General information for g7559.t2
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.t2 | isoform | g7559.t2 | 24521976 | 24524312 |
| chr_2 | g7559 | g7559.t2 | exon | g7559.t2.exon1 | 24521976 | 24523192 |
| chr_2 | g7559 | g7559.t2 | TTS | g7559.t2 | 24521992 | 24521992 |
| chr_2 | g7559 | g7559.t2 | cds | g7559.t2.CDS1 | 24523018 | 24523192 |
| chr_2 | g7559 | g7559.t2 | exon | g7559.t2.exon2 | 24523253 | 24524312 |
| chr_2 | g7559 | g7559.t2 | cds | g7559.t2.CDS2 | 24523253 | 24523638 |
| chr_2 | g7559 | g7559.t2 | TSS | g7559.t2 | 24524278 | 24524278 |
Sequences
>g7559.t2 Gene=g7559 Length=2277
ATGGGTAAAATTATGTTGGATATTTCACGCATGCACCGGTGAGAAAGAGTTTTGGGTAAA
ATGTTGTGAATTTTATTATCTCAAAGAAATCTTGACAATTTTAATCAATTTTTGTAAAAA
TTGTGATGAATTCTTCTGCGGACTTGTATTTAAAATGTGAAGTGTAAGAGAGCATATTGG
AATTTATTAAATTTTATTATCATTTCATTGGTTATTTTATCTTTTTTTATTTGCAGATTT
TTTATTTTTTCTCTCATCTAAAAAAAATTATTGATTTTTTCTTGTGTAAATCGTGAAACT
TTTATTTTTGACTTGATATTTTTTTGATTACCTTGGCTCCCTTTTTTGTGTTTGCGAAAA
CAAGTGATAGAGAGATTGATACATTACTGAAAACAATTTTTTGCAGTGAAGTTTTTAAAG
GACTAAATAAAACTCGTGGGCTCTTTTTGCGATATCGCGAACTTCAAAACGATACGAGTG
CAAGTGATCAACAAACGGACCTTGAGTATACAACTACTGAATTGAGAAACTCATTGAGAT
CAATTGAATGGGATCTTGAAGATTTAGAAGATACAATTGCAATAGCTGAGAAAAATCCAA
AACATAAAATCGACTTACAGGAACTAAATCAGCGAAGGAATTTCATAATTGCCACAAAAA
ATGAGATCAAGTCTATGAAAGATAAAATTAGTATTTTAAAGAATCGTGATAAAGATATAA
CTGCGATTCAGCCACTACTTGACGACGATCCTTCACCAAAGAACACTTCAAACAGTAATT
GCAACGGTAATACATCAAATTCTATTGGGAATAATTTAATGAGCAGTATGGCAGCAGCAA
GACACAGCGGTACTAAATATAAGAAACTCGAAAACATCAACGACAGTCCCAGTCATAATG
GAAACTTTAACAGTGACAGTGCTTTTATGGGCGAAACAATTTCAATTCAACAGAGAATGC
TACAATCTCAAGATTTACAAATCGATGTTTTGAGCGATTCAATAGGCACATTAAAAACCG
TTAGTCGACAAATTGGTGTAGAAATTGATGAGCAAGCTGTTATGCTAGATGAATTTGGTA
ATGAATTAGATGCCACAGACTCAAAATTGGATGCTACAATGAAGAAAGTTGGAAAAGTGC
TTCATTTATCAGGCAACGATAGACGTCAATGGATGGCAATTGGATTTCTGAGCATCCTTT
TAATAGTTGTGATAATTCTTTTCATAATTCTTTAAAAAGGCTAACAGGACACAACAGAAA
ACCCTAAATAAGACATTAATGAATAAAAACTGATCTCGTTATTGAAGTGCATAAAGTGAA
TTTGTGAGAAAATACTGATTTGTGTGTAAATAAGTGAAGTTTGATTTCTTCTTTAAAATG
TGAGGAAACATTTAAAATTATTAAGACAGAAGGAAAATGATTATATATATACATAGTCAA
CTATTTTTGTAGTTTTAAAATTTAGAATTTTTTCTTTCCTTTTATCCTATACCTTGTAGT
GATGATAAATTTTATATTTAATAAACTTTGAATGTGGAAATTTCCATTAATTTTCACTTC
TCAATTAAATGTAACACAAAAAATAATTGGCAACCAATTATTTAAAAAAATAATGGAAAA
ACCAACACAAAAGATGAAACCAATATTTATATCAAATTAATAATATGCAATAATATAATT
TTGATGTTTTTCACTCTTTTTTGTAGATAAAAATTTATCAAACTAAACAAAATAATAATC
TATTTAAATTATCTTCCTAAAAATGTCAAGAAAATATAAAGTCTAATACACACACAATAC
CTATATTTTAAATGTTTAATCAAATTACTTGATAACTCTAGTCAACTAGTGAGAAAATGA
AAAATTATTATGATATATAATATAGACACATAAACATCAATTTCATACATTTTGCATGTT
GGGATCAGAACAGAAAAAAATGATGTTTTCTGCAGCTAGATAATGAAAAGAAAATGATTA
AACATCAATTTTCAGTTTAGAATGAATTTATTACAACAAAACACAAAACAAAACTACGGT
TAATACAATATCAGCCAAATTTTCAATTCAAATTTCATTTATTTATTAAACGATAGAATA
AAGTGAATTAATTTTATCTTTAACCGTGATAACAAAATGAAGAAAATATATATCTCTGCA
ACAAAATACAATAATTTTCTCATAGACATTCCATCATACATTCTGTAATCTAACAAGAAG
AAATTAAAGCAGAAATAAAACAGAAATAATTTGATAAATTCAAAAGATCAATTTTTT
>g7559.t2 Gene=g7559 Length=186
MKDKISILKNRDKDITAIQPLLDDDPSPKNTSNSNCNGNTSNSIGNNLMSSMAAARHSGT
KYKKLENINDSPSHNGNFNSDSAFMGETISIQQRMLQSQDLQIDVLSDSIGTLKTVSRQI
GVEIDEQAVMLDEFGNELDATDSKLDATMKKVGKVLHLSGNDRRQWMAIGFLSILLIVVI
ILFIIL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g7559.t2 | CDD | cd15851 | SNARE_Syntaxin6 | 96 | 159 | 3.23129E-22 |
| 5 | g7559.t2 | Gene3D | G3DSA:1.20.5.110 | - | 100 | 165 | 1.2E-23 |
| 12 | g7559.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 18 | 39 | - |
| 13 | g7559.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 25 | 39 | - |
| 2 | g7559.t2 | PANTHER | PTHR19957 | SYNTAXIN | 79 | 186 | 2.9E-22 |
| 3 | g7559.t2 | PANTHER | PTHR19957:SF104 | SYNTAXIN-6 | 79 | 186 | 2.9E-22 |
| 1 | g7559.t2 | Pfam | PF05739 | SNARE domain | 130 | 182 | 3.5E-6 |
| 6 | g7559.t2 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 165 | - |
| 8 | g7559.t2 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 166 | 185 | - |
| 7 | g7559.t2 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 186 | 186 | - |
| 14 | g7559.t2 | ProSiteProfiles | PS50192 | t-SNARE coiled-coil homology domain profile. | 93 | 155 | 15.084 |
| 11 | g7559.t2 | SMART | SM00397 | tSNARE_6 | 88 | 155 | 1.7E-7 |
| 4 | g7559.t2 | SUPERFAMILY | SSF58038 | SNARE fusion complex | 88 | 156 | 1.05E-15 |
| 10 | g7559.t2 | 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.
