General information for g9258.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as U3 small nucleolar ribonucleoprotein protein IMP3.
Parent gene
- The parent gene g9258 is located on chr_1: 1344356..1344969 (- 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 | g9258 | g9258.t1 | TTS | g9258.t1 | 1344337 | 1344337 |
| chr_1 | g9258 | g9258.t1 | isoform | g9258.t1 | 1344356 | 1344969 |
| chr_1 | g9258 | g9258.t1 | exon | g9258.t1.exon1 | 1344356 | 1344767 |
| chr_1 | g9258 | g9258.t1 | cds | g9258.t1.CDS1 | 1344356 | 1344767 |
| chr_1 | g9258 | g9258.t1 | exon | g9258.t1.exon2 | 1344833 | 1344969 |
| chr_1 | g9258 | g9258.t1 | cds | g9258.t1.CDS2 | 1344833 | 1344969 |
| chr_1 | g9258 | g9258.t1 | TSS | g9258.t1 | 1345030 | 1345030 |
Sequences
>g9258.t1 Gene=g9258 Length=549
ATGGTGCGCAAATTAAAATATCATGAACAAAAATTGCTTAAGAAAGTTGATTTTCTTAAT
TGGAAAGTTGATAACAATCTGCAAGAAGTTAAAATCATGAAGAAATTTCACATTCATAAA
AGAGAAGACTACACAACATATAATGCATTATCGAGAAAGGTTAGAAACCTGGCAGAAAAG
ATTGCAAATGTAGATCAGAAACATCCATTTCGAACAGAAGTTAGTACACAGTTTTTAGAA
AAATTGTACATTATGGGATTAATACCGACAAAATGGGATCTGGAGCATGCTACAAAAGTA
TCAGCAAGTTCATTCTGTAGACGAAGATTGCCAGTTGTAATGGTTCGAAATAAGATGTCA
GAAAATATAAAGAATGCATCAACATTAGTAGAACAGGGCCACGTTAGAATTGGAACCGAT
ATAGTTAAAGATCCTGCATACCTAATCACACGCACTATGGAAGATTTTGTAACTTGGGTT
GATAGTAGTAAAATTAGACAGCACGTGTTGGAATATAATGATAATAAAGATGATTTTGAG
TTACTCTAA
>g9258.t1 Gene=g9258 Length=182
MVRKLKYHEQKLLKKVDFLNWKVDNNLQEVKIMKKFHIHKREDYTTYNALSRKVRNLAEK
IANVDQKHPFRTEVSTQFLEKLYIMGLIPTKWDLEHATKVSASSFCRRRLPVVMVRNKMS
ENIKNASTLVEQGHVRIGTDIVKDPAYLITRTMEDFVTWVDSSKIRQHVLEYNDNKDDFE
LL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g9258.t1 | CDD | cd00165 | S4 | 108 | 171 | 0.00107829 |
| 7 | g9258.t1 | Coils | Coil | Coil | 47 | 67 | - |
| 6 | g9258.t1 | Gene3D | G3DSA:3.10.290.10 | - | 109 | 180 | 3.5E-6 |
| 3 | g9258.t1 | PANTHER | PTHR11831:SF1 | U3 SMALL NUCLEOLAR RIBONUCLEOPROTEIN PROTEIN IMP3 | 1 | 181 | 1.6E-64 |
| 4 | g9258.t1 | PANTHER | PTHR11831 | 30S 40S RIBOSOMAL PROTEIN | 1 | 181 | 1.6E-64 |
| 1 | g9258.t1 | Pfam | PF00163 | Ribosomal protein S4/S9 N-terminal domain | 4 | 63 | 9.7E-9 |
| 2 | g9258.t1 | Pfam | PF01479 | S4 domain | 108 | 152 | 1.9E-8 |
| 10 | g9258.t1 | ProSiteProfiles | PS50889 | S4 RNA-binding domain profile. | 108 | 175 | 8.95 |
| 9 | g9258.t1 | SMART | SM01390 | Ribosomal_S4_2 | 4 | 107 | 4.0E-21 |
| 5 | g9258.t1 | SUPERFAMILY | SSF55174 | Alpha-L RNA-binding motif | 29 | 175 | 6.04E-13 |
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:0003723 | RNA binding | MF |
| GO:0019843 | rRNA binding | MF |
KEGG
Orthology
- This transcript has been annotated with K14560 (U3 small nucleolar ribonucleoprotein protein IMP3)
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.
