RetrogeneDB ID: | retro_btau_868 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 2:48559564..48560212(-) | ||
| 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: | ENSBTAG00000007570 | ||
| Aliases: | NDUFAF6, C14H8orf38 | ||
| Description: | NADH dehydrogenase (ubiquinone) complex I, assembly factor 6 [Source:UniProtKB/Swiss-Prot;Acc:A7YVD7] |
Retrocopy-Parental alignment summary:
>retro_btau_868
GAAAAAACTGTGAATGATTTATATTGTGACAGTCCACCACATCAGCGTGTGGCCACTGAACTATGGAAGGCTGTCAGAAA
ACATAATCTGACTAAAAGATGGCCTGTGAAAATCACTGATGAAAGAGAAAAGAATTTGGATGACAAAGTATATCATAACA
TCCAGAAACTAGGAAATTATGCTAAAAACACTCAGAGCTCTCTTCTTTATCTAACACTAGAAATATTGGGTATAAAGGAT
CTTCATGCAAATCATGCCACAAATCACACTGGAAAAACGCAAGGCATTGTCACTTGCTTGAGAGCAACACCCTGTCATGG
TAGCAGAAGAAAGCTGTCCCTTCCCATGGGTATTTGTATGCCGCGTGGTGTTTCACAAGAGGATTTTCTACAAAAGAGCC
AAAATGAAAATGTGAGAGATGTGGTGTATGACACTGCCAGCCAGGCACACTTGCACCTAAAGCATGCTAGGTCCTTCCAC
GAAAGTGTTCTTGTGAAAGCGTTTCCTGCTTTTGCACAGACAGTTGCTCTGGAGGACTATTTAAAGAAAATCCGACAAGT
GGATTTTGATCTATTCCACCCATCTTTACAGCAGAAGAATAGTTTACTTCCATTATCTTTATATATTCAGTCGTGGAGAA
AAAGATAT
ORF - retro_btau_868 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 81.94 % |
| Parental protein coverage: | 64.86 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | KKTVDDIYSDNPPHQPVAIELWKAVRRHNLTKRWLMKIIDEREKNLDDKAYRNIQELENYAENTQSSLLY |
| .KTV.D.Y.D.PPHQ.VA.ELWKAVR.HNLTKRW..KI.DEREKNLDDK.Y.NIQ.L.NYA.NTQSSLLY | |
| Retrocopy | EKTVNDLYCDSPPHQRVATELWKAVRKHNLTKRWPVKITDEREKNLDDKVYHNIQKLGNYAKNTQSSLLY |
| Parental | LTLEILGIKDLHADHAASHIGKAQGIVTCLRATPYHGSRRRVFLPMDICMLHGVSQEDFLRKSQDRNVRD |
| LTLEILGIKDLHA.HA..H.GK.QGIVTCLRATP.HGSRR...LPM.ICM..GVSQEDFL.KSQ..NVRD | |
| Retrocopy | LTLEILGIKDLHANHATNHTGKTQGIVTCLRATPCHGSRRKLSLPMGICMPRGVSQEDFLQKSQNENVRD |
| Parental | VVYDVASQAHLHLKHARSFHRSIPVKAFPAFLQTVALEDYLKKIQQVDFDLFHPSLQRKNTLLPLSLYIQ |
| VVYD.ASQAHLHLKHARSFH.S..VKAFPAF.QTVALEDYLKKI.QVDFDLFHPSLQ.KN.LLPLSLYIQ | |
| Retrocopy | VVYDTASQAHLHLKHARSFHESVLVKAFPAFAQTVALEDYLKKIRQVDFDLFHPSLQQKNSLLPLSLYIQ |
| Parental | SWRKRY |
| SWRKRY | |
| Retrocopy | SWRKRY |
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 |
|---|---|---|
| ERP005899_liver | 0 .00 RPM | 7 .43 RPM |
| ERP005899_muscle | 0 .00 RPM | 6 .39 RPM |
| SRP017611_brain | 0 .00 RPM | 14 .98 RPM |
| SRP017611_kidney | 0 .00 RPM | 18 .31 RPM |
| SRP017611_liver | 0 .00 RPM | 5 .89 RPM |
| SRP030211_testis | 0 .02 RPM | 10 .94 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_868 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_868 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_868 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000007570 | 1 retrocopy |
retro_btau_868 ,
|
| Canis familiaris | ENSCAFG00000009419 | 1 retrocopy | |
| Equus caballus | ENSECAG00000019146 | 1 retrocopy | |
| Oryctolagus cuniculus | ENSOCUG00000006635 | 1 retrocopy |