General information for g2774.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Synaptic vesicle glycoprotein 2C.
Parent gene
- The parent gene g2774 is located on chr_3: 20151011..20151666 (+ 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_3 | g2774 | g2774.t1 | TSS | g2774.t1 | 20148927 | 20148927 |
| chr_3 | g2774 | g2774.t1 | isoform | g2774.t1 | 20149182 | 20151120 |
| chr_3 | g2774 | g2774.t1 | exon | g2774.t1.exon1 | 20149182 | 20150612 |
| chr_3 | g2774 | g2774.t1 | cds | g2774.t1.CDS1 | 20149182 | 20150612 |
| chr_3 | g2774 | g2774.t1 | exon | g2774.t1.exon2 | 20150676 | 20150934 |
| chr_3 | g2774 | g2774.t1 | cds | g2774.t1.CDS2 | 20150676 | 20150934 |
| chr_3 | g2774 | g2774.t1 | exon | g2774.t1.exon3 | 20150996 | 20151120 |
| chr_3 | g2774 | g2774.t1 | cds | g2774.t1.CDS3 | 20150996 | 20151120 |
| chr_3 | g2774 | g2774.t1 | TTS | g2774.t1 | 20151667 | 20151667 |
Sequences
>g2774.t1 Gene=g2774 Length=1815
ATGGTAGATTCTGAAACTGATCAAAAACACGTCAACGAATCCAATGTAACAAACGGTGGC
GAAAGCCAACAGCACCAAGTCAACAGACTTACAATAGAAGAAGTTGTGCCAAAGAGAAAA
ATTTCTCCTGCTATACTACAAACAACAAGTGCAATAGGTCCATTGCGAACGGGCGACAAA
GATCAAATTGAACGCGAAGAGCAATATCGTCCACTCGATCCAGAGCGCGGAGCGGGCGAT
GATCTTGTGGCGCAATCTTTTCATCAACTGCCACCTCCATACTCACCAGACAATGATGGC
ATTGCAAGAGCAGATTTTGAGCGTGCCATTGAGCTCACGGGATATGGAAAATTTCACTAT
ATTTTGCTCGCCATTTGCGGTCTCGTAAGTACGAGTGAAGAAATGGATGTGATTTCAATG
AGTTTCATTCTACCATCAGCACAGTGTGATTTAAATCTCAATACGCACACTAAAGGATGG
CTAAATTGCATCATTTTCATTGGTATGATGGTTGGTGCATATGTTTGGGGATCAATTGCT
GATTCACTTGGACGCAAACGTGTACTAATTGTCATTTCATTCATGAATGCCGCTTGCATT
GTTGCCTCATCATTTTCGCAAAATTATGAGCTTTTCATGCTCTTTCGATTCTTAAATGGA
GCCGCTTTGGGTGGCGCAGGACCTGTCATATGGAGTTATTTTGCTGAATTTCAACCGTTA
CATAAGCGTGGTTCAATGTTGAGTTTTATGGCTGCTTTCTGGACAATTGGAAATTTATTG
GTTGCTTCACTTGCATGGCTCATCATTCCTACAGATATTGGTTTTGAAACTAAAGAATTT
GTCTACAATTCATGGCGTGTCTTTTTAGTTCTTTGTGCCATTCCATCATTCATTGTCGGC
ATTTTATTGCTCTATTTGCCAGAATCACCTAAATTCTTACTTTCATGTGGTAGATTTGAA
GAAGCCATGGCCATCTTTCGCGGTATTTATGTTACAAATACTGGTAATGATCCATCAATG
TATCCTGTTAAAGAACTTCTTATTGATGATCAACTAAGAGCAGAACTTGAAGAAGTCAAA
AAACCAATTAAAAATAAATACAAGCGAACATTTTTGAAAATTGCTGAGAATAGCAAGGAT
CTTTTTACAAGTCCAATTCTCAAATTCACAATGGTTTCAATTGTCATTAACTTTACATTC
CATATTGGCTATTATGGACTGATGATGTGGTTCCCAGAACTTTTCAATAGATTTGATGAT
TATGCTGAATTTCATCCTGATGTTAAAGATGTTGGCGTTTGTGAAGTAACTGATTTTGTT
GTAAAACAACATCAAACTGCTGGTCATGAATGCAATGATCATATTCCTAGCACAGTTTTC
TTAGAATCACTCATTACTGTTGCATCAGCTTTACCTGCAAATGTTATTGCTGTTCTTGGA
ATGGACAGATTAGGAAGAAAATTCTTTTTAGTGACTGGCACAGTTTCAGCTGGTATTTGC
TCGATGTTGATGTATTTTGTATCGAATAAAGTTGAAAATTTGATTGTCAGTGCAACATTT
AGTGCAGTGATATCATGTGCTAATGCTGCTCTTGATTGCCTCATCACAGAAGTTTTTCCA
ACGAATTTAAGAGCTACTGGTGTTGCCATATCAATGGTTGCTGCTAGATTAGGTGGCATT
ATTGGAAATGTTGTGATTGCAACACTTTTGGATACATATTGTCCAGCACCAACATTTATT
GTGGCAGCATTACTCGCTGGAGGTGGTTTAATGTGTCTGTTTCTACCCAATACAACAAGA
AAAGCACTTTCTTGA
>g2774.t1 Gene=g2774 Length=604
MVDSETDQKHVNESNVTNGGESQQHQVNRLTIEEVVPKRKISPAILQTTSAIGPLRTGDK
DQIEREEQYRPLDPERGAGDDLVAQSFHQLPPPYSPDNDGIARADFERAIELTGYGKFHY
ILLAICGLVSTSEEMDVISMSFILPSAQCDLNLNTHTKGWLNCIIFIGMMVGAYVWGSIA
DSLGRKRVLIVISFMNAACIVASSFSQNYELFMLFRFLNGAALGGAGPVIWSYFAEFQPL
HKRGSMLSFMAAFWTIGNLLVASLAWLIIPTDIGFETKEFVYNSWRVFLVLCAIPSFIVG
ILLLYLPESPKFLLSCGRFEEAMAIFRGIYVTNTGNDPSMYPVKELLIDDQLRAELEEVK
KPIKNKYKRTFLKIAENSKDLFTSPILKFTMVSIVINFTFHIGYYGLMMWFPELFNRFDD
YAEFHPDVKDVGVCEVTDFVVKQHQTAGHECNDHIPSTVFLESLITVASALPANVIAVLG
MDRLGRKFFLVTGTVSAGICSMLMYFVSNKVENLIVSATFSAVISCANAALDCLITEVFP
TNLRATGVAISMVAARLGGIIGNVVIATLLDTYCPAPTFIVAALLAGGGLMCLFLPNTTR
KALS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g2774.t1 | Coils | Coil | Coil | 600 | 604 | - |
| 43 | g2774.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 29 | - |
| 42 | g2774.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 11 | 29 | - |
| 3 | g2774.t1 | PANTHER | PTHR24064 | SOLUTE CARRIER FAMILY 22 MEMBER | 81 | 604 | 1.7E-247 |
| 4 | g2774.t1 | PANTHER | PTHR24064:SF544 | LP17136P | 81 | 604 | 1.7E-247 |
| 1 | g2774.t1 | Pfam | PF00083 | Sugar (and other) transporter | 132 | 398 | 1.1E-30 |
| 2 | g2774.t1 | Pfam | PF07690 | Major Facilitator Superfamily | 468 | 599 | 6.2E-10 |
| 18 | g2774.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 158 | - |
| 28 | g2774.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 159 | 176 | - |
| 8 | g2774.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 177 | 187 | - |
| 29 | g2774.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 188 | 205 | - |
| 15 | g2774.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 206 | 210 | - |
| 25 | g2774.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 211 | 234 | - |
| 11 | g2774.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 235 | 245 | - |
| 21 | g2774.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 246 | 269 | - |
| 16 | g2774.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 270 | 284 | - |
| 26 | g2774.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 285 | 306 | - |
| 7 | g2774.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 307 | 388 | - |
| 27 | g2774.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 389 | 411 | - |
| 14 | g2774.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 412 | 462 | - |
| 23 | g2774.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 463 | 481 | - |
| 12 | g2774.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 482 | 487 | - |
| 24 | g2774.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 488 | 508 | - |
| 13 | g2774.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 509 | 513 | - |
| 22 | g2774.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 514 | 535 | - |
| 10 | g2774.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 536 | 546 | - |
| 19 | g2774.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 547 | 570 | - |
| 17 | g2774.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 571 | 575 | - |
| 20 | g2774.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 576 | 595 | - |
| 9 | g2774.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 596 | 604 | - |
| 40 | g2774.t1 | ProSitePatterns | PS00217 | Sugar transport proteins signature 2. | 218 | 243 | - |
| 41 | g2774.t1 | ProSitePatterns | PS00216 | Sugar transport proteins signature 1. | 477 | 494 | - |
| 44 | g2774.t1 | ProSiteProfiles | PS50850 | Major facilitator superfamily (MFS) profile. | 120 | 600 | 38.792 |
| 5 | g2774.t1 | SUPERFAMILY | SSF103473 | MFS general substrate transporter | 105 | 596 | 5.23E-66 |
| 31 | g2774.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 158 | 180 | - |
| 32 | g2774.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 212 | 234 | - |
| 38 | g2774.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 247 | 269 | - |
| 33 | g2774.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 284 | 306 | - |
| 36 | g2774.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 389 | 411 | - |
| 37 | g2774.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 459 | 481 | - |
| 39 | g2774.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 488 | 507 | - |
| 30 | g2774.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 513 | 535 | - |
| 35 | g2774.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 548 | 570 | - |
| 34 | g2774.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 575 | 597 | - |
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:0055085 | transmembrane transport | BP |
| GO:0016021 | integral component of membrane | CC |
| GO:0022857 | transmembrane transporter activity | MF |
KEGG
Orthology
- This transcript has been annotated with K06258 (MFS transporter, VNT family, synaptic vesicle glycoprotein 2)
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.
