RetrogeneDB ID: | retro_cfam_1063 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 22:4663137..4663376(-) | ||
| Located in intron of: | ENSCAFG00000004478 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SNAPC5 | ||
| Ensembl ID: | ENSCAFG00000017304 | ||
| Aliases: | None | ||
| Description: | small nuclear RNA activating complex, polypeptide 5, 19kDa [Source:HGNC Symbol;Acc:15484] |
Retrocopy-Parental alignment summary:
>retro_cfam_1063
ACGCTGCTCCGGCTGAAGGTGGCCCTGACGACCAGCTGAATCGGCTCAAGGTTGAAGAACTAGCCCTCCAGTCAATGATT
AGTTCGAGGAGAGGAGATGAGATGCTTTATTCTCACCTTGCACCTCAACAGTCACATGATATGCTGGTGCATGTGGACAA
TGAAGCATCAGTCACAACCAAACTGCACTGGAGTTGAGCACAAGATGTGCCCGAAGAGTAGTAGGAGGAAGAAGCAGAT
ORF - retro_cfam_1063 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 71.08 % |
| Parental protein coverage: | 82.0 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | TLLRLKAAL-HDQLNRLKVEELALQSMISSRRGDETLSSQPAPEQSHDQMLVHVDNEASINQTALELSTR |
| TLLRLK.AL..DQLNRLKVEELALQSMISSRRGDE.L.S..AP.QSHD.MLVHVDNEAS...T.L..S.. | |
| Retrocopy | TLLRLKVAL<DDQLNRLKVEELALQSMISSRRGDEMLYSHLAPQQSHD-MLVHVDNEASVT-TKLHWS*A |
| Parental | SHVLEEEEEEEEE |
| ..V.EE..EEE.. | |
| Retrocopy | QDVPEE**EEEAD |
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 | 5 .25 RPM |
| SRP017611_brain | 0 .08 RPM | 3 .26 RPM |
| SRP017611_kidney | 0 .00 RPM | 3 .50 RPM |
| SRP017611_liver | 0 .22 RPM | 1 .45 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_1063 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_1063 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_1063 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 12 parental genes, and 12 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000017304 | 1 retrocopy |
retro_cfam_1063 ,
|
| Callithrix jacchus | ENSCJAG00000007484 | 1 retrocopy | |
| Dasypus novemcinctus | ENSDNOG00000006689 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000003693 | 1 retrocopy | |
| Macropus eugenii | ENSMEUG00000003990 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000016841 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000032398 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000012935 | 1 retrocopy | |
| Oryctolagus cuniculus | ENSOCUG00000008791 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000010156 | 1 retrocopy | |
| Ictidomys tridecemlineatus | ENSSTOG00000009201 | 1 retrocopy | |
| Tupaia belangeri | ENSTBEG00000014333 | 1 retrocopy |