RetrogeneDB ID: | retro_cfam_1944 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 8:23701454..23702049(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
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_1944
TCCCACCTCCTAGCCATCATCTTGCCACTGCTCACAACCTGGAAGTCCGGCTCTTGTGCGGGGATTTCAGGGAAGAGCCA
GGTCCTGTTTGCTGTGTTCACTGGCCGGTACCTGGACCTCTTCACCAACTGCATCTCACTGTACAACAGGTGCATGAAGG
TGGTCTGCACTGCCTGATCCTTCACCACAGTCTGGCTGATTTACAGCAAGTTCAAAGCCACTTAGGATGGGAACCATGAC
ACATTCCGAGTGGAGTTCCCCGTTGTTCCCACGGCCATCCTGGCATTCCTGGTCAACCATGACTTCACCCTCTAGAGGTC
CTCTGGACCTTCTCCATCTACCTGGGGTCGGTAGCCATCCTGCCGCAGCCGTTCACGGTGAGCAAGAGGGCGGAGGCCGA
GACCATCCCCAGCCACTGCCCGTTTGCTCTGGGCGTCCACCGCTGCTTTCTCGCTTCCACTGGCTCTGGCGCTACCTCTC
CGAGGGCTTCTTCGACCTCATTGCCATCGTAGCAGGCCTAGTCCAGACTGTCCTCTACTGCGATTCCTTCCACCTCTACA
TCACCAAAGTCCTGAAGGGGAAGGAGCGGAGTTTG
ORF - retro_cfam_1944 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 68.81 % |
| Parental protein coverage: | 94.34 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | SHLAAIVILLLKIWKTRSCAGISGKSQLLFALVFTTRYLDLFTSFISLYNTSMKLIYIACSYATVYLIYM |
| SHL.AI...LL..WK..SCAGISGKSQ.LFA.VFT.RYLDLFT..ISLYN..MK....A.S..TV.LIY. | |
| Retrocopy | SHLLAIILPLLTTWKSGSCAGISGKSQVLFA-VFTGRYLDLFTNCISLYNRCMKVVCTA*SFTTVWLIYS |
| Parental | KFKATYDGNHDTFRVEFLVVPVGGLSFLVNHDFS-PLEILWTFSIYLESVAILPQLFMISKTGEAETITT |
| KFKAT.DGNHDTFRVEF.VVP...L.FLVNHDF..PLE.LWTFSIYL.SVAILPQ.F..SK..EAETI.. | |
| Retrocopy | KFKAT*DGNHDTFRVEFPVVPTAILAFLVNHDFT<PLEVLWTFSIYLGSVAILPQPFTVSKRAEAETIPS |
| Parental | HYLFFLGLYRA-LYLVNWIWRFYFEGFFDLIAVVAGVVQTILYCDFFYLYITKVLKGKKLSL |
| H..F.LG..R..L....W.WR...EGFFDLIA.VAG.VQT.LYCD.F.LYITKVLKGK..SL | |
| Retrocopy | HCPFALGVHRC<LSRFHWLWRYLSEGFFDLIAIVAGLVQTVLYCDSFHLYITKVLKGKERSL |
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 .08 RPM | 63 .42 RPM |
| SRP017611_brain | 0 .08 RPM | 40 .81 RPM |
| SRP017611_kidney | 0 .20 RPM | 123 .36 RPM |
| SRP017611_liver | 0 .07 RPM | 77 .44 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_1944 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_1944 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_1944 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 |