General information for g4424.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g4424 is located on chr_2: 2114568..2115133 (- 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 | g4424 | g4424.t2 | TTS | g4424.t2 | 2114178 | 2114178 |
| chr_2 | g4424 | g4424.t2 | isoform | g4424.t2 | 2114250 | 2115133 |
| chr_2 | g4424 | g4424.t2 | exon | g4424.t2.exon1 | 2114250 | 2114498 |
| chr_2 | g4424 | g4424.t2 | cds | g4424.t2.CDS1 | 2114250 | 2114498 |
| chr_2 | g4424 | g4424.t2 | exon | g4424.t2.exon2 | 2114555 | 2114767 |
| chr_2 | g4424 | g4424.t2 | cds | g4424.t2.CDS2 | 2114555 | 2114656 |
| chr_2 | g4424 | g4424.t2 | exon | g4424.t2.exon3 | 2114825 | 2115017 |
| chr_2 | g4424 | g4424.t2 | exon | g4424.t2.exon4 | 2115071 | 2115133 |
| chr_2 | g4424 | g4424.t2 | TSS | g4424.t2 | 2115424 | 2115424 |
Sequences
>g4424.t2 Gene=g4424 Length=718
ATGTCTAACACAAGTGAGGCATGCATCAAATATACTTTGTTCATTTTCAACTTTATATTT
GTGATCACTGGGATCATAATTTTGAGTGTAGGCTTGTCAGTCCAAGGAGTCTACCATGGA
TATAGTGAATTTTTGAGCAGTCAATTTTTGACCTTGCCCGTATTTCTTGTCGTTATTGGA
AGCATAATTTTCTTTGTTGCATTCTTTGGCTGCTATGGAGCTATGCGTGAAAATTACTGC
ATGATATTGACTGTTATTTTGTGGATTATTAACAATAATATTTATTCTCGAATTGGCGGC
TGGCATTACTGGATATATTTTGAAAAATTCTACAAGTTCACTCATTTCAGCTACTCTTGA
ACCTACTATGCATGACTATACGAATCCTGATAAAAAACATATAACTTATGCATGGGATGA
TATTCAAAGTAAATTTTCTTGCTGTGGACTTGAAAGCTTTGAAGATTGGCAAAAAGCTGT
TAATGGCACACCATTAAGTTGCTGTGAGATTCCTCATGGTATCTTGGATAAATTCACATG
TGAGAATGGCACAGAAACATTGCATAGTGAAGGATGCGTGAAATCTTTTGGTAATTTCAT
TCAGTCACATGCAAAGTCATTGGGTGTTGCGGGAATAGTCTTAGCTATAGTGCAGCTATT
TGGTTTATTATTTGCATGTATAATTACAAGAACTATTAAAAAACATCGTGGGTATTAA
>g4424.t2 Gene=g4424 Length=116
MHDYTNPDKKHITYAWDDIQSKFSCCGLESFEDWQKAVNGTPLSCCEIPHGILDKFTCEN
GTETLHSEGCVKSFGNFIQSHAKSLGVAGIVLAIVQLFGLLFACIITRTIKKHRGY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g4424.t2 | CDD | cd03127 | tetraspanin_LEL | 1 | 82 | 3.48049E-16 |
| 6 | g4424.t2 | Gene3D | G3DSA:1.10.1450.10 | Tetraspanin | 1 | 81 | 2.0E-10 |
| 2 | g4424.t2 | PANTHER | PTHR19282 | TETRASPANIN | 9 | 111 | 1.0E-17 |
| 3 | g4424.t2 | PANTHER | PTHR19282:SF446 | TETRASPANIN | 9 | 111 | 1.0E-17 |
| 1 | g4424.t2 | Pfam | PF00335 | Tetraspanin family | 10 | 107 | 2.0E-21 |
| 8 | g4424.t2 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 84 | - |
| 9 | g4424.t2 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 85 | 106 | - |
| 7 | g4424.t2 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 107 | 116 | - |
| 5 | g4424.t2 | SUPERFAMILY | SSF48652 | Tetraspanin | 2 | 81 | 2.62E-12 |
| 4 | g4424.t2 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 84 | 106 | - |
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:0016021 | integral component of membrane | CC |
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