General information for g3854.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Pre-mRNA cleavage complex 2 protein Pcf11.
Parent gene
- The parent gene g3854 is located on chr_3: 28372690..28379817 (+ strand)
Gene structure
- The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.
| Chromosome | Gene | Transcript | Category | ID | Start | End |
|---|---|---|---|---|---|---|
| chr_3 | g3854 | g3854.t4 | TSS | g3854.t4 | 28371998 | 28371998 |
| chr_3 | g3854 | g3854.t4 | isoform | g3854.t4 | 28372120 | 28374342 |
| chr_3 | g3854 | g3854.t4 | exon | g3854.t4.exon1 | 28372120 | 28372126 |
| chr_3 | g3854 | g3854.t4 | exon | g3854.t4.exon2 | 28372594 | 28372854 |
| chr_3 | g3854 | g3854.t4 | cds | g3854.t4.CDS1 | 28372690 | 28372854 |
| chr_3 | g3854 | g3854.t4 | exon | g3854.t4.exon3 | 28374130 | 28374255 |
| chr_3 | g3854 | g3854.t4 | cds | g3854.t4.CDS2 | 28374130 | 28374255 |
| chr_3 | g3854 | g3854.t4 | exon | g3854.t4.exon4 | 28374324 | 28374342 |
| chr_3 | g3854 | g3854.t4 | cds | g3854.t4.CDS3 | 28374324 | 28374341 |
| chr_3 | g3854 | g3854.t4 | TTS | g3854.t4 | NA | NA |
Sequences
>g3854.t4 Gene=g3854 Length=413
CCTAAAGATTAAATTTAATCAGCCTGTATAGAATCGAGAAAACTTGTGATTGTGTATTTT
ATAAAATTGTAAAGAGTTTGTAAACATTTCAATCATCAAAAATATGGACTCTGTAAAGGA
AAAGGAAATTGAAGAGGAGTATCTTTCTTCTTTAATGGATCTTAATGTCAATAGTAAACC
CCTAATCAATATGCTAACAATGTTAGCCGAGGACAATCTCGAAAATGCAGCTATTATCGT
GCGAGCGATTGAAAAACACATCTTACAGGTGTCTCCGGAAATTAAACTCCCAATTCTCTA
TTTAATTGATTCCATCGTGAAAAATGTCGGTGATAAATACAAACAACTTTTTGCCCAAAA
TATTGTTAACATATTTTGTGGAGTTTTTGAGAAGGTGAATGAAAAAGTTCGCG
>g3854.t4 Gene=g3854 Length=103
MDSVKEKEIEEEYLSSLMDLNVNSKPLINMLTMLAEDNLENAAIIVRAIEKHILQVSPEI
KLPILYLIDSIVKNVGDKYKQLFAQNIVNIFCGVFEKVNEKVR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g3854.t4 | CDD | cd16982 | CID_Pcf11 | 11 | 103 | 0.000 |
| 6 | g3854.t4 | Gene3D | G3DSA:1.25.40.90 | - | 2 | 103 | 0.000 |
| 2 | g3854.t4 | PANTHER | PTHR15921:SF3 | PRE-MRNA CLEAVAGE COMPLEX 2 PROTEIN PCF11 | 7 | 103 | 0.000 |
| 3 | g3854.t4 | PANTHER | PTHR15921 | PRE-MRNA CLEAVAGE COMPLEX II | 7 | 103 | 0.000 |
| 1 | g3854.t4 | Pfam | PF04818 | CID domain | 20 | 101 | 0.000 |
| 8 | g3854.t4 | ProSiteProfiles | PS51391 | CID domain profile. | 5 | 103 | 31.642 |
| 7 | g3854.t4 | ProSiteProfiles | PS50179 | VHS domain profile. | 28 | 103 | 8.566 |
| 5 | g3854.t4 | SMART | SM00582 | 558neu5 | 8 | 103 | 0.000 |
| 4 | g3854.t4 | SUPERFAMILY | SSF48464 | ENTH/VHS domain | 7 | 103 | 0.000 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0006886 | intracellular protein transport | BP |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
Expression
Transcript expression in Pv11 cells
TPM values are indicated as average +/- STDEV. 
Differential expression
Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.
