General information for g5225.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t1 | isoform | g5225.t1 | 7920018 | 7920802 |
| chr_2 | g5225 | g5225.t1 | exon | g5225.t1.exon1 | 7920018 | 7920020 |
| chr_2 | g5225 | g5225.t1 | cds | g5225.t1.CDS1 | 7920018 | 7920020 |
| chr_2 | g5225 | g5225.t1 | exon | g5225.t1.exon2 | 7920089 | 7920139 |
| chr_2 | g5225 | g5225.t1 | cds | g5225.t1.CDS2 | 7920089 | 7920139 |
| chr_2 | g5225 | g5225.t1 | exon | g5225.t1.exon3 | 7920204 | 7920472 |
| chr_2 | g5225 | g5225.t1 | cds | g5225.t1.CDS3 | 7920204 | 7920472 |
| chr_2 | g5225 | g5225.t1 | exon | g5225.t1.exon4 | 7920529 | 7920802 |
| chr_2 | g5225 | g5225.t1 | cds | g5225.t1.CDS4 | 7920529 | 7920802 |
| chr_2 | g5225 | g5225.t1 | TTS | g5225.t1 | 7920908 | 7920908 |
| chr_2 | g5225 | g5225.t1 | TSS | g5225.t1 | NA | NA |
Sequences
>g5225.t1 Gene=g5225 Length=597
ATGGGAAATAAGAAAAACAATGCTCGTCGTGTGGCAATTCAAAAATTGGCTCAACTTAAA
AGAACGATTAGCTTGAAAGACAATCGTTTAAAAGAAAAAGATCGTATAACAAAACCCAAG
AAGCAGGATCCAAATGAATTAAAAGTCATTGAAAAGCCAAAACAATCATCTGCTCTTTTC
TTTAGCTACAACACTCAACTTGGTCCACCATATCACATCATTTTAGATACCAATTTTATC
AATTTTAGCATTAAAAATAAACTGGATATCATCAAGAGCCTTATGGATTGTCTTTATGCA
AAATGTTTTCCGTATATTACAGATTGTGTACGAGGTGAGTTAGAGAAGATGGGTCAAAAA
TACAAATTAGCATTGAAAATAATCAAAGATAAACGATTTGAGAGACTACCATGCATGCAT
AAAGGAACGTATGCTGACGATTGCATAGTTGATCGTGTGACACAACACAAATGCTATATT
GTTGCAACCAATGATAAAGACTTAAGAAGGCGAATAAGAAAAATTCCAGGAGTACCTATA
ATGAATGTTTCTCAAAGTAAATATACAATCGAACGAATGGGAGATTCGTTTGATTAA
>g5225.t1 Gene=g5225 Length=198
MGNKKNNARRVAIQKLAQLKRTISLKDNRLKEKDRITKPKKQDPNELKVIEKPKQSSALF
FSYNTQLGPPYHIILDTNFINFSIKNKLDIIKSLMDCLYAKCFPYITDCVRGELEKMGQK
YKLALKIIKDKRFERLPCMHKGTYADDCIVDRVTQHKCYIVATNDKDLRRRIRKIPGVPI
MNVSQSKYTIERMGDSFD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g5225.t1 | CDD | cd09864 | PIN_Fcf1-like | 61 | 191 | 0 |
| 6 | g5225.t1 | Gene3D | G3DSA:3.40.50.1010 | - | 51 | 197 | 0 |
| 2 | g5225.t1 | PANTHER | PTHR12416:SF2 | RRNA-PROCESSING PROTEIN FCF1 HOMOLOG | 13 | 196 | 0 |
| 3 | g5225.t1 | PANTHER | PTHR12416 | UNCHARACTERIZED | 13 | 196 | 0 |
| 1 | g5225.t1 | Pfam | PF04900 | Fcf1 | 96 | 192 | 0 |
| 5 | g5225.t1 | SMART | SM00670 | PIN_9 | 71 | 170 | 0 |
| 4 | g5225.t1 | SUPERFAMILY | SSF88723 | PIN domain-like | 69 | 193 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5225/g5225.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5225.t1.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.
