General information for g2967.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative U5 small nuclear ribonucleoprotein 40 kDa protein.
Parent gene
- The parent gene g2967 is located on chr_3: 21622217..21623088 (+ 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 | g2967 | g2967.t4 | TSS | g2967.t4 | 21621293 | 21621293 |
| chr_3 | g2967 | g2967.t4 | isoform | g2967.t4 | 21622217 | 21622594 |
| chr_3 | g2967 | g2967.t4 | exon | g2967.t4.exon1 | 21622217 | 21622594 |
| chr_3 | g2967 | g2967.t4 | cds | g2967.t4.CDS1 | 21622277 | 21622594 |
| chr_3 | g2967 | g2967.t4 | TTS | g2967.t4 | 21623081 | 21623081 |
Sequences
>g2967.t4 Gene=g2967 Length=378
ACTGATACAATTACTGGTTTAAAATTATCTCCATGTGGTTCATATGTTCTTTCAAATTCG
ATGGATAACACTTGCAGAATTTGGGACATTAGACCATATTGTTCACAAGATCGATGTAAA
TCAGTTTTTCAGGGACATTCCCATAATTTTGAGAAAAATCTTTTAAGATGTGCATGGAGT
TCAGATGGCACAATGATTTCAGCTGGATCGGCGGATAGATTTGTTTATATTTGGGACGTT
AATTCTAAGAAGATTCTATACAAACTCCCTGGTCATTTAGGAGCTGTAAATGATGTTGAT
TTTTCACCAAAAGAAGAAATTATTCTCAGTGGTTCTTCAGATAAGACTCTATACATGGGT
GAATTACTAGAAAATTAG
>g2967.t4 Gene=g2967 Length=105
MDNTCRIWDIRPYCSQDRCKSVFQGHSHNFEKNLLRCAWSSDGTMISAGSADRFVYIWDV
NSKKILYKLPGHLGAVNDVDFSPKEEIILSGSSDKTLYMGELLEN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g2967.t4 | Gene3D | G3DSA:2.130.10.10 | - | 1 | 103 | 5.0E-31 |
| 3 | g2967.t4 | PANTHER | PTHR44006 | U5 SMALL NUCLEAR RIBONUCLEOPROTEIN 40 KDA PROTEIN | 1 | 102 | 3.6E-43 |
| 2 | g2967.t4 | Pfam | PF00400 | WD domain, G-beta repeat | 18 | 59 | 1.2E-6 |
| 1 | g2967.t4 | Pfam | PF00400 | WD domain, G-beta repeat | 65 | 98 | 4.0E-5 |
| 7 | g2967.t4 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 46 | 60 | - |
| 9 | g2967.t4 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 1 | 105 | 19.986 |
| 11 | g2967.t4 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 38 | 68 | 10.676 |
| 10 | g2967.t4 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 69 | 105 | 11.143 |
| 6 | g2967.t4 | SMART | SM00320 | WD40_4 | 16 | 59 | 3.4E-6 |
| 5 | g2967.t4 | SMART | SM00320 | WD40_4 | 62 | 101 | 3.6E-5 |
| 4 | g2967.t4 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 2 | 98 | 2.66E-23 |
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.
