RetrogeneDB ID: | retro_cfam_318 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 1:70421911..70422546(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCAFG00000001208 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | KDELR2 | ||
| Ensembl ID: | ENSCAFG00000015746 | ||
| Aliases: | None | ||
| Description: | KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 2 [Source:HGNC Symbol;Acc:6305] |
Retrocopy-Parental alignment summary:
>retro_cfam_318
ATGAATCTCTTCTGATTCCTGGGAGACCTCTCCCACCTCCTAGCCATCATCTTGCTACCGCTTAAAATCTGGAAGTCCCG
CTCTTGTGCCGGGATTTCAGGGAAGAGCCAGGTCCTGTTTGCTGTGGTGTTCACTGCCCGGTACCTGGACCTCCTCACCA
ACTACATCTCACTGTACAACACGTACATGAAGGTGGTCTACATTGCCTGTTCCTTCACCACAGTCTGGATGATTTACAGC
AAGTTCAAAGCCACTTATGATGGGAACCATGACACATTCCGAGTGGAGTTCCTCGTTGTTCCCACGGCCATCCTGGCATT
CCTGGTCAACCATGACTTTACCCTCTAGAGATCCTCTGGACCTTCTCCATCTACCTGGAGTTGGTAGCCATCCTGCCACA
GCTGTTCACGGTGAGCAAGACGGGGAAGGCAGAGACCATCACCAGCCACTACCTGTTTGCTCTGGGCGTCTACCGCACGC
TTTATCTCTGCAACTGGATCTGGCGCTACCACTTCGAGGGCTTCTTCGACCTCATTGCCATCGTAGCAGGCCTAGTCCAG
ACTGTCCTCTACTGCGATTTCTTCTACCTCTACATCACCAAAGTCCTGAAGGGGAAGAAGCTGAGTTTGCCGGCG
ORF - retro_cfam_318 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 79.81 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MNIFRLTGDLSHLAAIVILLLKIWKTRSCAGISGKSQLLFALVFTTRYLDLFTSFISLYNTSMKLIYIAC |
| MN.F...GDLSHL.AI..L.LKIWK.RSCAGISGKSQ.LFA.VFT.RYLDL.T..ISLYNT.MK..YIAC | |
| Retrocopy | MNLF*FLGDLSHLLAIILLPLKIWKSRSCAGISGKSQVLFAVVFTARYLDLLTNYISLYNTYMKVVYIAC |
| Parental | SYATVYLIYMKFKATYDGNHDTFRVEFLVVPVGGLSFLVNHDFS-PLEILWTFSIYLESVAILPQLFMIS |
| S..TV..IY.KFKATYDGNHDTFRVEFLVVP...L.FLVNHDF..PLEILWTFSIYLE.VAILPQLF..S | |
| Retrocopy | SFTTVWMIYSKFKATYDGNHDTFRVEFLVVPTAILAFLVNHDFT<PLEILWTFSIYLELVAILPQLFTVS |
| Parental | KTGEAETITTHYLFFLGLYRALYLVNWIWRFYFEGFFDLIAVVAGVVQTILYCDFFYLYITKVLKGKKLS |
| KTG.AETIT.HYLF.LG.YR.LYL.NWIWR..FEGFFDLIA.VAG.VQT.LYCDFFYLYITKVLKGKKLS | |
| Retrocopy | KTGKAETITSHYLFALGVYRTLYLCNWIWRYHFEGFFDLIAIVAGLVQTVLYCDFFYLYITKVLKGKKLS |
| Parental | LPA |
| LPA | |
| Retrocopy | LPA |
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 | 3 .65 RPM | 63 .42 RPM |
| SRP017611_brain | 2 .94 RPM | 40 .81 RPM |
| SRP017611_kidney | 7 .26 RPM | 123 .36 RPM |
| SRP017611_liver | 5 .51 RPM | 77 .44 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_318 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_318 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_318 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 5 parental genes, and 6 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000015746 | 2 retrocopies |
retro_cfam_1944, retro_cfam_318 ,
|
| Choloepus hoffmanni | ENSCHOG00000000125 | 1 retrocopy | |
| Dasypus novemcinctus | ENSDNOG00000009897 | 1 retrocopy | |
| Echinops telfairi | ENSETEG00000016544 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000007832 | 1 retrocopy |