General information for g9954.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative U3 small nucleolar RNA-associated protein 4-like protein.
Parent gene
- The parent gene g9954 is located on chr_1: 6182205..6184148 (+ 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_1 | g9954 | g9954.t2 | TSS | g9954.t2 | 6179926 | 6179926 |
| chr_1 | g9954 | g9954.t2 | isoform | g9954.t2 | 6179971 | 6180918 |
| chr_1 | g9954 | g9954.t2 | exon | g9954.t2.exon1 | 6179971 | 6180077 |
| chr_1 | g9954 | g9954.t2 | cds | g9954.t2.CDS1 | 6179971 | 6180077 |
| chr_1 | g9954 | g9954.t2 | exon | g9954.t2.exon2 | 6180141 | 6180918 |
| chr_1 | g9954 | g9954.t2 | cds | g9954.t2.CDS2 | 6180141 | 6180918 |
| chr_1 | g9954 | g9954.t2 | TTS | g9954.t2 | NA | NA |
Sequences
>g9954.t2 Gene=g9954 Length=885
ATGGTGAGAGAAATAAAATTACATGGAATTAAATGCTACAATATATTAGCAAGAGGTATT
AAGCATTTAGCTTATTCAAAAGAGCTCAGTAAATTAGCTGTTCTTCGAAATGATTTTAGT
ATAGAAATATGGAATTTTACTAATGCTCCTTTTATTGAGCGTGTTATACCTGGTACAATT
GATTGTGCTCTTGAACAAGTCTGTTGGATAGACAAAAGATTATTTTCTATCTCAATATCT
GGTTTTGGTTTGATTGAATGGGATCTTAAAACATTGAGCGTTAAAAGAAAATTGATGCTA
ACAGGAGATAAAGGAATATGCATTGACTATCATAAAAAAACACAAAGAATTGCAGTTGGA
ACTGAAGAAGGATTTATAAATATCTTCGATGTAAGTGATGATGATTTGCAATATGTGAAA
ATTTTAGATCGTCAAGATAATAGAATTGTTTGTTGTAAATTCAATGAGTCCGGTGATAGT
ATTGTATCGGGGTCAACAGATGCTGTAAAAATATGGAGTATCAAAACTGGACATGTAATT
CATAAAATGAGCACAGGGAGAGTTGATAAATTTCAAGAAACCATTGTTTGGTGTGTTCAA
GTTCTAAAAGATTTTACAATTATAACTGGCGATTCAAGAGGAAGAGTCACATTTTGGGAT
GGTAATATTGGAACGCAAATTGATTGGGTTCAAGCATCGAATGAGGATATCATGTGTCTT
ACAGTGTCTGAAGATCAAAATTCCTTTTTCTGTTCTGGTGTTGAACAAGTTGTAAGAAAG
TATGTGAAAATCACAAACACAAGAGATAACCAGAAGTTTGATCAGTGGATTCGAAATGCA
AAGCGATACAAATTACATACACATGATATTTTGACATTAACTATG
>g9954.t2 Gene=g9954 Length=295
MVREIKLHGIKCYNILARGIKHLAYSKELSKLAVLRNDFSIEIWNFTNAPFIERVIPGTI
DCALEQVCWIDKRLFSISISGFGLIEWDLKTLSVKRKLMLTGDKGICIDYHKKTQRIAVG
TEEGFINIFDVSDDDLQYVKILDRQDNRIVCCKFNESGDSIVSGSTDAVKIWSIKTGHVI
HKMSTGRVDKFQETIVWCVQVLKDFTIITGDSRGRVTFWDGNIGTQIDWVQASNEDIMCL
TVSEDQNSFFCSGVEQVVRKYVKITNTRDNQKFDQWIRNAKRYKLHTHDILTLTM
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g9954.t2 | Gene3D | G3DSA:2.130.10.10 | - | 3 | 290 | 0.0e+00 |
| 1 | g9954.t2 | PANTHER | PTHR44163 | U3 SMALL NUCLEOLAR RNA-ASSOCIATED PROTEIN 4 HOMOLOG | 4 | 294 | 0.0e+00 |
| 5 | g9954.t2 | SMART | SM00320 | WD40_4 | 9 | 45 | 1.8e+02 |
| 7 | g9954.t2 | SMART | SM00320 | WD40_4 | 93 | 130 | 7.1e+00 |
| 6 | g9954.t2 | SMART | SM00320 | WD40_4 | 135 | 173 | 4.9e-03 |
| 4 | g9954.t2 | SMART | SM00320 | WD40_4 | 176 | 220 | 1.4e+01 |
| 3 | g9954.t2 | SMART | SM00320 | WD40_4 | 223 | 262 | 2.0e+02 |
| 2 | g9954.t2 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 18 | 261 | 0.0e+00 |
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.
