RetrogeneDB ID: | retro_cfam_316 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 1:67721857..67722685(-) | ||
| Located in intron of: | ENSCAFG00000001106 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | THOC6 | ||
| Ensembl ID: | ENSCAFG00000019317 | ||
| Aliases: | None | ||
| Description: | THO complex 6 homolog (Drosophila) [Source:HGNC Symbol;Acc:28369] |
Retrocopy-Parental alignment summary:
>retro_cfam_316
AAGAAGCCAGTGGTGACATTCCAAGCCCATGATGGGCCGGTCTACAGCATGGTCTCCACGGATCGACATCTGCTCAGTGC
TGGGGATGGGGAAGTGAAGGCCTGGCTTTGGGCAGAGATCCTCAAGAAGGGTTGTAAGGAGCTGTGGCAGCGTCAGCCCC
CATACAGGACCAGCCTAGAAGTGCCTGAGATCAATGCTTTGCTTCTCGTCCCCAAGGAGAATTCTCTCATCCTGGCAGGG
GGAGACTGTCAGTTGCATACGATGGACCTTGAGACCGGGACCTTCACACGGGCCCTCCGGGGCCACACAGACTATGTCCA
CTGCCTGGCACTGCGGGAGCGGAGTCCTGAGGTGCTGTCAGGTGGAGAGGATGGAGCCGTGCGACTTTGGGACCTCCGCA
CAGCCAAGGAAGTCCAGACCATTGAGGTATGTAAGCATGAGGAGTGCTCGAGGCCACACAATGGGCGTTGGATCGGCTGT
TTGGCCACTGACTCAGACTGGATGGTCTGTGGAGGAGGCCCAGCACTCACCCTCTGGCACCTCCGATCCTCCACACCCAC
AACTATTTTCCCCATACGGGCGCCACAGAAACACGTCACCTTCTACCAGGACCTGATTCTGTCAGCTGGCCAGGGCCTCT
GTGTCAACCAGTGGCAGCTGAGTGGGGAGCTCAAGGCGCAGGTGCCTGGCTCCTCCCTAGGGCTGCTCAGCCTCAGTCTC
AACCAGCAGCCAGCAGCACCCGAGTGCAAGGTCCTGACAGACACAGGTAACAGCTGCCGCATGGATGTCTTCACGAATCT
CGGCTACCGCGCCTTCCCCTTGTCCTTC
ORF - retro_cfam_316 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 96.01 % |
| Parental protein coverage: | 80.94 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | KKPVVTFQAHDGPVYSMVSTDRHLLSAGDGEVKAWLWAEILKKGCKELWRRQPPYRTSLEVPEINALLLV |
| KKPVVTFQAHDGPVYSMVSTDRHLLSAGDGEVKAWLWAEILKKGCKELW.RQPPYRTSLEVPEINALLLV | |
| Retrocopy | KKPVVTFQAHDGPVYSMVSTDRHLLSAGDGEVKAWLWAEILKKGCKELWQRQPPYRTSLEVPEINALLLV |
| Parental | PKENSLILAGGDCQLHTMDLETGTFTRALRGHTDYVHCLALRERSPEVLSGGEDGAVRLWDLRTAKEVQT |
| PKENSLILAGGDCQLHTMDLETGTFTRALRGHTDYVHCLALRERSPEVLSGGEDGAVRLWDLRTAKEVQT | |
| Retrocopy | PKENSLILAGGDCQLHTMDLETGTFTRALRGHTDYVHCLALRERSPEVLSGGEDGAVRLWDLRTAKEVQT |
| Parental | IEVYKHEECSRPHNGRWISCLATDSDWMVCGGGPALTLWHLRSSTPTTIFPIRVPQKHVTFYQDLILSAG |
| IEV.KHEECSRPHNGRWI.CLATDSDWMVCGGGPALTLWHLRSSTPTTIFPIR.PQKHVTFYQDLILSAG | |
| Retrocopy | IEVCKHEECSRPHNGRWIGCLATDSDWMVCGGGPALTLWHLRSSTPTTIFPIRAPQKHVTFYQDLILSAG |
| Parental | QGRCVNQWQLSGELKAQVPGSSPGLLSLSLNQQPAAPECKVLTAAGNSSRVDVFTNLGYRAFSLSF |
| QG.CVNQWQLSGELKAQVPGSS.GLLSLSLNQQPAAPECKVLT..GNS.R.DVFTNLGYRAF.LSF | |
| Retrocopy | QGLCVNQWQLSGELKAQVPGSSLGLLSLSLNQQPAAPECKVLTDTGNSCRMDVFTNLGYRAFPLSF |
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 | 14 .91 RPM |
| SRP017611_brain | 0 .00 RPM | 8 .26 RPM |
| SRP017611_kidney | 0 .00 RPM | 7 .99 RPM |
| SRP017611_liver | 0 .00 RPM | 4 .57 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_316 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_316 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_316 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000019317 | 1 retrocopy |
retro_cfam_316 ,
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