General information for g5225.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative rRNA-processing protein FCF1-like protein.
Parent gene
- The parent gene g5225 is located on chr_2: 7920802..7922942 (+ 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_2 | g5225 | g5225.t2 | isoform | g5225.t2 | 7920018 | 7920802 |
| chr_2 | g5225 | g5225.t2 | exon | g5225.t2.exon1 | 7920018 | 7920020 |
| chr_2 | g5225 | g5225.t2 | exon | g5225.t2.exon2 | 7920089 | 7920143 |
| chr_2 | g5225 | g5225.t2 | exon | g5225.t2.exon3 | 7920204 | 7920472 |
| chr_2 | g5225 | g5225.t2 | cds | g5225.t2.CDS1 | 7920432 | 7920472 |
| chr_2 | g5225 | g5225.t2 | exon | g5225.t2.exon4 | 7920529 | 7920802 |
| chr_2 | g5225 | g5225.t2 | cds | g5225.t2.CDS2 | 7920529 | 7920802 |
| chr_2 | g5225 | g5225.t2 | TTS | g5225.t2 | 7920908 | 7920908 |
| chr_2 | g5225 | g5225.t2 | TSS | g5225.t2 | NA | NA |
Sequences
>g5225.t2 Gene=g5225 Length=601
ATGGGAAATAAGAAAAACAATGCTCGTCGTGTGGCAATTCAAAAATTGGCTCAAGTAACT
TAAAAGAACGATTAGCTTGAAAGACAATCGTTTAAAAGAAAAAGATCGTATAACAAAACC
CAAGAAGCAGGATCCAAATGAATTAAAAGTCATTGAAAAGCCAAAACAATCATCTGCTCT
TTTCTTTAGCTACAACACTCAACTTGGTCCACCATATCACATCATTTTAGATACCAATTT
TATCAATTTTAGCATTAAAAATAAACTGGATATCATCAAGAGCCTTATGGATTGTCTTTA
TGCAAAATGTTTTCCGTATATTACAGATTGTGTACGAGGTGAGTTAGAGAAGATGGGTCA
AAAATACAAATTAGCATTGAAAATAATCAAAGATAAACGATTTGAGAGACTACCATGCAT
GCATAAAGGAACGTATGCTGACGATTGCATAGTTGATCGTGTGACACAACACAAATGCTA
TATTGTTGCAACCAATGATAAAGACTTAAGAAGGCGAATAAGAAAAATTCCAGGAGTACC
TATAATGAATGTTTCTCAAAGTAAATATACAATCGAACGAATGGGAGATTCGTTTGATTA
A
>g5225.t2 Gene=g5225 Length=104
MDCLYAKCFPYITDCVRGELEKMGQKYKLALKIIKDKRFERLPCMHKGTYADDCIVDRVT
QHKCYIVATNDKDLRRRIRKIPGVPIMNVSQSKYTIERMGDSFD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g5225.t2 | CDD | cd09864 | PIN_Fcf1-like | 1 | 97 | 0 |
| 5 | g5225.t2 | Gene3D | G3DSA:3.40.50.1010 | - | 1 | 103 | 0 |
| 2 | g5225.t2 | PANTHER | PTHR12416:SF2 | RRNA-PROCESSING PROTEIN FCF1 HOMOLOG | 1 | 102 | 0 |
| 3 | g5225.t2 | PANTHER | PTHR12416 | UNCHARACTERIZED | 1 | 102 | 0 |
| 1 | g5225.t2 | Pfam | PF04900 | Fcf1 | 2 | 98 | 0 |
| 4 | g5225.t2 | SUPERFAMILY | SSF88723 | PIN domain-like | 2 | 99 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5225/g5225.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5225.t2.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0032040 | small-subunit processome | CC |
KEGG
Orthology
- This transcript has been annotated with K14566 (U3 small nucleolar RNA-associated protein 24)
Pathway
- This transcript belongs to the following pathways
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.
