General information for g5029.t1
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.t1 | isoform | g5029.t1 | 6508789 | 6524270 |
| chr_2 | g5029 | g5029.t1 | exon | g5029.t1.exon1 | 6508789 | 6508942 |
| chr_2 | g5029 | g5029.t1 | cds | g5029.t1.CDS1 | 6508789 | 6508942 |
| chr_2 | g5029 | g5029.t1 | exon | g5029.t1.exon2 | 6509012 | 6509250 |
| chr_2 | g5029 | g5029.t1 | cds | g5029.t1.CDS2 | 6509012 | 6509250 |
| chr_2 | g5029 | g5029.t1 | exon | g5029.t1.exon3 | 6511956 | 6512054 |
| chr_2 | g5029 | g5029.t1 | cds | g5029.t1.CDS3 | 6511956 | 6512054 |
| chr_2 | g5029 | g5029.t1 | exon | g5029.t1.exon4 | 6512124 | 6512318 |
| chr_2 | g5029 | g5029.t1 | cds | g5029.t1.CDS4 | 6512124 | 6512318 |
| chr_2 | g5029 | g5029.t1 | exon | g5029.t1.exon5 | 6512712 | 6512888 |
| chr_2 | g5029 | g5029.t1 | cds | g5029.t1.CDS5 | 6512712 | 6512888 |
| chr_2 | g5029 | g5029.t1 | exon | g5029.t1.exon6 | 6519413 | 6519527 |
| chr_2 | g5029 | g5029.t1 | cds | g5029.t1.CDS6 | 6519413 | 6519527 |
| chr_2 | g5029 | g5029.t1 | exon | g5029.t1.exon7 | 6519674 | 6519807 |
| chr_2 | g5029 | g5029.t1 | cds | g5029.t1.CDS7 | 6519674 | 6519807 |
| chr_2 | g5029 | g5029.t1 | exon | g5029.t1.exon8 | 6524070 | 6524270 |
| chr_2 | g5029 | g5029.t1 | cds | g5029.t1.CDS8 | 6524070 | 6524270 |
| chr_2 | g5029 | g5029.t1 | TTS | g5029.t1 | 6525139 | 6525139 |
| chr_2 | g5029 | g5029.t1 | TSS | g5029.t1 | NA | NA |
Sequences
>g5029.t1 Gene=g5029 Length=1314
ATGGCACCAGGATTACAGAGATTATTAGTGAAGCGTGAGACGGCAGCAGATGAAGATTAT
GAAGAGCCAGCGACGACTCTTGCCACACACATTTTTGGCAAGCATCTGCATAAAGTTAGA
ATTACGACTCCAACAACAACTACTGAAGGAGAAGAGGAAGAAACAACGGAGGCAACACAA
CGCACGATGACACAAAAAGTGCAAGACGTTGGCGTAATTGTAACAAATAAATTGGCAGAG
AAAACGGGCATTCCAACGTGGGGTGTTGTTGCAATTTTTATTCTTATTGCGCTCATCATT
CTTGGTATATGTGGATTTTGCATTCGACGATGTTTCCGCAAACGACGTTCTAAAGATGGA
AAAAAGGGAATGAAAGGCGTTGATCTCAAATCGGTTCAACCTGATATGGAAGAGTTAACT
GATAATGCCGAAGAGCATGAAGATGAAGGTAGTAAACAGAGTGAACAAAAGCTCGGAAAA
TTGCAATATAAGCTGGAGTATGATTTCAACTCGAACAGTTTAGCTGTTAGCGTTATTAAA
GCTGAAGAATTGCCTGCTCTTGATATGGGTGGAACATCGGATCCTTATGTTAAAGTTTAT
CTACTTCCTGATAAGAAGAAAAAGTTTGAAACCAAAGTGCACCGAAAAACTCTCAATCCC
GAATTCAATGAAACATTTGTGTTCAAGAATCTACCATATGCTGAGGCAATGAACAAGACT
CTGGTATTTGCCATATTTGATTTTGATCGATTCTCTAAGCATGACCAAATTGGTGAAGTT
AAAGTTCCACTTTGTCAAATTGATTTGGCTCAAACTATTGAAGAATGGCGTGAATTGCAA
AGTGTTGAAGGAGAAGGTGGTCAGGAAAAGTTGGGCGACATTTGCTTCTCATTGAGATAC
GTTCCAACCGCTGGCAAGTTGACGGTCGTAATATTGGAAGCTAAGAATCTGAAGAAGATG
GATGTTGGTGGATTATCAGATCCATATGTTAAGATAGCAATAATGCAGAATGGAAAGCGT
TTAAAGAAAAAGAAAACAAGTATCAAGAAATGTACATTGAATCCATACTACAATGAGTCG
TTTTCATTTGAAGTACCATTCGAACAAATACAAAAAGTAAATTTGGTTGTAACGGTTGTC
GATTACGACAGGATCGGTACATCTGAGCCAATTGGGAAGGTAGTTCTGGGATACAACGCT
ACTGGCACTGAATTAAGACACTGGTCAGATATGCTTGCATCCCCGAGGAGACCTATTGCT
CAATGGCACACGCTTAAAGATCCAGAAGAAGAGATGCCGGGTGATAAGAAGTAA
>g5029.t1 Gene=g5029 Length=437
MAPGLQRLLVKRETAADEDYEEPATTLATHIFGKHLHKVRITTPTTTTEGEEEETTEATQ
RTMTQKVQDVGVIVTNKLAEKTGIPTWGVVAIFILIALIILGICGFCIRRCFRKRRSKDG
KKGMKGVDLKSVQPDMEELTDNAEEHEDEGSKQSEQKLGKLQYKLEYDFNSNSLAVSVIK
AEELPALDMGGTSDPYVKVYLLPDKKKKFETKVHRKTLNPEFNETFVFKNLPYAEAMNKT
LVFAIFDFDRFSKHDQIGEVKVPLCQIDLAQTIEEWRELQSVEGEGGQEKLGDICFSLRY
VPTAGKLTVVILEAKNLKKMDVGGLSDPYVKIAIMQNGKRLKKKKTSIKKCTLNPYYNES
FSFEVPFEQIQKVNLVVTVVDYDRIGTSEPIGKVVLGYNATGTELRHWSDMLASPRRPIA
QWHTLKDPEEEMPGDKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 21 | g5029.t1 | CDD | cd08385 | C2A_Synaptotagmin-1-5-6-9-10 | 157 | 281 | 2.05221E-82 |
| 20 | g5029.t1 | CDD | cd08402 | C2B_Synaptotagmin-1 | 291 | 426 | 4.80843E-96 |
| 16 | g5029.t1 | Coils | Coil | Coil | 129 | 156 | - |
| 15 | g5029.t1 | Gene3D | G3DSA:2.60.40.150 | - | 143 | 283 | 2.9E-46 |
| 14 | g5029.t1 | Gene3D | G3DSA:2.60.40.150 | - | 284 | 432 | 2.9E-55 |
| 25 | g5029.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 123 | 155 | - |
| 3 | g5029.t1 | PANTHER | PTHR10024 | SYNAPTOTAGMIN | 42 | 431 | 9.2E-169 |
| 4 | g5029.t1 | PANTHER | PTHR10024:SF239 | SYNAPTOTAGMIN-1 | 42 | 431 | 9.2E-169 |
| 11 | g5029.t1 | PRINTS | PR00360 | C2 domain signature | 189 | 201 | 2.7E-10 |
| 10 | g5029.t1 | PRINTS | PR00360 | C2 domain signature | 216 | 229 | 2.7E-10 |
| 9 | g5029.t1 | PRINTS | PR00360 | C2 domain signature | 241 | 249 | 2.7E-10 |
| 8 | g5029.t1 | PRINTS | PR00399 | Synaptotagmin signature | 294 | 309 | 2.2E-16 |
| 6 | g5029.t1 | PRINTS | PR00399 | Synaptotagmin signature | 309 | 322 | 2.2E-16 |
| 7 | g5029.t1 | PRINTS | PR00399 | Synaptotagmin signature | 366 | 381 | 2.2E-16 |
| 5 | g5029.t1 | PRINTS | PR00399 | Synaptotagmin signature | 386 | 396 | 2.2E-16 |
| 1 | g5029.t1 | Pfam | PF00168 | C2 domain | 173 | 279 | 3.3E-27 |
| 2 | g5029.t1 | Pfam | PF00168 | C2 domain | 305 | 409 | 2.9E-23 |
| 18 | g5029.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 86 | - |
| 19 | g5029.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 87 | 108 | - |
| 17 | g5029.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 109 | 437 | - |
| 26 | g5029.t1 | ProSiteProfiles | PS50004 | C2 domain profile. | 171 | 261 | 20.935 |
| 27 | g5029.t1 | ProSiteProfiles | PS50004 | C2 domain profile. | 304 | 395 | 21.201 |
| 24 | g5029.t1 | SMART | SM00239 | C2_3c | 173 | 276 | 4.3E-22 |
| 23 | g5029.t1 | SMART | SM00239 | C2_3c | 306 | 420 | 3.5E-24 |
| 12 | g5029.t1 | SUPERFAMILY | SSF49562 | C2 domain (Calcium/lipid-binding domain, CaLB) | 151 | 283 | 3.56E-40 |
| 13 | g5029.t1 | SUPERFAMILY | SSF49562 | C2 domain (Calcium/lipid-binding domain, CaLB) | 291 | 425 | 1.21E-40 |
| 22 | g5029.t1 | 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.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5029.t1.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.
