General information for g2919.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative U1 small nuclear ribonucleoprotein C.
Parent gene
- The parent gene g2919 is located on chr_3: 21253618..21254232 (+ 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 | g2919 | g2919.t1 | TSS | g2919.t1 | 21253522 | 21253522 |
| chr_3 | g2919 | g2919.t1 | isoform | g2919.t1 | 21253618 | 21254232 |
| chr_3 | g2919 | g2919.t1 | exon | g2919.t1.exon1 | 21253618 | 21253780 |
| chr_3 | g2919 | g2919.t1 | cds | g2919.t1.CDS1 | 21253618 | 21253780 |
| chr_3 | g2919 | g2919.t1 | exon | g2919.t1.exon2 | 21253897 | 21253921 |
| chr_3 | g2919 | g2919.t1 | cds | g2919.t1.CDS2 | 21253897 | 21253921 |
| chr_3 | g2919 | g2919.t1 | exon | g2919.t1.exon3 | 21254067 | 21254232 |
| chr_3 | g2919 | g2919.t1 | cds | g2919.t1.CDS3 | 21254067 | 21254232 |
| chr_3 | g2919 | g2919.t1 | TTS | g2919.t1 | 21254346 | 21254346 |
Sequences
>g2919.t1 Gene=g2919 Length=354
ATGCCGAAATATTACTGCGATTATTGCGATACTTTTCTTACGCACGATTCACCTTCAGTC
CGTAAAACACATTGCACTGGAAGAAAGCATAAAGATAATGTAAAATTTTATTATCAAAAA
TGGATGGAAGAACAAGCACAACATTTAATTGATGCTACTACAGCTGCATTTAAGGCCGGA
AAAATTAGTTCTAATCCGTTTGCTCAACCACCACCGATGATGATGAATCCGCAGAGACCG
AATTTGAATGTGCCACCACCAATGAACTATCCACCGTTGAACATTCCACCTCCAAATTTC
AGCATGCCGCCGAATTTTCCACCAGCAGCTAATTTTGGGCCACCGATGAAATAA
>g2919.t1 Gene=g2919 Length=117
MPKYYCDYCDTFLTHDSPSVRKTHCTGRKHKDNVKFYYQKWMEEQAQHLIDATTAAFKAG
KISSNPFAQPPPMMMNPQRPNLNVPPPMNYPPLNIPPPNFSMPPNFPPAANFGPPMK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g2919.t1 | Gene3D | G3DSA:3.30.160.60 | Classic Zinc Finger | 1 | 61 | 0.00000 |
| 3 | g2919.t1 | Hamap | MF_03153 | U1 small nuclear ribonucleoprotein C [SNRPC]. | 1 | 116 | 11.01279 |
| 2 | g2919.t1 | PANTHER | PTHR31148 | U1 SMALL NUCLEAR RIBONUCLEOPROTEIN C | 1 | 114 | 0.00000 |
| 6 | g2919.t1 | PIRSF | PIRSF037969 | U1-C | 1 | 117 | 0.00000 |
| 1 | g2919.t1 | Pfam | PF06220 | U1 zinc finger | 1 | 38 | 0.00000 |
| 8 | g2919.t1 | ProSiteProfiles | PS50171 | Zinc finger matrin-type profile. | 4 | 36 | 13.44900 |
| 7 | g2919.t1 | SMART | SM00451 | ZnF_U1_5 | 1 | 37 | 0.00000 |
| 4 | g2919.t1 | SUPERFAMILY | SSF57667 | beta-beta-alpha zinc fingers | 1 | 58 | 0.00000 |
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:0005685 | U1 snRNP | CC |
| GO:0005634 | nucleus | CC |
| GO:0000398 | mRNA splicing, via spliceosome | BP |
| GO:0008270 | zinc ion binding | MF |
| GO:0003676 | nucleic acid binding | MF |
| GO:0000387 | spliceosomal snRNP assembly | BP |
KEGG
Orthology
- This transcript has been annotated with K11095 (U1 small nuclear ribonucleoprotein C)
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.
