General information for g7559.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Syntaxin-6.
Parent gene
- The parent gene g7559 is located on chr_2: 24523018..24524312 (- 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 | g7559 | g7559.t3 | isoform | g7559.t3 | 24521976 | 24524312 |
| chr_2 | g7559 | g7559.t3 | exon | g7559.t3.exon1 | 24521976 | 24523192 |
| chr_2 | g7559 | g7559.t3 | TTS | g7559.t3 | 24521992 | 24521992 |
| chr_2 | g7559 | g7559.t3 | cds | g7559.t3.CDS1 | 24523018 | 24523192 |
| chr_2 | g7559 | g7559.t3 | exon | g7559.t3.exon2 | 24523253 | 24524076 |
| chr_2 | g7559 | g7559.t3 | cds | g7559.t3.CDS2 | 24523253 | 24523638 |
| chr_2 | g7559 | g7559.t3 | exon | g7559.t3.exon3 | 24524150 | 24524312 |
| chr_2 | g7559 | g7559.t3 | TSS | g7559.t3 | 24524278 | 24524278 |
Sequences
>g7559.t3 Gene=g7559 Length=2204
ATGGGTAAAATTATGTTGGATATTTCACGCATGCACCGGTGAGAAAGAGTTTTGGGTAAA
ATGTTGTGAATTTTATTATCTCAAAGAAATCTTGACAATTTTAATCAATTTTTGTAAAAA
TTGTGATGAATTCTTCTGCGGACTTGTATTTAAAATGTGAAGTATTTTTTATTTTTTCTC
TCATCTAAAAAAAATTATTGATTTTTTCTTGTGTAAATCGTGAAACTTTTATTTTTGACT
TGATATTTTTTTGATTACCTTGGCTCCCTTTTTTGTGTTTGCGAAAACAAGTGATAGAGA
GATTGATACATTACTGAAAACAATTTTTTGCAGTGAAGTTTTTAAAGGACTAAATAAAAC
TCGTGGGCTCTTTTTGCGATATCGCGAACTTCAAAACGATACGAGTGCAAGTGATCAACA
AACGGACCTTGAGTATACAACTACTGAATTGAGAAACTCATTGAGATCAATTGAATGGGA
TCTTGAAGATTTAGAAGATACAATTGCAATAGCTGAGAAAAATCCAAAACATAAAATCGA
CTTACAGGAACTAAATCAGCGAAGGAATTTCATAATTGCCACAAAAAATGAGATCAAGTC
TATGAAAGATAAAATTAGTATTTTAAAGAATCGTGATAAAGATATAACTGCGATTCAGCC
ACTACTTGACGACGATCCTTCACCAAAGAACACTTCAAACAGTAATTGCAACGGTAATAC
ATCAAATTCTATTGGGAATAATTTAATGAGCAGTATGGCAGCAGCAAGACACAGCGGTAC
TAAATATAAGAAACTCGAAAACATCAACGACAGTCCCAGTCATAATGGAAACTTTAACAG
TGACAGTGCTTTTATGGGCGAAACAATTTCAATTCAACAGAGAATGCTACAATCTCAAGA
TTTACAAATCGATGTTTTGAGCGATTCAATAGGCACATTAAAAACCGTTAGTCGACAAAT
TGGTGTAGAAATTGATGAGCAAGCTGTTATGCTAGATGAATTTGGTAATGAATTAGATGC
CACAGACTCAAAATTGGATGCTACAATGAAGAAAGTTGGAAAAGTGCTTCATTTATCAGG
CAACGATAGACGTCAATGGATGGCAATTGGATTTCTGAGCATCCTTTTAATAGTTGTGAT
AATTCTTTTCATAATTCTTTAAAAAGGCTAACAGGACACAACAGAAAACCCTAAATAAGA
CATTAATGAATAAAAACTGATCTCGTTATTGAAGTGCATAAAGTGAATTTGTGAGAAAAT
ACTGATTTGTGTGTAAATAAGTGAAGTTTGATTTCTTCTTTAAAATGTGAGGAAACATTT
AAAATTATTAAGACAGAAGGAAAATGATTATATATATACATAGTCAACTATTTTTGTAGT
TTTAAAATTTAGAATTTTTTCTTTCCTTTTATCCTATACCTTGTAGTGATGATAAATTTT
ATATTTAATAAACTTTGAATGTGGAAATTTCCATTAATTTTCACTTCTCAATTAAATGTA
ACACAAAAAATAATTGGCAACCAATTATTTAAAAAAATAATGGAAAAACCAACACAAAAG
ATGAAACCAATATTTATATCAAATTAATAATATGCAATAATATAATTTTGATGTTTTTCA
CTCTTTTTTGTAGATAAAAATTTATCAAACTAAACAAAATAATAATCTATTTAAATTATC
TTCCTAAAAATGTCAAGAAAATATAAAGTCTAATACACACACAATACCTATATTTTAAAT
GTTTAATCAAATTACTTGATAACTCTAGTCAACTAGTGAGAAAATGAAAAATTATTATGA
TATATAATATAGACACATAAACATCAATTTCATACATTTTGCATGTTGGGATCAGAACAG
AAAAAAATGATGTTTTCTGCAGCTAGATAATGAAAAGAAAATGATTAAACATCAATTTTC
AGTTTAGAATGAATTTATTACAACAAAACACAAAACAAAACTACGGTTAATACAATATCA
GCCAAATTTTCAATTCAAATTTCATTTATTTATTAAACGATAGAATAAAGTGAATTAATT
TTATCTTTAACCGTGATAACAAAATGAAGAAAATATATATCTCTGCAACAAAATACAATA
ATTTTCTCATAGACATTCCATCATACATTCTGTAATCTAACAAGAAGAAATTAAAGCAGA
AATAAAACAGAAATAATTTGATAAATTCAAAAGATCAATTTTTT
>g7559.t3 Gene=g7559 Length=186
MKDKISILKNRDKDITAIQPLLDDDPSPKNTSNSNCNGNTSNSIGNNLMSSMAAARHSGT
KYKKLENINDSPSHNGNFNSDSAFMGETISIQQRMLQSQDLQIDVLSDSIGTLKTVSRQI
GVEIDEQAVMLDEFGNELDATDSKLDATMKKVGKVLHLSGNDRRQWMAIGFLSILLIVVI
ILFIIL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g7559.t3 | CDD | cd15851 | SNARE_Syntaxin6 | 96 | 159 | 3.23129E-22 |
| 5 | g7559.t3 | Gene3D | G3DSA:1.20.5.110 | - | 100 | 165 | 1.2E-23 |
| 12 | g7559.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 18 | 39 | - |
| 13 | g7559.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 25 | 39 | - |
| 2 | g7559.t3 | PANTHER | PTHR19957 | SYNTAXIN | 79 | 186 | 2.9E-22 |
| 3 | g7559.t3 | PANTHER | PTHR19957:SF104 | SYNTAXIN-6 | 79 | 186 | 2.9E-22 |
| 1 | g7559.t3 | Pfam | PF05739 | SNARE domain | 130 | 182 | 3.5E-6 |
| 6 | g7559.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 165 | - |
| 8 | g7559.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 166 | 185 | - |
| 7 | g7559.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 186 | 186 | - |
| 14 | g7559.t3 | ProSiteProfiles | PS50192 | t-SNARE coiled-coil homology domain profile. | 93 | 155 | 15.084 |
| 11 | g7559.t3 | SMART | SM00397 | tSNARE_6 | 88 | 155 | 1.7E-7 |
| 4 | g7559.t3 | SUPERFAMILY | SSF58038 | SNARE fusion complex | 88 | 156 | 1.05E-15 |
| 10 | g7559.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 166 | 185 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
