RetrogeneDB ID: | retro_cfam_439 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 11:6635557..6635965(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | FAM96A | ||
| Ensembl ID: | ENSCAFG00000017035 | ||
| Aliases: | None | ||
| Description: | family with sequence similarity 96, member A [Source:HGNC Symbol;Acc:26235] |
Retrocopy-Parental alignment summary:
>retro_cfam_439
GGAGCTGCCTGGCATCCGGGGACCATGGAAGAGGAAGCGCTAGGGGGTTATGATTTGATTCGAACTATCCGGGACCCAGA
GAAGCCCAATACTTTAGGAGACCTGGAAGTGGTAACAGAAAGTAATGTGAAGATTCAGGAAATAAATGAAGACTATCTGG
TTATTATCAGGTTCAGGCCAACAGTACCTCACTGCTCTTTGGCAACCCTTATTGGGCTGTGTTTATGAGAAAAACTTCAC
TGGTGTTTACCATTAAAACATAAGTTGGAAATCTACATTCCTGAAGGAACCCACTCAAAGGGGAAGACATCAACAAGCAG
ATAAATGACAAAGAGCGAGTGGCAGCTGCAATGGAAAACCCCAACCAACCTAAGGGAAATTGTGGAACAGTGTGTCCTTG
AACCTGAC
ORF - retro_cfam_439 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80.58 % |
| Parental protein coverage: | 83.95 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | GAARQPRIMEEKALEVYDLIRTIRDPEKPNTLEELEVVTESSVEVQEINEEDYLVIIRFTPTVPHCSLAT |
| GAA..P..MEE.AL..YDLIRTIRDPEKPNTL..LEVVTES.V..QEINE.DYLVIIRF.PTVPHCSLAT | |
| Retrocopy | GAAWHPGTMEEEALGGYDLIRTIRDPEKPNTLGDLEVVTESNVKIQEINE-DYLVIIRFRPTVPHCSLAT |
| Parental | LIGLCLRVKLQRCLPFKHKLEIYISEGTHSTE-EDINKQINDKERVAAAM-ENP-NLREIVEQCVLEPD |
| LIGLCL..KL..CLP.KHKLEIYI.EGTHS...EDINKQINDKERVAAAM...P.NLREIVEQCVLEPD | |
| Retrocopy | LIGLCL*EKLHWCLPLKHKLEIYIPEGTHSKG<EDINKQINDKERVAAAM>KTPTNLREIVEQCVLEPD |
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 | 21 .13 RPM |
| SRP017611_brain | 0 .00 RPM | 14 .61 RPM |
| SRP017611_kidney | 0 .00 RPM | 88 .03 RPM |
| SRP017611_liver | 0 .00 RPM | 49 .96 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_439 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_439 was not experimentally validated.