RetrogeneDB ID: | retro_cfam_1272 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 28:6412038..6412392(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CNBP | ||
| Ensembl ID: | ENSCAFG00000004320 | ||
| Aliases: | None | ||
| Description: | Canis lupus familiaris CCHC-type zinc finger, nucleic acid binding protein (CNBP), transcript variant 1, mRNA. [Source:RefSeq mRNA;Acc:NM_001252264] |
Retrocopy-Parental alignment summary:
>retro_cfam_1272
ATGAGCAGCAACAAATGTTTCAAGTGTGGACCATCTAGCTATTGGGCCCCGGAATGCTCTACTGGTGGAGGCTGTGGTCA
TGGAACGAGAAGTCATGGCAGAGGTGGTTTTACCTCCAATAGAGATTTCCAGTTTGTTTCCTTATCTCTTCCAGACACCT
GTTATCACTGTGGTAAGTCTGGTTATCTTCCAAGAATTGTGATCTTCAAAAGGATGCCTCCTGTAATTGCACTAGAGGTG
GCCTCATGATCAAGGACTGCCAGGAGCCTGAAAGAGAAAGAGCAATGCTGCTACCACTGTGGCAAACTAGGCCATTTGTC
TCATGACTGTGACCATGCGGATAAGCAGAAGTGC
ORF - retro_cfam_1272 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 67.48 % |
| Parental protein coverage: | 67.6 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | MSSNECFKCGRSGHWARECPTGGGRGRGMRSRGRGGFTSDRGFQFVSSSLPDICYRCGESGHL-AKDCDL |
| MSSN.CFKCG.S..WA.EC.TGGG.G.G.RS.GRGGFTS.R.FQFVS.SLPD.CY.CG.SG.L..K.CDL | |
| Retrocopy | MSSNKCFKCGPSSYWAPECSTGGGCGHGTRSHGRGGFTSNRDFQFVSLSLPDTCYHCGKSGYL<SKNCDL |
| Parental | QEDVEACYNCGRGGHIAKDCKEPKRER-EQCCYNCGKPGHLARDCDHADEQKC |
| Q.D..A..NC.RGG...KDC.EP.RER...C.Y.CGK.GHL..DCDHAD.QKC | |
| Retrocopy | QKD--ASCNCTRGGLMIKDCQEPERER>QCC-YHCGKLGHLSHDCDHADKQKC |
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 | 281 .52 RPM |
| SRP017611_brain | 0 .00 RPM | 156 .16 RPM |
| SRP017611_kidney | 0 .00 RPM | 330 .52 RPM |
| SRP017611_liver | 0 .00 RPM | 100 .29 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_1272 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_1272 was not experimentally validated.