RetrogeneDB ID: | retro_cfam_23 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | X:57603524..57603962(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCAFG00000032517 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
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_23
ATGAGCAGTAAAGAATGTTTCAGGTGTGGACGCTCTGGCCACTGGGCCAGGGGATGCCCTAGAGTAGGAGGGAGTCGAGG
GCGCGGAGCTAGAGGCCGTGGCAGAGGTTCTCCGTGCAGTTCCACCAACCTACCTGACATCTGTTACCGCTGTGGTAAGT
CTGGTCATCATGCTAAGAATTGTGACCTTCTCGAGGACATCTGCTACAACTGTGGGAGAAGTGGCCACATCGCTAAAGAC
TGTATTGAGCCTAAAAGAGAGAGAGAGCAGTGCTGTTACACTTGTGGCCGACCAGGCCATCTGGCTCGTGATTGTGACCG
TCAGGAAGAGCAGAAGTGCTACTCTTGCGGTGAATATGGCCACATTCAGAAAGACTGCACCCAAGTTAAGTGTTACCGTT
GTGGCGAGACAGGCCACGTGGCCATCAACTGCAGCAAA
ORF - retro_cfam_23 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 78.23 % |
| Parental protein coverage: | 69.27 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | SRGRGGFTSDRGFQFVSSSLPDICYRCGESGHLAKDCDLQEDVEACYNCGRGGHIAKDCKEPKREREQCC |
| SRGRG.....RG....S..LPDICYRCG.SGH.AK.CDL.ED...CYNCGR.GHIAKDC.EPKREREQCC | |
| Retrocopy | SRGRGARGRGRGSPCSSTNLPDICYRCGKSGHHAKNCDLLEDI--CYNCGRSGHIAKDCIEPKREREQCC |
| Parental | YNCGKPGHLARDCDHADEQKCYSCGEFGHIQKDCTKVKCYRCGETGHVAINCSK |
| Y.CG.PGHLARDCD...EQKCYSCGE.GHIQKDCT.VKCYRCGETGHVAINCSK | |
| Retrocopy | YTCGRPGHLARDCDRQEEQKCYSCGEYGHIQKDCTQVKCYRCGETGHVAINCSK |
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_23 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_23 was not experimentally validated.