RetrogeneDB ID: | retro_cfam_1644 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 4:13351930..13352495(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCAFG00000012971 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | FAM57A | ||
| Ensembl ID: | ENSCAFG00000019129 | ||
| Aliases: | None | ||
| Description: | family with sequence similarity 57, member A [Source:HGNC Symbol;Acc:29646] |
Retrocopy-Parental alignment summary:
>retro_cfam_1644
CACTGGCTTGCCCGAGAGTATGTCTGGTTCTTGATTCCGTACATGATCTGTGACTTCTATGCCATGTACCTCTGTGAGTG
GTACCGAACCAGAGACCAGAACCACAGACACTCCCTCACCACTTTTCGAAACTTCCTAAGTAAAAACCACCTCATGGTCA
TGCACCACACAGTCATCCTGTTTGTCCTTGTGCCAGTTTCACAGAGGCTTAGGGGAGACCTTGGAGACTTCTTTGTTGGC
TGCATCTTCATGGCAAAACTGAGCACTCCGTTTGTGTTACTGGGCAGAGTCCTGATTCAGCTAAAGCAGCAGCACACCCT
TCTGTACAAAGTGAACGGAATCCTCATGCTGACCACCTTCCTTTCCTGTCGGATCCTCCTCTTCCCTTTCATGTACAGGT
CTTATGGCCAACAGCAGGGACTCAGCCCACTCTGAGTGCCATTCAGCATCCCTTTACTGCAATGTGGCCAATGCCTTCCT
CATTGCTCCCCAGATCTACTGGTTCTCTCTGCTGTGCAAGAAAGCAACCCGGCTCTTTGACACCGCCCCAGCCAAAAAGG
ATGGC
ORF - retro_cfam_1644 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 93.19 % |
| Parental protein coverage: | 73.26 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | HWLAREYVWFLIPYMIYDSYAMYLCEWYRTRDQNHRHSLTTFRNFLSKNRLMVAHHAVILFVLVPVAQRL |
| HWLAREYVWFLIPYMI.D.YAMYLCEWYRTRDQNHRHSLTTFRNFLSKN.LMV.HH.VILFVLVPV.QRL | |
| Retrocopy | HWLAREYVWFLIPYMICDFYAMYLCEWYRTRDQNHRHSLTTFRNFLSKNHLMVMHHTVILFVLVPVSQRL |
| Parental | RGDLGDFFVGCIFMAELSTPFVSLGRVLIQLKQQHTLLYKVNGILTLTTFLSCRILLFPFMYWSYGQQQG |
| RGDLGDFFVGCIFMA.LSTPFV.LGRVLIQLKQQHTLLYKVNGIL.LTTFLSCRILLFPFMY.SYGQQQG | |
| Retrocopy | RGDLGDFFVGCIFMAKLSTPFVLLGRVLIQLKQQHTLLYKVNGILMLTTFLSCRILLFPFMYRSYGQQQG |
| Parental | LSPLRVPFSI-PF-YCNVANAFLIAPQIYWFSLLCKKATRLFDTAPAKKDG |
| LSPL.VPFSI.PF.YCNVANAFLIAPQIYWFSLLCKKATRLFDTAPAKKDG | |
| Retrocopy | LSPL*VPFSI<PF<YCNVANAFLIAPQIYWFSLLCKKATRLFDTAPAKKDG |
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 .04 RPM | 43 .34 RPM |
| SRP017611_brain | 0 .00 RPM | 12 .70 RPM |
| SRP017611_kidney | 0 .00 RPM | 11 .82 RPM |
| SRP017611_liver | 0 .00 RPM | 6 .82 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_1644 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_1644 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_1644 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000019129 | 1 retrocopy |
retro_cfam_1644 ,
|
| Echinops telfairi | ENSETEG00000019235 | 1 retrocopy | |
| Loxodonta africana | ENSLAFG00000017562 | 1 retrocopy | |
| Microcebus murinus | ENSMICG00000009347 | 1 retrocopy |