RetrogeneDB ID: | retro_cfam_776 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 17:36535784..36536309(-) | ||
| Located in intron of: | ENSCAFG00000007149 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ERCC1 | ||
| Ensembl ID: | ENSCAFG00000004448 | ||
| Aliases: | None | ||
| Description: | excision repair cross-complementing rodent repair deficiency, complementation group 1 (includes overlapping antisense sequence) [Source:HGNC Symbol;Acc:3433] |
Retrocopy-Parental alignment summary:
>retro_cfam_776
CAGAGGGGCAACCCTGTGCTGAAGTTTGTGCGGAATGTGCCCTGGGAATTTGGTGACGTGCTTCCCGACTATGTGCTGGG
CCAGAGCACCTGTGCCCTGTTCCTCAGCCTCCGCTACCACAATCTCCACCCGGACTACCTCCACGAGCGGCTGCAGAGCC
TGGGGAAGAGTTTTGCGCTGCGGGTCCTGCTGGTCCAGGTGGACGTGAAAGATCCTCAGCAGGCCCTCAAGGAGCTGGCT
AAGATGTGCATCCTGGCCTACTGCACCCTGGTCCTCGCCTGGAGCCCCGAGGAGGCTGGGCGGTACCTGGAGACTTACAA
AGCCTATGAGCAGAAGCCGGCCAACCTCCTGATGGAGAAGCTGGAGCAGGACTTCGTCTCCCGGGTGACTGAATGCCTGA
CCACCGTGAAGTCAGTCAATAAAACAGACAGCCAGACCCTCCTGACAACTTTTGGGTCTCTGGAACAGCTCATGACCGCA
TCGAGGGAAGATCTGGCTTTGTGTCCAGGCCTGGGGCCCCAGAAG
ORF - retro_cfam_776 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 97.71 % |
| Parental protein coverage: | 54.18 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | QRGNPVLKFVRNVPWEFGDVLPDYVLGQSTCALFLSLRYHNLHPDYIHERLQSLGKSFALRVLLVQVDVK |
| QRGNPVLKFVRNVPWEFGDVLPDYVLGQSTCALFLSLRYHNLHPDY.HERLQSLGKSFALRVLLVQVDVK | |
| Retrocopy | QRGNPVLKFVRNVPWEFGDVLPDYVLGQSTCALFLSLRYHNLHPDYLHERLQSLGKSFALRVLLVQVDVK |
| Parental | DPQQALKELAKMCILADCTLVLAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLTTVKSVN |
| DPQQALKELAKMCILA.CTLVLAWSPEEAGRYLETYKAYEQKPA.LLMEKLEQDFVSRVTECLTTVKSVN | |
| Retrocopy | DPQQALKELAKMCILAYCTLVLAWSPEEAGRYLETYKAYEQKPANLLMEKLEQDFVSRVTECLTTVKSVN |
| Parental | KTDSQTLLTTFGSLEQLMAASREDLALCPGLGPQK |
| KTDSQTLLTTFGSLEQLM.ASREDLALCPGLGPQK | |
| Retrocopy | KTDSQTLLTTFGSLEQLMTASREDLALCPGLGPQK |
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 .71 RPM | 12 .77 RPM |
| SRP017611_brain | 0 .00 RPM | 11 .04 RPM |
| SRP017611_kidney | 0 .26 RPM | 16 .18 RPM |
| SRP017611_liver | 0 .00 RPM | 6 .74 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_776 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_776 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_776 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Anolis carolinensis | ENSACAG00000014643 | 2 retrocopies | |
| Canis familiaris | ENSCAFG00000004448 | 1 retrocopy |
retro_cfam_776 ,
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