Gene loci information

Transcript annotation

  • This transcript has been annotated as Synaptotagmin-7.

Parent gene

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.t2 isoform g17509.t2 13736988 13748019
chr_4 g17509 g17509.t2 exon g17509.t2.exon1 13736988 13737115
chr_4 g17509 g17509.t2 cds g17509.t2.CDS1 13736988 13737115
chr_4 g17509 g17509.t2 exon g17509.t2.exon2 13746714 13746813
chr_4 g17509 g17509.t2 cds g17509.t2.CDS2 13746714 13746813
chr_4 g17509 g17509.t2 exon g17509.t2.exon3 13746881 13747009
chr_4 g17509 g17509.t2 cds g17509.t2.CDS3 13746881 13747009
chr_4 g17509 g17509.t2 exon g17509.t2.exon4 13747072 13747308
chr_4 g17509 g17509.t2 cds g17509.t2.CDS4 13747072 13747308
chr_4 g17509 g17509.t2 exon g17509.t2.exon5 13747472 13747580
chr_4 g17509 g17509.t2 cds g17509.t2.CDS5 13747472 13747580
chr_4 g17509 g17509.t2 exon g17509.t2.exon6 13747644 13747856
chr_4 g17509 g17509.t2 cds g17509.t2.CDS6 13747644 13747856
chr_4 g17509 g17509.t2 exon g17509.t2.exon7 13747919 13748019
chr_4 g17509 g17509.t2 cds g17509.t2.CDS7 13747919 13748019
chr_4 g17509 g17509.t2 TSS g17509.t2 NA NA
chr_4 g17509 g17509.t2 TTS g17509.t2 NA NA

Sequences

>g17509.t2 Gene=g17509 Length=1017
ATGATTGTCGCCCTATTCGAATACTATTCTACGGCAGTAGTAACGCCGACAACGGCGCTG
CAACAAGAGCAAGCACCAAATACATCATCAAGTCTCAATGTTAATGATCCTAATCATATC
AGCATCAGGTCATCAAGTACGCAGATCAAATCACCTGCTGGCTCAAGCTCCGGTGGAGAC
GATTCACGTGCTGTGGCAGCAATGAACAAGGACAAAGATAATTCGACTCAGAATCGAAGT
GTATCGATGGTTGACATGTACATTGATAATTCAGAACCAAGTGAAAATGTTGGACAAATT
CATTTTTCACTTGAATATGATTTCCAAAATACAACATTGATTCTTAAAGTTATTCAGGGC
AAAGAATTGCCAGCAAAAGACTTGAGTGGCACATCAGATCCGTATGTTCGTGTCACACTC
CTGCCCGATAAGAAGCATCGCCTCGAGACGAAAATTAAGCGACGCACGCTAAATCCACGT
TGGAATGAGACATTCTACTTTGAGGGTTTCCCAGTACAAAAGCTCCAATCTAGGATACTT
CACCTCCATGTTTTCGATTATGATCGTTTCTCAAGAGACGATTCTATCGGCGAGTGTGGA
GAATTGCTTTGTTCATTGTGTTATCATCCATCAAATTCCATACTTACATTAACGCTGGTT
AAAGCACGTAATTTGAAGGCAAAAGATATCAATGGAAAATCAGATCCATACACAAAAGTC
TGGCTACAATTTGGCGATAAACGTATTGAAAAGCGCAAAACGCCGATTTTCAAGTGCAAC
CTCAATCCACATTTTAATGAATCTTTTAGCTTCAATGTACCGTGGGAAAAAATTCGAGAA
TGTTCACTTGATGTGATGGTGATGGATTTTGATAACATAGGACGTAATGAACTGATTGGG
AGAATATTGCTAGCGGGCAAAAATGGTTCGGGTGCATCAGAAACGAAGCACTGGCAGGAC
ATGATATCTAAACCAAGACAAACAATTGTGCAATGGCATCGATTGAAGCCAGAATAA

>g17509.t2 Gene=g17509 Length=338
MIVALFEYYSTAVVTPTTALQQEQAPNTSSSLNVNDPNHISIRSSSTQIKSPAGSSSGGD
DSRAVAAMNKDKDNSTQNRSVSMVDMYIDNSEPSENVGQIHFSLEYDFQNTTLILKVIQG
KELPAKDLSGTSDPYVRVTLLPDKKHRLETKIKRRTLNPRWNETFYFEGFPVQKLQSRIL
HLHVFDYDRFSRDDSIGECGELLCSLCYHPSNSILTLTLVKARNLKAKDINGKSDPYTKV
WLQFGDKRIEKRKTPIFKCNLNPHFNESFSFNVPWEKIRECSLDVMVMDFDNIGRNELIG
RILLAGKNGSGASETKHWQDMISKPRQTIVQWHRLKPE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
18 g17509.t2 CDD cd08405 C2B_Synaptotagmin-7 199 336 0.000
16 g17509.t2 Gene3D G3DSA:2.60.40.150 - 88 199 0.000
17 g17509.t2 Gene3D G3DSA:2.60.40.150 - 200 336 0.000
4 g17509.t2 PANTHER PTHR10024 SYNAPTOTAGMIN 19 198 0.000
6 g17509.t2 PANTHER PTHR10024:SF344 SYNAPTOTAGMIN-7 19 198 0.000
3 g17509.t2 PANTHER PTHR10024 SYNAPTOTAGMIN 198 336 0.000
5 g17509.t2 PANTHER PTHR10024:SF344 SYNAPTOTAGMIN-7 198 336 0.000
7 g17509.t2 PRINTS PR00399 Synaptotagmin signature 100 115 0.000
13 g17509.t2 PRINTS PR00360 C2 domain signature 128 140 0.000
12 g17509.t2 PRINTS PR00360 C2 domain signature 155 168 0.000
11 g17509.t2 PRINTS PR00360 C2 domain signature 180 188 0.000
8 g17509.t2 PRINTS PR00399 Synaptotagmin signature 217 230 0.000
10 g17509.t2 PRINTS PR00399 Synaptotagmin signature 274 289 0.000
9 g17509.t2 PRINTS PR00399 Synaptotagmin signature 294 304 0.000
1 g17509.t2 Pfam PF00168 C2 domain 112 199 0.000
2 g17509.t2 Pfam PF00168 C2 domain 214 318 0.000
22 g17509.t2 ProSiteProfiles PS50004 C2 domain profile. 112 200 20.728
21 g17509.t2 ProSiteProfiles PS50004 C2 domain profile. 215 303 17.679
20 g17509.t2 SMART SM00239 C2_3c 112 212 0.000
19 g17509.t2 SMART SM00239 C2_3c 214 330 0.000
15 g17509.t2 SUPERFAMILY SSF49562 C2 domain (Calcium/lipid-binding domain, CaLB) 91 199 0.000
14 g17509.t2 SUPERFAMILY SSF49562 C2 domain (Calcium/lipid-binding domain, CaLB) 200 336 0.000

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

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