RetrogeneDB ID: | retro_ecab_141 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 1:120956445..120957041(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | NDUFAF6 | ||
| Ensembl ID: | ENSECAG00000019146 | ||
| Aliases: | None | ||
| Description: | NADH dehydrogenase (ubiquinone) complex I, assembly factor 6 [Source:HGNC Symbol;Acc:28625] |
Retrocopy-Parental alignment summary:
>retro_ecab_141
TGGAAAGCTGCTGTCAAGAAACATAATTTGACTAAAAGATGGCTTATGAGAGTCATTGATGAAGGAGAAAAAAATTGGAT
GACAAAGCATATTGCAATATCCAGGAACTGGAAAATTATGCTGAAAACACACAGAACTCTCTTCTTTATTTGACACCAGA
AATATTGGGTATAATGACCTTCATGAAGATCATGTCACAAGCCACACTGGAAAAGCACAAGGTATTGTCACATGCTTGAG
AGCAACGTCCTATAGTGGTAGCAGAAGAAGGGTGTGCCCTCCCTTGAATATTTATATCTTTGACCAATACAACACATGGG
GTTTCACAAGAGGATGTTCTATGAAGAACCGAGGTAAAAATGTGAGAGATGCAATATATGTCATTTCTAGCCAGGCCTAC
TTGCACTGACAGCAGGCTAGGTCCTTACATACAAAGTGTTCTTGTGAAAGCATTTCCTATTTTTCTTCTGGTTCCTCTGG
AGGACTATTTAGAGAAAATTCAACAAGTGGATTTTAATATATTCCACCCATCTTTACAGGAGAAGAATACATTGCTTCCA
TTATCTTTGTATGTTCAGTCATAGAAAAAAAGATAT
ORF - retro_ecab_141 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 69.95 % |
| Parental protein coverage: | 72.76 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | WKA-VKKHNLTKRWLMKIVDEREKN-LDDKAYRNIQELESYAENTQSSLLYLTLEILGI-KDLHADHAAS |
| WKA.VKKHNLTKRWLM...DE.EKN.LDDKAY.NIQELE.YAENTQ.SLLYLT.EILGI..DLH.DH..S | |
| Retrocopy | WKAAVKKHNLTKRWLMRVIDEGEKN<LDDKAYCNIQELENYAENTQNSLLYLTPEILGI<NDLHEDHVTS |
| Parental | HIGKAQGIVTCLRAMPYHGSRRRVFLPMDICMLHGVSQEDFLR----KNRDKNVRDVIYDIASQAHLHLK |
| H.GKAQGIVTCLRA..Y.GSRRRV..P..I..........F.R....KNR.KNVRD.IY.I.SQA.LH.. | |
| Retrocopy | HTGKAQGIVTCLRATSYSGSRRRVCPPLNIYIFDQYNTWGFTRGCSMKNRGKNVRDAIYVISSQAYLH*Q |
| Parental | HARSFH-KSVPVKAFPAFLQTVALEDYLKKIQQVDFDIFHPSLQQKNTLLPLSLYIRSWRKRY |
| .ARS.H..SV.VKAFP.FL..V.LEDYL.KIQQVDF.IFHPSLQ.KNTLLPLSLY..S..KRY | |
| Retrocopy | QARSLH>QSVLVKAFPIFL-LVPLEDYLEKIQQVDFNIFHPSLQEKNTLLPLSLYVQS*KKRY |
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 | 0 .47 RPM |
| SRP021940_cerebellum | 0 .00 RPM | 2 .54 RPM |
| SRP021940_embryo | 0 .00 RPM | 3 .27 RPM |
| SRP021940_placental_villous | 0 .00 RPM | 3 .70 RPM |
| SRP021940_synovial_membrane | 0 .00 RPM | 2 .11 RPM |
| SRP021940_testis | 0 .00 RPM | 1 .02 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_141 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_141 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_141 has 1 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Canis familiaris | retro_cfam_1423 |
Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000007570 | 1 retrocopy | |
| Canis familiaris | ENSCAFG00000009419 | 1 retrocopy | |
| Equus caballus | ENSECAG00000019146 | 1 retrocopy |
retro_ecab_141 ,
|
| Oryctolagus cuniculus | ENSOCUG00000006635 | 1 retrocopy |