General information for g5029.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Synaptotagmin 1.
Parent gene
- The parent gene g5029 is located on chr_2: 6524270..6525947 (+ 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 | g5029 | g5029.t3 | isoform | g5029.t3 | 6508789 | 6524270 |
| chr_2 | g5029 | g5029.t3 | exon | g5029.t3.exon1 | 6508789 | 6508942 |
| chr_2 | g5029 | g5029.t3 | cds | g5029.t3.CDS1 | 6508789 | 6508942 |
| chr_2 | g5029 | g5029.t3 | exon | g5029.t3.exon2 | 6509012 | 6509283 |
| chr_2 | g5029 | g5029.t3 | cds | g5029.t3.CDS2 | 6509012 | 6509283 |
| chr_2 | g5029 | g5029.t3 | exon | g5029.t3.exon3 | 6511956 | 6512054 |
| chr_2 | g5029 | g5029.t3 | cds | g5029.t3.CDS3 | 6511956 | 6512054 |
| chr_2 | g5029 | g5029.t3 | exon | g5029.t3.exon4 | 6512124 | 6512318 |
| chr_2 | g5029 | g5029.t3 | cds | g5029.t3.CDS4 | 6512124 | 6512318 |
| chr_2 | g5029 | g5029.t3 | exon | g5029.t3.exon5 | 6512712 | 6512888 |
| chr_2 | g5029 | g5029.t3 | cds | g5029.t3.CDS5 | 6512712 | 6512888 |
| chr_2 | g5029 | g5029.t3 | exon | g5029.t3.exon6 | 6519419 | 6519527 |
| chr_2 | g5029 | g5029.t3 | cds | g5029.t3.CDS6 | 6519419 | 6519527 |
| chr_2 | g5029 | g5029.t3 | exon | g5029.t3.exon7 | 6519674 | 6519807 |
| chr_2 | g5029 | g5029.t3 | cds | g5029.t3.CDS7 | 6519674 | 6519807 |
| chr_2 | g5029 | g5029.t3 | exon | g5029.t3.exon8 | 6524070 | 6524270 |
| chr_2 | g5029 | g5029.t3 | cds | g5029.t3.CDS8 | 6524070 | 6524270 |
| chr_2 | g5029 | g5029.t3 | TTS | g5029.t3 | 6525139 | 6525139 |
| chr_2 | g5029 | g5029.t3 | TSS | g5029.t3 | NA | NA |
Sequences
>g5029.t3 Gene=g5029 Length=1341
ATGGCACCAGGATTACAGAGATTATTAGTGAAGCGTGAGACGGCAGCAGATGAAGATTAT
GAAGAGCCAGCGACGACTCTTGCCACACACATTTTTGGCAAGCATCTGCATAAAGTTAGA
ATTACGACTCCAACAACAACTACTGAAGGAGAAGAGGAAGAAACAACGGAGGCAACACAA
CGCACGATGACACAAAAAGTGCAAGACGTTGGCGTAATTGTAACAAATAAATTGGCAGAG
AAAACGGGCATTCCAACGTGGGGTGTTGTTGCAATTTTTATTCTTATTGCGCTCATCATT
CTTGGTATATGTGGATTTTGCATTCGACGATGTTTCCGCAAACGACGTTCTAAAGATGGA
AAAAAGGGAATGAAAGGCGTTGATCTCAAATCGGTACAGTTACTTGGATCCGCTTATAAA
GAAAAGGTTCAACCTGATATGGAAGAGTTAACTGATAATGCCGAAGAGCATGAAGATGAA
GGTAGTAAACAGAGTGAACAAAAGCTCGGAAAATTGCAATATAAGCTGGAGTATGATTTC
AACTCGAACAGTTTAGCTGTTAGCGTTATTAAAGCTGAAGAATTGCCTGCTCTTGATATG
GGTGGAACATCGGATCCTTATGTTAAAGTTTATCTACTTCCTGATAAGAAGAAAAAGTTT
GAAACCAAAGTGCACCGAAAAACTCTCAATCCCGAATTCAATGAAACATTTGTGTTCAAG
AATCTACCATATGCTGAGGCAATGAACAAGACTCTGGTATTTGCCATATTTGATTTTGAT
CGATTCTCTAAGCATGACCAAATTGGTGAAGTTAAAGTTCCACTTTGTCAAATTGATTTG
GCTCAAACTATTGAAGAATGGCGTGAATTGCAAAGTGTTGAAGGAGAAGGTGGTCAGTTG
GGCGACATTTGCTTCTCATTGAGATACGTTCCAACCGCTGGCAAGTTGACGGTCGTAATA
TTGGAAGCTAAGAATCTGAAGAAGATGGATGTTGGTGGATTATCAGATCCATATGTTAAG
ATAGCAATAATGCAGAATGGAAAGCGTTTAAAGAAAAAGAAAACAAGTATCAAGAAATGT
ACATTGAATCCATACTACAATGAGTCGTTTTCATTTGAAGTACCATTCGAACAAATACAA
AAAGTAAATTTGGTTGTAACGGTTGTCGATTACGACAGGATCGGTACATCTGAGCCAATT
GGGAAGGTAGTTCTGGGATACAACGCTACTGGCACTGAATTAAGACACTGGTCAGATATG
CTTGCATCCCCGAGGAGACCTATTGCTCAATGGCACACGCTTAAAGATCCAGAAGAAGAG
ATGCCGGGTGATAAGAAGTAA
>g5029.t3 Gene=g5029 Length=446
MAPGLQRLLVKRETAADEDYEEPATTLATHIFGKHLHKVRITTPTTTTEGEEEETTEATQ
RTMTQKVQDVGVIVTNKLAEKTGIPTWGVVAIFILIALIILGICGFCIRRCFRKRRSKDG
KKGMKGVDLKSVQLLGSAYKEKVQPDMEELTDNAEEHEDEGSKQSEQKLGKLQYKLEYDF
NSNSLAVSVIKAEELPALDMGGTSDPYVKVYLLPDKKKKFETKVHRKTLNPEFNETFVFK
NLPYAEAMNKTLVFAIFDFDRFSKHDQIGEVKVPLCQIDLAQTIEEWRELQSVEGEGGQL
GDICFSLRYVPTAGKLTVVILEAKNLKKMDVGGLSDPYVKIAIMQNGKRLKKKKTSIKKC
TLNPYYNESFSFEVPFEQIQKVNLVVTVVDYDRIGTSEPIGKVVLGYNATGTELRHWSDM
LASPRRPIAQWHTLKDPEEEMPGDKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 21 | g5029.t3 | CDD | cd08385 | C2A_Synaptotagmin-1-5-6-9-10 | 168 | 292 | 2.40069E-82 |
| 20 | g5029.t3 | CDD | cd08402 | C2B_Synaptotagmin-1 | 300 | 435 | 6.37648E-96 |
| 16 | g5029.t3 | Coils | Coil | Coil | 140 | 167 | - |
| 14 | g5029.t3 | Gene3D | G3DSA:2.60.40.150 | - | 154 | 294 | 3.2E-46 |
| 15 | g5029.t3 | Gene3D | G3DSA:2.60.40.150 | - | 295 | 441 | 1.5E-54 |
| 3 | g5029.t3 | PANTHER | PTHR10024 | SYNAPTOTAGMIN | 42 | 440 | 2.9E-170 |
| 4 | g5029.t3 | PANTHER | PTHR10024:SF239 | SYNAPTOTAGMIN-1 | 42 | 440 | 2.9E-170 |
| 11 | g5029.t3 | PRINTS | PR00360 | C2 domain signature | 200 | 212 | 2.9E-10 |
| 10 | g5029.t3 | PRINTS | PR00360 | C2 domain signature | 227 | 240 | 2.9E-10 |
| 9 | g5029.t3 | PRINTS | PR00360 | C2 domain signature | 252 | 260 | 2.9E-10 |
| 8 | g5029.t3 | PRINTS | PR00399 | Synaptotagmin signature | 303 | 318 | 2.4E-16 |
| 7 | g5029.t3 | PRINTS | PR00399 | Synaptotagmin signature | 318 | 331 | 2.4E-16 |
| 6 | g5029.t3 | PRINTS | PR00399 | Synaptotagmin signature | 375 | 390 | 2.4E-16 |
| 5 | g5029.t3 | PRINTS | PR00399 | Synaptotagmin signature | 395 | 405 | 2.4E-16 |
| 2 | g5029.t3 | Pfam | PF00168 | C2 domain | 184 | 290 | 3.4E-27 |
| 1 | g5029.t3 | Pfam | PF00168 | C2 domain | 314 | 418 | 3.0E-23 |
| 18 | g5029.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 86 | - |
| 19 | g5029.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 87 | 108 | - |
| 17 | g5029.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 109 | 446 | - |
| 26 | g5029.t3 | ProSiteProfiles | PS50004 | C2 domain profile. | 182 | 272 | 20.935 |
| 25 | g5029.t3 | ProSiteProfiles | PS50004 | C2 domain profile. | 313 | 404 | 21.201 |
| 24 | g5029.t3 | SMART | SM00239 | C2_3c | 184 | 287 | 4.3E-22 |
| 23 | g5029.t3 | SMART | SM00239 | C2_3c | 315 | 429 | 3.5E-24 |
| 13 | g5029.t3 | SUPERFAMILY | SSF49562 | C2 domain (Calcium/lipid-binding domain, CaLB) | 162 | 294 | 3.87E-40 |
| 12 | g5029.t3 | SUPERFAMILY | SSF49562 | C2 domain (Calcium/lipid-binding domain, CaLB) | 300 | 434 | 1.25E-40 |
| 22 | g5029.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 86 | 108 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5029/g5029.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5029.t3.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0016020 | membrane | CC |
| GO:0007269 | neurotransmitter secretion | BP |
| GO:0005544 | calcium-dependent phospholipid binding | MF |
| GO:0008021 | synaptic vesicle | CC |
KEGG
Orthology
- This transcript has been annotated with K15290 (synaptotagmin-1)
Pathway
- This transcript belongs to the following 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