAGAATGAAGGGCTTTTTGCTCTATATAAAGGGTTTTGGCC
AAATTGGTTGAGACTTGGACCTTGGAACATCATTTTCTTTGTGACATGTGAGCGGCTGAAGAAACTGGATTTG
ORF - retro_ecab_383 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 86.94 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MSALNWKPFVYGGLASITAECGTFPIDLTKTRLQIQGQTNDANFKEIRYRGMLHALVRIGREEGLKALYS |
| M.ALN.KPFVYGGLASI.AECGTFPIDLTK..LQIQ.QTNDAN.KEIRYRG.LHA.V.IGREEGLKAL.. | |
| Retrocopy | MAALNRKPFVYGGLASIPAECGTFPIDLTKMWLQIQWQTNDANLKEIRYRGVLHAFVTIGREEGLKAL*V |
| Parental | GIAPAMLRQASYGTIKIGTYQSLKRLFVERPEDETLLINVVCGILSGVISSTIANPTDVLKIRMQAQSST |
| GIAPAMLRQASYGT.KIGT.QSLKRLFVERPE.ETLLINVVCGILSGV.SS.IANPTDVLKIRMQAQSS. | |
| Retrocopy | GIAPAMLRQASYGTVKIGT*QSLKRLFVERPEGETLLINVVCGILSGVLSSAIANPTDVLKIRMQAQSSS |
| Parental | IQGGMIGNFINIYQQEGTRGLWKGVSLTAQRAAIVVGVELPVYDLTKKHLILSGLMGDTVYTHFLSSFTC |
| IQGGMIG.FIN.YQQEG.RGLWKGVSLTAQRA.IVVG.EL.V.DL.KKHLIL.GLMGD.V.THFLSSFT. | |
| Retrocopy | IQGGMIGSFINNYQQEGPRGLWKGVSLTAQRAPIVVGLELRVCDLAKKHLILWGLMGDPVSTHFLSSFT* |
| Parental | GLAGALASNPVDVVRTRMMNQRVLRDGSCPGYTGTLDCLLQTWKNEGFFALYKGFWPNWLRLGPWNIIFF |
| GLAGALASNPV.VVRT..MNQRVLRDG.C.GYTGTLDCLLQTWKNEG.FALYKGFWPNWLRLGPWNIIFF | |
| Retrocopy | GLAGALASNPVEVVRTPVMNQRVLRDGTCCGYTGTLDCLLQTWKNEGLFALYKGFWPNWLRLGPWNIIFF |
| Parental | VTYEQLKKLDL |
| VT.E.LKKLDL | |
| Retrocopy | VTCERLKKLDL |
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 | 7 .14 RPM |
| SRP021940_cerebellum | 0 .05 RPM | 12 .20 RPM |
| SRP021940_embryo | 0 .00 RPM | 12 .20 RPM |
| SRP021940_placental_villous | 0 .05 RPM | 9 .29 RPM |
| SRP021940_synovial_membrane | 0 .00 RPM | 7 .06 RPM |
| SRP021940_testis | 0 .13 RPM | 92 .33 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_383 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_383 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_383 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 | ENSECAG00000017334 | 1 retrocopy |
retro_ecab_383 ,
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