RetrogeneDB ID: | retro_cfam_868 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 19:22809819..22810309(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCAFG00000004335 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ISOC2 | ||
| Ensembl ID: | ENSCAFG00000002580 | ||
| Aliases: | None | ||
| Description: | isochorismatase domain containing 2 [Source:HGNC Symbol;Acc:26278] |
Retrocopy-Parental alignment summary:
>retro_cfam_868
ATGGCAACTGTGAGGTCCAACCTGGGCTGAGTCCTCCCTGGATCATCCATCCTGTTCCTGTGTGACATGCAGAAGCTCTG
CCAAATCGCATACTTTCCCCATATTGTCTCTGTGGCTGCCATGCTCAAGGTGGCCAGGCTGCTGGAGGTACCTACCAGCT
GTGCTGACAGAGCAGTACCCAGAAGTCCTGGGCCCCACAGGCCCCAAGCTGGGGGCTCAAGGCCTGCAGCCAGTAGCCAA
AACTTGCTTCAGCATGGTGCCTGCAGTGCAACGGGAGCTGGATACATGGCCCCAGCTGTGTTCTGTGCTCCTCTGTGGCA
TTGAGACACAGGCCTGCATCCTGAATACCACCCTGGACCTCTTGGACCGGGGGCTGCAGGTCCATGTGGTGGTGGACGGC
TGCTCTTCTCGAAGCCAGGTGGACAGGCTAGTAGCCCTGGCCAGGATGCGGCAGAGTAGCGCCTTCCTCTCCACCAGCAA
AGGGCTGATT
ORF - retro_cfam_868 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 82.53 % |
| Parental protein coverage: | 80.39 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MATMRSNLGRVLPGSSILFLCDMQEKFRHIAYFPQIVSVAARMLKVARLLEVPAVLTEQ-YPEGLG-PTV |
| MAT.RSNLG.VLPGSSILFLCDMQ.K...IAYFP.IVSVAA.MLKVARLLEVP........P...G.PT. | |
| Retrocopy | MATVRSNLG*VLPGSSILFLCDMQ-KLCQIAYFPHIVSVAA-MLKVARLLEVPTSCADRAVPRSPG>PTG |
| Parental | PELGAQGLRPVAKTCFSMVPAVQKELESRPQLCSVLLCGIETQACILNTTLDLLDRGLQVHVVVDGCSSR |
| P.LGAQGL.PVAKTCFSMVPAVQ.EL...PQLCSVLLCGIETQACILNTTLDLLDRGLQVHVVVDGCSSR | |
| Retrocopy | PKLGAQGLQPVAKTCFSMVPAVQRELDTWPQLCSVLLCGIETQACILNTTLDLLDRGLQVHVVVDGCSSR |
| Parental | SQVDRLVALARMRQSGAFLSTSEGLI |
| SQVDRLVALARMRQS.AFLSTS.GLI | |
| Retrocopy | SQVDRLVALARMRQSSAFLSTSKGLI |
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 | 23 .77 RPM |
| SRP017611_brain | 0 .00 RPM | 17 .70 RPM |
| SRP017611_kidney | 0 .00 RPM | 34 .60 RPM |
| SRP017611_liver | 0 .00 RPM | 11 .96 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_868 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_868 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_868 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 | ENSCAFG00000002580 | 1 retrocopy |
retro_cfam_868 ,
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