General information for g7559.t6
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.t6 | TTS | g7559.t6 | 24521992 | 24521992 |
| chr_2 | g7559 | g7559.t6 | isoform | g7559.t6 | 24522558 | 24524312 |
| chr_2 | g7559 | g7559.t6 | exon | g7559.t6.exon1 | 24522558 | 24523192 |
| chr_2 | g7559 | g7559.t6 | cds | g7559.t6.CDS1 | 24523018 | 24523192 |
| chr_2 | g7559 | g7559.t6 | exon | g7559.t6.exon2 | 24523253 | 24523906 |
| chr_2 | g7559 | g7559.t6 | cds | g7559.t6.CDS2 | 24523253 | 24523638 |
| chr_2 | g7559 | g7559.t6 | exon | g7559.t6.exon3 | 24524157 | 24524312 |
| chr_2 | g7559 | g7559.t6 | TSS | g7559.t6 | 24524278 | 24524278 |
Sequences
>g7559.t6 Gene=g7559 Length=1445
ATGGGTAAAATTATGTTGGATATTTCACGCATGCACCGGTGAGAAAGAGTTTTGGGTAAA
ATGTTGTGAATTTTATTATCTCAAAGAAATCTTGACAATTTTAATCAATTTTTGTAAAAA
TTGTGATGAATTCTTCTGCGGACTTGTATTTAAAATTGAAGTTTTTAAAGGACTAAATAA
AACTCGTGGGCTCTTTTTGCGATATCGCGAACTTCAAAACGATACGAGTGCAAGTGATCA
ACAAACGGACCTTGAGTATACAACTACTGAATTGAGAAACTCATTGAGATCAATTGAATG
GGATCTTGAAGATTTAGAAGATACAATTGCAATAGCTGAGAAAAATCCAAAACATAAAAT
CGACTTACAGGAACTAAATCAGCGAAGGAATTTCATAATTGCCACAAAAAATGAGATCAA
GTCTATGAAAGATAAAATTAGTATTTTAAAGAATCGTGATAAAGATATAACTGCGATTCA
GCCACTACTTGACGACGATCCTTCACCAAAGAACACTTCAAACAGTAATTGCAACGGTAA
TACATCAAATTCTATTGGGAATAATTTAATGAGCAGTATGGCAGCAGCAAGACACAGCGG
TACTAAATATAAGAAACTCGAAAACATCAACGACAGTCCCAGTCATAATGGAAACTTTAA
CAGTGACAGTGCTTTTATGGGCGAAACAATTTCAATTCAACAGAGAATGCTACAATCTCA
AGATTTACAAATCGATGTTTTGAGCGATTCAATAGGCACATTAAAAACCGTTAGTCGACA
AATTGGTGTAGAAATTGATGAGCAAGCTGTTATGCTAGATGAATTTGGTAATGAATTAGA
TGCCACAGACTCAAAATTGGATGCTACAATGAAGAAAGTTGGAAAAGTGCTTCATTTATC
AGGCAACGATAGACGTCAATGGATGGCAATTGGATTTCTGAGCATCCTTTTAATAGTTGT
GATAATTCTTTTCATAATTCTTTAAAAAGGCTAACAGGACACAACAGAAAACCCTAAATA
AGACATTAATGAATAAAAACTGATCTCGTTATTGAAGTGCATAAAGTGAATTTGTGAGAA
AATACTGATTTGTGTGTAAATAAGTGAAGTTTGATTTCTTCTTTAAAATGTGAGGAAACA
TTTAAAATTATTAAGACAGAAGGAAAATGATTATATATATACATAGTCAACTATTTTTGT
AGTTTTAAAATTTAGAATTTTTTCTTTCCTTTTATCCTATACCTTGTAGTGATGATAAAT
TTTATATTTAATAAACTTTGAATGTGGAAATTTCCATTAATTTTCACTTCTCAATTAAAT
GTAACACAAAAAATAATTGGCAACCAATTATTTAAAAAAATAATGGAAAAACCAACACAA
AAGATGAAACCAATATTTATATCAAATTAATAATATGCAATAATATAATTTTGATGTTTT
TCACT
>g7559.t6 Gene=g7559 Length=186
MKDKISILKNRDKDITAIQPLLDDDPSPKNTSNSNCNGNTSNSIGNNLMSSMAAARHSGT
KYKKLENINDSPSHNGNFNSDSAFMGETISIQQRMLQSQDLQIDVLSDSIGTLKTVSRQI
GVEIDEQAVMLDEFGNELDATDSKLDATMKKVGKVLHLSGNDRRQWMAIGFLSILLIVVI
ILFIIL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g7559.t6 | CDD | cd15851 | SNARE_Syntaxin6 | 96 | 159 | 3.23129E-22 |
| 5 | g7559.t6 | Gene3D | G3DSA:1.20.5.110 | - | 100 | 165 | 1.2E-23 |
| 12 | g7559.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 18 | 39 | - |
| 13 | g7559.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 25 | 39 | - |
| 2 | g7559.t6 | PANTHER | PTHR19957 | SYNTAXIN | 79 | 186 | 2.9E-22 |
| 3 | g7559.t6 | PANTHER | PTHR19957:SF104 | SYNTAXIN-6 | 79 | 186 | 2.9E-22 |
| 1 | g7559.t6 | Pfam | PF05739 | SNARE domain | 130 | 182 | 3.5E-6 |
| 6 | g7559.t6 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 165 | - |
| 8 | g7559.t6 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 166 | 185 | - |
| 7 | g7559.t6 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 186 | 186 | - |
| 14 | g7559.t6 | ProSiteProfiles | PS50192 | t-SNARE coiled-coil homology domain profile. | 93 | 155 | 15.084 |
| 11 | g7559.t6 | SMART | SM00397 | tSNARE_6 | 88 | 155 | 1.7E-7 |
| 4 | g7559.t6 | SUPERFAMILY | SSF58038 | SNARE fusion complex | 88 | 156 | 1.05E-15 |
| 10 | g7559.t6 | 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.
