RetrogeneDB ID: | retro_cfam_1423 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 30:35873706..35874233(-) | ||
| 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: | ENSCAFG00000009419 | ||
| Aliases: | None | ||
| Description: | NADH dehydrogenase (ubiquinone) complex I, assembly factor 6 [Source:HGNC Symbol;Acc:28625] |
Retrocopy-Parental alignment summary:
>retro_cfam_1423
GCTATCAAAAGATATACTCTGATCAAAATATGGCTTATGAAAACCATTGGTAGAAGAGACAAAATTCGGATGACAAAGCA
TATCATAACATCCAAGAACTGAAAAATTATGCTGAAAATGCACAAAACTCTCTCTTCATTTAACACTGGAAGTATGGGGT
AAAAAGGAACTTCATACAGACCATGCCCAAGTCACACTGGAAAAGCACAGGGCATTGTCACATGCTTGAGAACAACGCCC
TATCATGGTAGCAGAAGAAGGGTGTTCCTTCCCTTGGATATTTGCATGTTTGACAAACACAATACATGGTGTTTCTCTTG
GAAGAACCAAGATATAAATCTGAGAGATGAAATATTTATGTCCTTGCTGGCCCAGCATGCTGGGCACTTAAAGCATGCTA
GACCTTTCGACAAAAGTGTTCTCATGAAAACATTTCCTGCTTTTCTTTGAATTGCTCTGGAGGACTGCTTAAAGAAAGTT
CAACAAAGAATTTTTATATATTCCACCCATCTTCACAGCAGAAGAAT
ORF - retro_cfam_1423 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 63.19 % |
| Parental protein coverage: | 52.99 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | AVKRHNLTKRWLMKIIDEREK-NLDDKAYRNIQELENYAENTQSSL-LYLTLEILGVKDLHADHAA-SHI |
| A.KR..L.K.WLMK.I..R.K.N.DDKAY.NIQEL.NYAEN.Q.SL.L.LTLE..G.K.LH.DHA..SH. | |
| Retrocopy | AIKRYTLIKIWLMKTIGRRDK<NSDDKAYHNIQELKNYAENAQNSL<LHLTLEVWGKKELHTDHAQ<SHT |
| Parental | GKAQGIVTCLRATPYHGSRRRVFLPMDICMLHGVSQEDFLRKNQDKNVRDVIY-DIASQAHLHLKHARSF |
| GKAQGIVTCLR.TPYHGSRRRVFLP.DICM........F..KNQD.N.RD.I......Q...HLKHAR.F | |
| Retrocopy | GKAQGIVTCLRTTPYHGSRRRVFLPLDICMFDKHNTWCFSWKNQDINLRDEIFMSLLAQHAGHLKHARPF |
| Parental | HKSVPVKAFPAFLQTVALENYLKRIQQ-VDFDIFHPSLQQKD |
| .KSV..K.FPAFL...ALE..LK..QQ...F.IFHPS.QQK. | |
| Retrocopy | DKSVLMKTFPAFL-*IALEDCLKKVQQ<KNFYIFHPSSQQKN |
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 |
|---|---|---|
| SRP012049_cerebellum | 0 .00 RPM | 14 .83 RPM |
| SRP017611_brain | 0 .00 RPM | 18 .50 RPM |
| SRP017611_kidney | 0 .00 RPM | 17 .04 RPM |
| SRP017611_liver | 0 .00 RPM | 3 .99 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_1423 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_1423 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_1423 has 1 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Equus caballus | retro_ecab_141 |
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 |
retro_cfam_1423 ,
|
| Equus caballus | ENSECAG00000019146 | 1 retrocopy | |
| Oryctolagus cuniculus | ENSOCUG00000006635 | 1 retrocopy |