RetrogeneDB ID: | retro_cfam_1136 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 24:43667672..43668349(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PHAX | ||
| Ensembl ID: | ENSCAFG00000000590 | ||
| Aliases: | None | ||
| Description: | phosphorylated adaptor for RNA export [Source:HGNC Symbol;Acc:10241] |
Retrocopy-Parental alignment summary:
>retro_cfam_1136
CAGAGCAGCCAGAAACCACGTGTGCCTGGACCTAAGAAGGTGACACCATCCGGGGTGCTGGGCTACCGGAAGAGAATCGA
GGCGCAGTGGCCACTCGGTATCTTGGGAGTGGAGGGTGCTGTTGACAGAACCAGACGATGGGGGACCTACAATTATTTGC
TTGCTAGGAAACTTAAGAGGAAATCTTGAGAACATACAAAGGAATCAGACAAAGACCTAGATGAATAGAAGCGTGGTGGC
AAAAAAATGAGATCAAAGGGAGAGAAAAATGGGCGAGGTCACCTCACCCAGAACTGACCCGTTAAAGACAGGCCTGGGGA
CAGACTAGAAATGACCTGTACCGGCCAGTATCAGATCACGGAGGACGATCCACATGAGAAAGCGGCTGATAAAATTTCTT
TCGGGTTGCAGGCACCAAAGAAAGATCTGATAGCACAAGGAGTGAGGATAATTGGGAACAAAAAGGCAAATGAACTGATA
GAAATGCCAAAGTTGAACAAAATGCGGCTGGCCTTTTCATGATGGATGCTACTTGAAGAAGAACACCAGGTGGTGTTTTC
CCAGATCTCCTGGGAAACATTCCTAGTGTCGGCGAGGAACAAATTAAGGATGTTTTCTACACTGAAAATCAAAAGGAGTA
TGAACATGAAAAGGCTGCTAGGAAGAGAACACAAGTG
ORF - retro_cfam_1136 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 64.94 % |
| Parental protein coverage: | 62.91 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | QSSQKPLVPGGKKVNNIWGAVLQEQNQDAVATELGILGMEGTIDKSRQSETYNYLLAKKLKRESQEHTKE |
| QSSQKP.VPG.KKV......VL...........LGILG.EG..D..R...TYNYLLA.KLKR.S.EHTKE | |
| Retrocopy | QSSQKPRVPGPKKVTP--SGVLGYRKRIEAQWPLGILGVEGAVDRTRRWGTYNYLLARKLKRKS*EHTKE |
| Parental | LDKELDEYMHGGKKMGSKEEENGQGHLKRKRPVKDRLGDRLEMNYKGRYEITEDDAQEKVADEISFRLQE |
| .DK.LDE...GGKKM.SK.E.NG.GHL....PVKDR.GDRLEM...G.Y.ITEDD..EK.AD.ISF.LQ. | |
| Retrocopy | SDKDLDE*KRGGKKMRSKGEKNGRGHLTQN*PVKDRPGDRLEMTCTGQYQITEDDPHEKAADKISFGLQA |
| Parental | PKKDLIARVVRIIGNKKAIELLME-TAEVEQNG-GLFIMNGSRRRTPGGVFLNLLKNTPSISEEQIKDIF |
| PKKDLIA..VRIIGNKKA.E.L.E..A.VEQN..GLF.M....RRTPGGVF..LL.N.PS..EEQIKD.F | |
| Retrocopy | PKKDLIAQGVRIIGNKKANE-LIE<NAKVEQNAAGLFMMDAT*RRTPGGVFPDLLGNIPSVGEEQIKDVF |
| Parental | YIENQKEYENKKAARKRRTQV |
| Y.ENQKEYE..KAARK.RTQV | |
| Retrocopy | YTENQKEYEHEKAARK-RTQV |
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 | 11 .68 RPM |
| SRP017611_brain | 0 .00 RPM | 8 .26 RPM |
| SRP017611_kidney | 0 .00 RPM | 9 .97 RPM |
| SRP017611_liver | 0 .00 RPM | 4 .86 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_1136 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_1136 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_1136 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Ailuropoda melanoleuca | ENSAMEG00000010042 | 1 retrocopy | |
| Canis familiaris | ENSCAFG00000000590 | 2 retrocopies |
retro_cfam_1136 , retro_cfam_1701,
|
| Myotis lucifugus | ENSMLUG00000000184 | 1 retrocopy |