General information for g3792.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 116 kDa U5 small nuclear ribonucleoprotein component.
Parent gene
- The parent gene g3792 is located on chr_3: 27970663..27973631 (- 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 | g3792 | g3792.t2 | isoform | g3792.t2 | 27970567 | 27971821 |
| chr_3 | g3792 | g3792.t2 | exon | g3792.t2.exon1 | 27970567 | 27971821 |
| chr_3 | g3792 | g3792.t2 | cds | g3792.t2.CDS1 | 27970663 | 27971766 |
| chr_3 | g3792 | g3792.t2 | TSS | g3792.t2 | NA | NA |
| chr_3 | g3792 | g3792.t2 | TTS | g3792.t2 | NA | NA |
Sequences
>g3792.t2 Gene=g3792 Length=1255
ACAGAGTATCATAAAAATTGCAGTTGAACCTGTTAATCCATCTGAATTACCAAAAATGCT
TGATGGTTTGAGAAAAGTGAACAAAAGTTACCCACTTTTATCAACTCGTGTTGAAGAGTC
TGGTGAGCATGTAATTTTAGGTACTGGAGAACTTTATCTAGATTGTGTTATGCATGACTT
GAGAAAAATGTATTCAGAAATTGACATTAAAGTTGCCGATCCAGTTACAATGTTTACAGA
AACATGTGTAGAAACTTCAGCAATCAAATGTTTCTCAGAAACTCCAAACAAAAAGAATAA
AATCACCATGATTTCGGAACCACTCGAGAAAGGATTAGCAGAGGATATTGAAAATGAAAA
TGTTTCAATAAATTGGAGTAAAAAGAAAATTGGTGAATTCTTCCAAAAAACATATGATTG
GGATTTGCTTGCGGCACGTTCAATTTGGTCATTTGGTCCAGATAATTGTGGTGCAAATAT
TCTTGTTGATGACACATTACCATCAGAGGTTGACAAATCTTTATTGCTCTCAATTAAAGA
TTCAATAGTTCAAGGATTTCAATGGGCTACAAGGGAAGGTCCATTGTGTGAAGAGCCAAT
TAGAAATGTAAAATTTAAAGTATTGGATGCAGTGATTGCAAACGAACCTATACACAGAGG
AGGTGGTCAAATTATTCCAACTGCTCGGCGCGTTTCATATTCTGCATTTTTAATGGCAAC
ACCAAGATTAATGGAACCATATTTATTTGTCGAAGTTCAAGCTCCAGCTGATTGTGTATC
ATCTGTTTATACAGTGTTAGCGAAAAGACGTGGACATGTGACACAAGATGCTCCAATACC
AGGTTCTCCTTTATATATTGTCAAAGCTTTTATTCCAGCAATTGATTCGTTTGGATTTGA
AACGGATTTGAGAACACACACTCAAGGACAAGCATTTTGTCAATCAGTCTTTCATCACTG
GCAAATAGTACCAGGTGATCCTCTAGACAAATCAATCATCATTCGACCACTTGAACCACA
ACCAGCTACACATTTAGCACGTGAATTTATGATTAAAACTCGTCGACGCAAGGGTCTTTC
TGAAGATGTCTCTATCAACAAATTCTTTGATGATCCAATGTTGCTCGAGTTAGCAAAACA
AGATGTTTTATTAAATTAAGTAAATTTTCATTTAAAATTTCAATAAACGGTCACTTTAAT
ATTTAAAAAACTAAGCAATTTTTTTTGGTCTAAAAAAATTTCATGTTGTTCTTTC
>g3792.t2 Gene=g3792 Length=367
MLDGLRKVNKSYPLLSTRVEESGEHVILGTGELYLDCVMHDLRKMYSEIDIKVADPVTMF
TETCVETSAIKCFSETPNKKNKITMISEPLEKGLAEDIENENVSINWSKKKIGEFFQKTY
DWDLLAARSIWSFGPDNCGANILVDDTLPSEVDKSLLLSIKDSIVQGFQWATREGPLCEE
PIRNVKFKVLDAVIANEPIHRGGGQIIPTARRVSYSAFLMATPRLMEPYLFVEVQAPADC
VSSVYTVLAKRRGHVTQDAPIPGSPLYIVKAFIPAIDSFGFETDLRTHTQGQAFCQSVFH
HWQIVPGDPLDKSIIIRPLEPQPATHLAREFMIKTRRRKGLSEDVSINKFFDDPMLLELA
KQDVLLN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g3792.t2 | CDD | cd01683 | EF2_IV_snRNP | 55 | 232 | 0 |
| 13 | g3792.t2 | CDD | cd04098 | eEF2_C_snRNP | 227 | 306 | 0 |
| 11 | g3792.t2 | Gene3D | G3DSA:3.30.70.870 | Elongation Factor G (Translational Gtpase) | 1 | 58 | 0 |
| 12 | g3792.t2 | Gene3D | G3DSA:3.30.70.240 | - | 62 | 341 | 0 |
| 10 | g3792.t2 | Gene3D | G3DSA:3.30.230.10 | - | 67 | 344 | 0 |
| 3 | g3792.t2 | PANTHER | PTHR42908:SF6 | 116 KDA U5 SMALL NUCLEAR RIBONUCLEOPROTEIN COMPONENT | 1 | 361 | 0 |
| 4 | g3792.t2 | PANTHER | PTHR42908 | TRANSLATION ELONGATION FACTOR-RELATED | 1 | 361 | 0 |
| 1 | g3792.t2 | Pfam | PF03764 | Elongation factor G, domain IV | 104 | 221 | 0 |
| 2 | g3792.t2 | Pfam | PF00679 | Elongation factor G C-terminus | 224 | 312 | 0 |
| 8 | g3792.t2 | SMART | SM00889 | EFG_IV_2 | 102 | 222 | 0 |
| 9 | g3792.t2 | SMART | SM00838 | EFG_C_a | 224 | 313 | 0 |
| 7 | g3792.t2 | SUPERFAMILY | SSF54980 | EF-G C-terminal domain-like | 1 | 56 | 0 |
| 5 | g3792.t2 | SUPERFAMILY | SSF54211 | Ribosomal protein S5 domain 2-like | 59 | 226 | 0 |
| 6 | g3792.t2 | SUPERFAMILY | SSF54980 | EF-G C-terminal domain-like | 227 | 313 | 0 |
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:0005525 | GTP binding | MF |
KEGG
Orthology
- This transcript has been annotated with K12852 (116 kDa U5 small nuclear ribonucleoprotein component)
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.
