General information for g17021.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Zinc finger matrin-type protein 2.
Parent gene
- The parent gene g17021 is located on chr_4: 12172747..12173334 (+ 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_4 | g17021 | g17021.t1 | TSS | g17021.t1 | 12172652 | 12172652 |
| chr_4 | g17021 | g17021.t1 | isoform | g17021.t1 | 12172747 | 12173334 |
| chr_4 | g17021 | g17021.t1 | exon | g17021.t1.exon1 | 12172747 | 12173334 |
| chr_4 | g17021 | g17021.t1 | cds | g17021.t1.CDS1 | 12172747 | 12173334 |
| chr_4 | g17021 | g17021.t1 | TTS | g17021.t1 | 12173206 | 12173206 |
Sequences
>g17021.t1 Gene=g17021 Length=588
ATGTCAATGCGACCGGATGATCATCGTAAAAAGTGGGACAAGAAAGAATATGAAAGGAAA
GCACTTGATCGTATACAAAAAATCAAAAAAGATGAAATTCCACTGCCAGAAGCTCCTCGC
GAAATGCTCAAAGTTCGTGACTACAAAGTCGATCTTGATAGTAAACTTGGTAAATCAATG
GTGATAAATAAAACAACACCAAGCAGTCAATCTGGTGGTTATTTTTGCAATGTTTGTGAT
TGCGTAGTAAAAGATTCAATTAATTTTTTGGATCATATTAATGGCAAAAAACATCAGCGG
AATCTCGGAATGTCAATGAAAGTTGAACGTAGCAGTTTGGAGCAAGTAAAAGAAAGATTT
AGTAAAAATAAGAGAAAAAATGAAGACAAACCTAAAGAATATGACCTTGAGCAGAGATTA
AAAGAAGCACAAGAAATGGAAGAAAAATTAAAAGAACAAAAAAGAGAAAAGAAAAAGAGA
AAAATTGATGAGGAACAAGCAGGAAGTTCTAATGATGGTGGTTTTGATGATGATATGATG
AGAATGATGGGTTTCAGTGGATTTGGTGGAAGTAAGAAAAATAATTAA
>g17021.t1 Gene=g17021 Length=195
MSMRPDDHRKKWDKKEYERKALDRIQKIKKDEIPLPEAPREMLKVRDYKVDLDSKLGKSM
VINKTTPSSQSGGYFCNVCDCVVKDSINFLDHINGKKHQRNLGMSMKVERSSLEQVKERF
SKNKRKNEDKPKEYDLEQRLKEAQEMEEKLKEQKREKKKRKIDEEQAGSSNDGGFDDDMM
RMMGFSGFGGSKKNN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g17021.t1 | Coils | Coil | Coil | 133 | 167 | - |
| 7 | g17021.t1 | Gene3D | G3DSA:3.30.160.60 | Classic Zinc Finger | 62 | 107 | 3.4E-7 |
| 6 | g17021.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 108 | 195 | - |
| 5 | g17021.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 111 | 167 | - |
| 2 | g17021.t1 | PANTHER | PTHR45986 | ZINC FINGER MATRIN-TYPE PROTEIN 2 | 4 | 193 | 4.0E-67 |
| 1 | g17021.t1 | Pfam | PF12171 | Zinc-finger double-stranded RNA-binding | 74 | 99 | 7.8E-6 |
| 4 | g17021.t1 | SMART | SM00451 | ZnF_U1_5 | 71 | 105 | 2.6E-10 |
| 3 | g17021.t1 | SUPERFAMILY | SSF57667 | beta-beta-alpha zinc fingers | 69 | 115 | 1.36E-9 |
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:0005681 | spliceosomal complex | CC |
| GO:0000398 | mRNA splicing, via spliceosome | BP |
| GO:0008270 | zinc ion binding | MF |
| GO:0003676 | nucleic acid binding | MF |
KEGG
Orthology
- This transcript has been annotated with K12848 (U4/U6.U5 tri-snRNP component SNU23)
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.
