General information for g3401.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative U3 small nucleolar RNA-associated protein 15-like protein.
Parent gene
- The parent gene g3401 is located on chr_3: 25199393..25200511 (- 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 | g3401 | g3401.t2 | TTS | g3401.t2 | 25198766 | 25198766 |
| chr_3 | g3401 | g3401.t2 | isoform | g3401.t2 | 25199393 | 25200359 |
| chr_3 | g3401 | g3401.t2 | exon | g3401.t2.exon1 | 25199393 | 25200359 |
| chr_3 | g3401 | g3401.t2 | cds | g3401.t2.CDS1 | 25199395 | 25199883 |
| chr_3 | g3401 | g3401.t2 | TSS | g3401.t2 | 25200569 | 25200569 |
Sequences
>g3401.t2 Gene=g3401 Length=967
CAGTATTTATTAAGGAATTTGGCGCTATAGATTATATTGATTTTAGTCCAATTGAACCAT
ATAACTTTGCTGCAACCTGTTCACTACGCGTACAAATTTATAATCCACTTACAAAACTTG
TTTTAAAAAATATTACAACATTTCAAAAAGAAGCATTCGGCGCAACATACAGAAATGACG
GTAAATTAATTGCAGCGGGTGATGATGAAGGAAAAGTAAGACTTTTTGATGCAAACACAA
AAACAATATTGAGAATATTTTCTGGTCATCGAGCTGCAGTGCATAGAACATATTTTGTCT
CTGATTTACATCATCTTGCTAGTTTTTCTGATGATAGAACAGTGAAATTATGGGATGTTG
GTACTGAAAAAATTGTATATACTTTTCGAGAACATAATGATTATATCAGAGCTGGAGCAG
TGAATCGTGCAAGTCCTCACACACTTATAAGCGGTGGTTACGATCATGTTATAAATATGT
ATGATACACGATCTGAAAAACGTGTAATGTCAGTCAATCATGGTAATCCAATAGAAGCAC
TCGTCTTTCATCCAAGTGGAGGTATCTTCATTTCAGCTGGCGGTAATGAAATCAAATTTT
GGGATGCTGTGGCAGGTGGACGTCTTTTAGGAACAATTTCTCAACATACCAAGACAGTTA
CATGTCTTTCAGTTAGTTCTGATGGCCGTCATTTAATTTCTGGTAGTCTCGATAGACATG
TCAAGTTTTTCAACACGTCAAACTATCAAATGATTCATAACATTAATTACACAAATTCAA
TTCTAAGCGTTGGAATTGCAAAAGATGGAAATACTTTAGCAGTTGGTCATGTTGATGGAA
CATTGGCAATTCACAGACGAGAAGAAAATTTCGATGATGATAAAATAGAACGAATTGAAA
GAGAAAAACGGAGAAAAGAGCGAACTTATCAAATTGCTGATGAAGTGATTGAGAAGCCAG
AACGAAA
>g3401.t2 Gene=g3401 Length=163
MYDTRSEKRVMSVNHGNPIEALVFHPSGGIFISAGGNEIKFWDAVAGGRLLGTISQHTKT
VTCLSVSSDGRHLISGSLDRHVKFFNTSNYQMIHNINYTNSILSVGIAKDGNTLAVGHVD
GTLAIHRREENFDDDKIERIEREKRRKERTYQIADEVIEKPER
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g3401.t2 | Coils | Coil | Coil | 137 | 157 | - |
| 9 | g3401.t2 | Gene3D | G3DSA:2.130.10.10 | - | 1 | 153 | 2.1E-28 |
| 3 | g3401.t2 | PANTHER | PTHR19924 | UTP15 U3 SMALL NUCLEOLAR RNA-ASSOCIATED PROTEIN 15 FAMILY MEMBER | 1 | 152 | 9.8E-43 |
| 4 | g3401.t2 | PANTHER | PTHR19924:SF30 | U3 SMALL NUCLEOLAR RNA-ASSOCIATED PROTEIN 15 HOMOLOG | 1 | 152 | 9.8E-43 |
| 2 | g3401.t2 | Pfam | PF00400 | WD domain, G-beta repeat | 14 | 43 | 0.028 |
| 1 | g3401.t2 | Pfam | PF00400 | WD domain, G-beta repeat | 48 | 86 | 2.8E-7 |
| 11 | g3401.t2 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 12 | 95 | 13.765 |
| 12 | g3401.t2 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 54 | 95 | 11.478 |
| 7 | g3401.t2 | SMART | SM00320 | WD40_4 | 6 | 43 | 0.0011 |
| 8 | g3401.t2 | SMART | SM00320 | WD40_4 | 47 | 86 | 2.8E-8 |
| 6 | g3401.t2 | SMART | SM00320 | WD40_4 | 89 | 127 | 0.62 |
| 5 | g3401.t2 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 2 | 135 | 7.69E-28 |
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:0005515 | protein binding | MF |
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.
