RetrogeneDB ID: | retro_cjac_4114 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | X:108335383..108335681(+) | ||
| Located in intron of: | ENSCJAG00000004880 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PFDN4 | ||
| Ensembl ID: | ENSCJAG00000002615 | ||
| Aliases: | None | ||
| Description: | prefoldin subunit 4 [Source:HGNC Symbol;Acc:8868] |
Retrocopy-Parental alignment summary:
>retro_cjac_4114
GCTGCAGAAGATGTCAGTTCTACTCTTGAATATCAACAAAAGACAAACAAATTTGCAAGGAATGTGAGTAGAATCACAGC
GCTGAAGGAAGAAACAGAAGTAAAAAGGAAACAACTCCAAAATTTAGAGGATGCTTACGATGACATTCTGCTTGCAGATG
ATGACTGCTTAATGATACCTTATCAAATTGATGTTTATTAGCCTTTCTCAAGATGAATCACAAGAAATGCTAGAAGAGGC
AAAGAAAAATTGGCAAGAAGAAACTGATGCCTTAGAATCCAGAATGGTATCACTTCAG
ORF - retro_cjac_4114 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 68.63 % |
| Parental protein coverage: | 75.37 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | AAEDVNVTFEDQQKINKFARNTSRITELKEEIEVKKKQLQNLEDACDDIMLADDDCLMIPYQIGDVFISH |
| AAEDV..T.E.QQK.NKFARN.SRIT.LKEE.EVK.KQLQNLEDA.DDI.LADDDCLMIPYQI.DV.... | |
| Retrocopy | AAEDVSSTLEYQQKTNKFARNVSRITALKEETEVKRKQLQNLEDAYDDILLADDDCLMIPYQI-DVY*PF |
| Parental | SQ-EETQEMLEEAKKNLQEEIDALESRVESIQ |
| S..E......E..K.N.QEE.DALESR..S.Q | |
| Retrocopy | SR>ESQEMLEEAKK-NWQEETDALESRMVSLQ |
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 .07 RPM | 3 .00 RPM |
| SRP051959_heart | 0 .11 RPM | 4 .91 RPM |
| SRP051959_kidney | 0 .13 RPM | 4 .53 RPM |
| SRP051959_liver | 0 .11 RPM | 3 .55 RPM |
| SRP051959_lung | 0 .05 RPM | 5 .30 RPM |
| SRP051959_lymph_node | 0 .02 RPM | 4 .45 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 5 .55 RPM |
| SRP051959_spleen | 0 .06 RPM | 5 .06 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_4114 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_4114 was not experimentally validated.