General information for g4154.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g4154 is located on chr_3: 31019483..31020175 (+ 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 | g4154 | g4154.t1 | isoform | g4154.t1 | 31019072 | 31020175 |
| chr_3 | g4154 | g4154.t1 | exon | g4154.t1.exon1 | 31019072 | 31019140 |
| chr_3 | g4154 | g4154.t1 | cds | g4154.t1.CDS1 | 31019072 | 31019140 |
| chr_3 | g4154 | g4154.t1 | exon | g4154.t1.exon2 | 31019481 | 31020044 |
| chr_3 | g4154 | g4154.t1 | cds | g4154.t1.CDS2 | 31019481 | 31020044 |
| chr_3 | g4154 | g4154.t1 | exon | g4154.t1.exon3 | 31020098 | 31020175 |
| chr_3 | g4154 | g4154.t1 | cds | g4154.t1.CDS3 | 31020098 | 31020175 |
| chr_3 | g4154 | g4154.t1 | TTS | g4154.t1 | 31020285 | 31020285 |
| chr_3 | g4154 | g4154.t1 | TSS | g4154.t1 | NA | NA |
Sequences
>g4154.t1 Gene=g4154 Length=711
ATGGTTAAATTAACATGTGCAGCTAGTTTACTTAAATATATAATTTTTAGTTTTAATTTT
ATTTGTGCAATTTTCGGAATTATTTTTATGTTTCATGGTGCACTAACGCTCGTCAAAATC
GGTGAAATAAGGTCATTTTTGCAAAATAAGCATTTAGATGATGCATCACTTGTTCCAACA
ATTATAATATGTGTAGGAATATTCATTTTTATTATTTCATTTCTTGGATGCTGTGGTGCA
ATGAAACAACAGAGAATATTTCTCGAAACCTATTCGATATGTCTCCTTGTACTGGTGATG
ATGCAAATTTTACTTGCTCTTCTGATTTTTTTATTTTTGGAAGATATTAATCGTGATAGT
TTGAAAAGTTTTACAAAAATGTGGCGTTTAAGATTTATGCCAGATAACCAAATGATGATT
GATATGGTTCAAACTTCAATTGAATGTTGTGGCTCAAATAACATGGATGACTATAGTTTT
GATCGAATACCACTTTCATGTTGTAAAAAGAATGTAGATGCATGCTCAAAAGATATTGCA
TTTCCATCAGGCTGTAAATTACTCTTAAAAAATGCAATAAATTCATCGGGACATACAATT
TCATACTTATGTATAATTACCGCTATTTTCGAGTTTTTAGCATCAATGATGGGATTTTTA
CTAAGTTCGCAGATAAGGAAAAATCATGGAAAAGGACGATGTTGTACTTAA
>g4154.t1 Gene=g4154 Length=236
MVKLTCAASLLKYIIFSFNFICAIFGIIFMFHGALTLVKIGEIRSFLQNKHLDDASLVPT
IIICVGIFIFIISFLGCCGAMKQQRIFLETYSICLLVLVMMQILLALLIFLFLEDINRDS
LKSFTKMWRLRFMPDNQMMIDMVQTSIECCGSNNMDDYSFDRIPLSCCKKNVDACSKDIA
FPSGCKLLLKNAINSSGHTISYLCIITAIFEFLASMMGFLLSSQIRKNHGKGRCCT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 20 | g4154.t1 | CDD | cd03127 | tetraspanin_LEL | 114 | 195 | 5.16671E-12 |
| 9 | g4154.t1 | Gene3D | G3DSA:1.10.1450.10 | Tetraspanin | 114 | 185 | 2.4E-9 |
| 2 | g4154.t1 | PANTHER | PTHR19282:SF273 | TETRASPANIN | 5 | 228 | 2.9E-28 |
| 3 | g4154.t1 | PANTHER | PTHR19282 | TETRASPANIN | 5 | 228 | 2.9E-28 |
| 19 | g4154.t1 | PIRSF | PIRSF002419 | Tetraspanin | 2 | 236 | 8.4E-35 |
| 5 | g4154.t1 | PRINTS | PR00259 | Transmembrane four family signature | 13 | 36 | 1.3E-19 |
| 4 | g4154.t1 | PRINTS | PR00259 | Transmembrane four family signature | 55 | 81 | 1.3E-19 |
| 7 | g4154.t1 | PRINTS | PR00259 | Transmembrane four family signature | 82 | 110 | 1.3E-19 |
| 6 | g4154.t1 | PRINTS | PR00259 | Transmembrane four family signature | 199 | 225 | 1.3E-19 |
| 1 | g4154.t1 | Pfam | PF00335 | Tetraspanin family | 11 | 222 | 3.2E-36 |
| 10 | g4154.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 11 | - |
| 17 | g4154.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 12 | 37 | - |
| 14 | g4154.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 38 | 56 | - |
| 16 | g4154.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 57 | 81 | - |
| 11 | g4154.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 82 | 92 | - |
| 18 | g4154.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 93 | 113 | - |
| 13 | g4154.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 114 | 199 | - |
| 15 | g4154.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 200 | 221 | - |
| 12 | g4154.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 222 | 236 | - |
| 8 | g4154.t1 | SUPERFAMILY | SSF48652 | Tetraspanin | 112 | 195 | 4.84E-11 |
| 24 | g4154.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 13 | 35 | - |
| 21 | g4154.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 55 | 77 | - |
| 23 | g4154.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 90 | 112 | - |
| 22 | g4154.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 199 | 221 | - |
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