General information for g17509.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Synaptotagmin-7.
Parent gene
- The parent gene g17509 is located on chr_4: 13736988..13748019 (+ 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_4 | g17509 | g17509.t1 | isoform | g17509.t1 | 13721693 | 13748019 |
| chr_4 | g17509 | g17509.t1 | exon | g17509.t1.exon1 | 13721693 | 13721696 |
| chr_4 | g17509 | g17509.t1 | cds | g17509.t1.CDS1 | 13721693 | 13721696 |
| chr_4 | g17509 | g17509.t1 | exon | g17509.t1.exon2 | 13722775 | 13723090 |
| chr_4 | g17509 | g17509.t1 | cds | g17509.t1.CDS2 | 13722775 | 13723090 |
| chr_4 | g17509 | g17509.t1 | exon | g17509.t1.exon3 | 13746714 | 13746813 |
| chr_4 | g17509 | g17509.t1 | cds | g17509.t1.CDS3 | 13746714 | 13746813 |
| chr_4 | g17509 | g17509.t1 | exon | g17509.t1.exon4 | 13746881 | 13747009 |
| chr_4 | g17509 | g17509.t1 | cds | g17509.t1.CDS4 | 13746881 | 13747009 |
| chr_4 | g17509 | g17509.t1 | exon | g17509.t1.exon5 | 13747072 | 13747308 |
| chr_4 | g17509 | g17509.t1 | cds | g17509.t1.CDS5 | 13747072 | 13747308 |
| chr_4 | g17509 | g17509.t1 | exon | g17509.t1.exon6 | 13747472 | 13747580 |
| chr_4 | g17509 | g17509.t1 | cds | g17509.t1.CDS6 | 13747472 | 13747580 |
| chr_4 | g17509 | g17509.t1 | exon | g17509.t1.exon7 | 13747644 | 13747856 |
| chr_4 | g17509 | g17509.t1 | cds | g17509.t1.CDS7 | 13747644 | 13747856 |
| chr_4 | g17509 | g17509.t1 | exon | g17509.t1.exon8 | 13747919 | 13748019 |
| chr_4 | g17509 | g17509.t1 | cds | g17509.t1.CDS8 | 13747919 | 13748019 |
| chr_4 | g17509 | g17509.t1 | TSS | g17509.t1 | NA | NA |
| chr_4 | g17509 | g17509.t1 | TTS | g17509.t1 | NA | NA |
Sequences
>g17509.t1 Gene=g17509 Length=1209
ATGGAGCTAGGAAAAATTGTATTGATTGGTGTCCTCTCGACACTTGGTATTATCACACTG
ATACTTGTTCTTTTGGCTGGTGCATATTTCTGGTGGCGTCATAAGCGTTCACAGCTTGAA
TTTGTTGAACCATGCGATGATCATGAAACGAGCAGTGCAAGTTTAAAATTTCAGCAGCTG
CTTGAAACACAGCAACAAGAGCAATTGCTTGAAGAGCAGAAAAAGCAGCAACAGCAACAA
CCACAACAGACTAGCGCACAAGCCAACAAAATTAACACGAAACTCAATGGATTCCTTAAC
CTCAAGACACCACTGATTGGGTCATCAAGTACGCAGATCAAATCACCTGCTGGCTCAAGC
TCCGGTGGAGACGATTCACGTGCTGTGGCAGCAATGAACAAGGACAAAGATAATTCGACT
CAGAATCGAAGTGTATCGATGGTTGACATGTACATTGATAATTCAGAACCAAGTGAAAAT
GTTGGACAAATTCATTTTTCACTTGAATATGATTTCCAAAATACAACATTGATTCTTAAA
GTTATTCAGGGCAAAGAATTGCCAGCAAAAGACTTGAGTGGCACATCAGATCCGTATGTT
CGTGTCACACTCCTGCCCGATAAGAAGCATCGCCTCGAGACGAAAATTAAGCGACGCACG
CTAAATCCACGTTGGAATGAGACATTCTACTTTGAGGGTTTCCCAGTACAAAAGCTCCAA
TCTAGGATACTTCACCTCCATGTTTTCGATTATGATCGTTTCTCAAGAGACGATTCTATC
GGCGAGTGTGGAGAATTGCTTTGTTCATTGTGTTATCATCCATCAAATTCCATACTTACA
TTAACGCTGGTTAAAGCACGTAATTTGAAGGCAAAAGATATCAATGGAAAATCAGATCCA
TACACAAAAGTCTGGCTACAATTTGGCGATAAACGTATTGAAAAGCGCAAAACGCCGATT
TTCAAGTGCAACCTCAATCCACATTTTAATGAATCTTTTAGCTTCAATGTACCGTGGGAA
AAAATTCGAGAATGTTCACTTGATGTGATGGTGATGGATTTTGATAACATAGGACGTAAT
GAACTGATTGGGAGAATATTGCTAGCGGGCAAAAATGGTTCGGGTGCATCAGAAACGAAG
CACTGGCAGGACATGATATCTAAACCAAGACAAACAATTGTGCAATGGCATCGATTGAAG
CCAGAATAA
>g17509.t1 Gene=g17509 Length=402
MELGKIVLIGVLSTLGIITLILVLLAGAYFWWRHKRSQLEFVEPCDDHETSSASLKFQQL
LETQQQEQLLEEQKKQQQQQPQQTSAQANKINTKLNGFLNLKTPLIGSSSTQIKSPAGSS
SGGDDSRAVAAMNKDKDNSTQNRSVSMVDMYIDNSEPSENVGQIHFSLEYDFQNTTLILK
VIQGKELPAKDLSGTSDPYVRVTLLPDKKHRLETKIKRRTLNPRWNETFYFEGFPVQKLQ
SRILHLHVFDYDRFSRDDSIGECGELLCSLCYHPSNSILTLTLVKARNLKAKDINGKSDP
YTKVWLQFGDKRIEKRKTPIFKCNLNPHFNESFSFNVPWEKIRECSLDVMVMDFDNIGRN
ELIGRILLAGKNGSGASETKHWQDMISKPRQTIVQWHRLKPE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 22 | g17509.t1 | CDD | cd08405 | C2B_Synaptotagmin-7 | 263 | 400 | 1.27869E-86 |
| 18 | g17509.t1 | Coils | Coil | Coil | 60 | 80 | - |
| 17 | g17509.t1 | Gene3D | G3DSA:2.60.40.150 | - | 152 | 263 | 5.3E-40 |
| 16 | g17509.t1 | Gene3D | G3DSA:2.60.40.150 | - | 264 | 400 | 1.7E-43 |
| 3 | g17509.t1 | PANTHER | PTHR10024 | SYNAPTOTAGMIN | 73 | 262 | 9.9E-109 |
| 5 | g17509.t1 | PANTHER | PTHR10024:SF344 | SYNAPTOTAGMIN-7 | 73 | 262 | 9.9E-109 |
| 4 | g17509.t1 | PANTHER | PTHR10024 | SYNAPTOTAGMIN | 262 | 400 | 9.9E-109 |
| 6 | g17509.t1 | PANTHER | PTHR10024:SF344 | SYNAPTOTAGMIN-7 | 262 | 400 | 9.9E-109 |
| 10 | g17509.t1 | PRINTS | PR00399 | Synaptotagmin signature | 164 | 179 | 6.7E-11 |
| 12 | g17509.t1 | PRINTS | PR00360 | C2 domain signature | 192 | 204 | 2.2E-9 |
| 13 | g17509.t1 | PRINTS | PR00360 | C2 domain signature | 219 | 232 | 2.2E-9 |
| 11 | g17509.t1 | PRINTS | PR00360 | C2 domain signature | 244 | 252 | 2.2E-9 |
| 7 | g17509.t1 | PRINTS | PR00399 | Synaptotagmin signature | 281 | 294 | 6.7E-11 |
| 8 | g17509.t1 | PRINTS | PR00399 | Synaptotagmin signature | 338 | 353 | 6.7E-11 |
| 9 | g17509.t1 | PRINTS | PR00399 | Synaptotagmin signature | 358 | 368 | 6.7E-11 |
| 1 | g17509.t1 | Pfam | PF00168 | C2 domain | 176 | 263 | 3.2E-24 |
| 2 | g17509.t1 | Pfam | PF00168 | C2 domain | 278 | 381 | 3.1E-19 |
| 20 | g17509.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 5 | - |
| 21 | g17509.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 6 | 32 | - |
| 19 | g17509.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 33 | 402 | - |
| 26 | g17509.t1 | ProSiteProfiles | PS50004 | C2 domain profile. | 176 | 264 | 20.728 |
| 27 | g17509.t1 | ProSiteProfiles | PS50004 | C2 domain profile. | 279 | 367 | 17.679 |
| 24 | g17509.t1 | SMART | SM00239 | C2_3c | 176 | 276 | 7.3E-16 |
| 25 | g17509.t1 | SMART | SM00239 | C2_3c | 278 | 394 | 7.1E-17 |
| 14 | g17509.t1 | SUPERFAMILY | SSF49562 | C2 domain (Calcium/lipid-binding domain, CaLB) | 155 | 263 | 2.87E-35 |
| 15 | g17509.t1 | SUPERFAMILY | SSF49562 | C2 domain (Calcium/lipid-binding domain, CaLB) | 264 | 400 | 1.15E-35 |
| 23 | g17509.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 7 | 29 | - |
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:0016020 | membrane | CC |
KEGG
Orthology
- This transcript has been annotated with K19907 (synaptotagmin-7)
Pathway
This gene does not belong to any pathways.
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