General information for g4996.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g4996 is located on chr_2: 6373229..6373738 (+ 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_2 | g4996 | g4996.t1 | TSS | g4996.t1 | 6373215 | 6373215 |
| chr_2 | g4996 | g4996.t1 | isoform | g4996.t1 | 6373229 | 6373738 |
| chr_2 | g4996 | g4996.t1 | exon | g4996.t1.exon1 | 6373229 | 6373738 |
| chr_2 | g4996 | g4996.t1 | cds | g4996.t1.CDS1 | 6373229 | 6373738 |
| chr_2 | g4996 | g4996.t1 | TTS | g4996.t1 | 6373821 | 6373821 |
Sequences
>g4996.t1 Gene=g4996 Length=510
ATGGCTAATTTTCGCCGAACTTGGGATAAAAAAGAATATCAATTAAAAGCTTTAAAACGT
GAACAAGATGAAAAAGAATCAAAGAATAAAGTACAAGAAGTAACGAAAGAGCTGTTGGAG
AAAGACTTAAAACTAAGAGCTAAACCAGTTTTGATTGGCAAGAAAATTTCTATAAAAAGT
TCATTTTCATCAAAAAACAATTTTCATTGTGAAATCTGTAACAGTACATGCAATGATTCT
AGTAGCTTTATATTGCATTTAAATAGTAAATATCATCAAAAGAATCTTGGAAAGAATGCT
AGCAATTCTGAAAGAAGCTCTTTGAAGCAAGTTCAAGAAAAATTTAAACAATTGAAAAGA
AAGAATGAAGACTCTTCAAAAATAATTCAAGCACATCCATCTAAAAAGTCAAAGAACATA
AACAATATGGAACAAAACGATATAATAGAAGATGATGAGATGAAAATGATGTTTGAAACA
ATTGGATTTACATCATTCAATAAGAAATGA
>g4996.t1 Gene=g4996 Length=169
MANFRRTWDKKEYQLKALKREQDEKESKNKVQEVTKELLEKDLKLRAKPVLIGKKISIKS
SFSSKNNFHCEICNSTCNDSSSFILHLNSKYHQKNLGKNASNSERSSLKQVQEKFKQLKR
KNEDSSKIIQAHPSKKSKNINNMEQNDIIEDDEMKMMFETIGFTSFNKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g4996.t1 | Coils | Coil | Coil | 15 | 35 | - |
| 5 | g4996.t1 | Coils | Coil | Coil | 101 | 128 | - |
| 4 | g4996.t1 | Gene3D | G3DSA:3.30.160.60 | Classic Zinc Finger | 57 | 102 | 3.6E-7 |
| 9 | g4996.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 117 | 145 | - |
| 10 | g4996.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 117 | 131 | - |
| 2 | g4996.t1 | PANTHER | PTHR45986 | ZINC FINGER MATRIN-TYPE PROTEIN 2 | 3 | 147 | 1.4E-18 |
| 1 | g4996.t1 | Pfam | PF12874 | Zinc-finger of C2H2 type | 68 | 92 | 8.8E-6 |
| 7 | g4996.t1 | ProSitePatterns | PS00028 | Zinc finger C2H2 type domain signature. | 70 | 92 | - |
| 8 | g4996.t1 | SMART | SM00451 | ZnF_U1_5 | 65 | 99 | 4.1E-4 |
| 3 | g4996.t1 | SUPERFAMILY | SSF57667 | beta-beta-alpha zinc fingers | 47 | 96 | 3.18E-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 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. There were no conditions that were differentially expressed