RetrogeneDB ID: | retro_cjac_350 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 5:102821719..102822097(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000022825 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ISCA1 | ||
| Ensembl ID: | ENSCJAG00000001940 | ||
| Aliases: | None | ||
| Description: | iron-sulfur cluster assembly 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:28660] |
Retrocopy-Parental alignment summary:
>retro_cjac_350
GATACTTCCTTAGTTGGGGCAACTGTCTGGGCTGTGTGTAAGAGGAAGCTGCAGCCCACCTGGGCCACCCTCACCCTAAC
ACTTTCAGCAGTAAGCAACATAAAACAATTTCTTAAAGATAACCCTGAGCATGTAGGTGTAAAAGCTGGTGTTCGAACCA
GGGCTGTAATGGCCTTTCTTATACTCTATACAAAGACAAGAAAAGATTCTGAGGAAGTTACACAAGATGGAATCAGAATA
TTCATTGAAAAGAAAGCACAGCCAACACTTTTAGGAACAGAAATAGACTACGCTGAAGACAAATTATCCAGTGAGTTTGT
GCCCAATAACCCAAACATGAAAGGAACTTGTGGCTGCGGAGAAAGTTTTAATATTTGA
ORF - retro_cjac_350 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 73.81 % |
| Parental protein coverage: | 71.59 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | SLVRATVRAVSKRKLQPTRAALTLTPAAVNKIKQLLKDKPEHVGVKVGVRTRGCNGLSYTLEYTKTKGDS |
| SLV.ATV.AV.KRKLQPT.A.LTLT..AV..IKQ.LKD.PEHVGVK.GVRTR..........YTKT..DS | |
| Retrocopy | SLVGATVWAVCKRKLQPTWATLTLTLSAVSNIKQFLKDNPEHVGVKAGVRTRAV--MAFLILYTKTRKDS |
| Parental | DEEVIQDGVRVFIEKKAQLTLLGTEMDYVEDKLSSEFVFNNPNIKGTCGCGESFNI |
| .EEV.QDG.R.FIEKKAQ.TLLGTE.DY.EDKLSSEFV.NNPN.KGTCGCGESFNI | |
| Retrocopy | -EEVTQDGIRIFIEKKAQPTLLGTEIDYAEDKLSSEFVPNNPNMKGTCGCGESFNI |
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 |
|---|---|---|
| SRP051959_colon | 0 .00 RPM | 9 .03 RPM |
| SRP051959_heart | 0 .00 RPM | 22 .63 RPM |
| SRP051959_kidney | 0 .00 RPM | 21 .76 RPM |
| SRP051959_liver | 0 .00 RPM | 18 .78 RPM |
| SRP051959_lung | 0 .00 RPM | 12 .44 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 10 .39 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 32 .41 RPM |
| SRP051959_spleen | 0 .00 RPM | 35 .00 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_350 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_350 was not experimentally validated.