General information for g9085.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Syndecan.
Parent gene
- The parent gene g9085 is located on chr_2: 35197443..35198822 (+ 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 | g9085 | g9085.t1 | TSS | g9085.t1 | 35191957 | 35191957 |
| chr_2 | g9085 | g9085.t1 | isoform | g9085.t1 | 35192485 | 35197619 |
| chr_2 | g9085 | g9085.t1 | exon | g9085.t1.exon1 | 35192485 | 35192598 |
| chr_2 | g9085 | g9085.t1 | cds | g9085.t1.CDS1 | 35192485 | 35192598 |
| chr_2 | g9085 | g9085.t1 | exon | g9085.t1.exon2 | 35195110 | 35195241 |
| chr_2 | g9085 | g9085.t1 | cds | g9085.t1.CDS2 | 35195110 | 35195241 |
| chr_2 | g9085 | g9085.t1 | exon | g9085.t1.exon3 | 35195632 | 35195950 |
| chr_2 | g9085 | g9085.t1 | cds | g9085.t1.CDS3 | 35195632 | 35195950 |
| chr_2 | g9085 | g9085.t1 | exon | g9085.t1.exon4 | 35197187 | 35197384 |
| chr_2 | g9085 | g9085.t1 | cds | g9085.t1.CDS4 | 35197187 | 35197384 |
| chr_2 | g9085 | g9085.t1 | exon | g9085.t1.exon5 | 35197444 | 35197619 |
| chr_2 | g9085 | g9085.t1 | cds | g9085.t1.CDS5 | 35197444 | 35197619 |
| chr_2 | g9085 | g9085.t1 | TTS | g9085.t1 | 35197707 | 35197707 |
Sequences
>g9085.t1 Gene=g9085 Length=939
ATGAATCTTAAAAGTTGGTGCAATATTAGTGGGATGAAAATGAACAACGCAAAATTATTC
ACTCTTACGTTAATTATATCAATCATATGGACATCTGGAGCTATAGCTGATCAGAAGATA
AAATCGAGCTCATTGTCTGAGCCAAAAGCAGAAAAATTGACATCAAATAAATTAAATAAT
AACAACAGAGATATTTATATCGATAGCGAAGACGATTTTGAGGGAAGTGGCGGCAGAAAA
GGCGAGGTTCACGATGCATTAGAGAATGAGAATGATGACGTTGATGGATCAGGCTCTGGA
GATGGATTTCCTGGTGATGATGAAGACGGTTTCAAACCAAAAGATAAGAACATAAAACCG
GACTATAATACAAATCAACCTCATCATTCAGGTGATGGTTCAGACCACGGTGTTGATAAT
GATGATGATGAAGAAGAAGAAATTAACAGAAAGAAAATTATTGAGGATCAAAAACCACCT
TCACCCACTGAAAAATCCGATGATATTTTCTTTGAGACTTCAACAGAAACTGACACTTAT
CCATCACAAACAGACGACGAAGATAGTGGTACAAACGATAACAGTAGAAAAACAGGTTTT
GAATATCCAGATAAGAAACCAGATTACGAAATTGATCCAACACATCGTGTTCCTGTCTCA
CCAACTGATTCAAGCAGTGGTAGCTCCGATAATGTGTTGATAATGAACACATCTAATGAG
GATCGCACGACGAGCTTTTTCGCTCAACCAGGTATTTTGGCAGCTGTCATTGGTGGAGCA
GTGGTTGGATTATTGTTTGCTATTTTAATAGTCATGTTTTGTGTTTATCGACTTCGAAAG
AAGGATGAAGGATCATATGCACTCGATGAGCCACAGAAACGATCACCACAAGCCAACTCA
TATACTAAAAATCATAATAATCGGGAATTTTATGCCTGA
>g9085.t1 Gene=g9085 Length=312
MNLKSWCNISGMKMNNAKLFTLTLIISIIWTSGAIADQKIKSSSLSEPKAEKLTSNKLNN
NNRDIYIDSEDDFEGSGGRKGEVHDALENENDDVDGSGSGDGFPGDDEDGFKPKDKNIKP
DYNTNQPHHSGDGSDHGVDNDDDEEEEINRKKIIEDQKPPSPTEKSDDIFFETSTETDTY
PSQTDDEDSGTNDNSRKTGFEYPDKKPDYEIDPTHRVPVSPTDSSSGSSDNVLIMNTSNE
DRTTSFFAQPGILAAVIGGAVVGLLFAILIVMFCVYRLRKKDEGSYALDEPQKRSPQANS
YTKNHNNREFYA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g9085.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 40 | 231 | - |
| 10 | g9085.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 40 | 63 | - |
| 7 | g9085.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 64 | 91 | - |
| 13 | g9085.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 105 | 122 | - |
| 11 | g9085.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 145 | 172 | - |
| 12 | g9085.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 173 | 188 | - |
| 6 | g9085.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 189 | 213 | - |
| 14 | g9085.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 285 | 312 | - |
| 8 | g9085.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 292 | 312 | - |
| 2 | g9085.t1 | PANTHER | PTHR10915:SF1 | SYNDECAN | 56 | 312 | 6.2E-53 |
| 3 | g9085.t1 | PANTHER | PTHR10915 | SYNDECAN | 56 | 312 | 6.2E-53 |
| 1 | g9085.t1 | Pfam | PF01034 | Syndecan domain | 245 | 310 | 2.6E-27 |
| 18 | g9085.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 36 | - |
| 19 | g9085.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 18 | - |
| 20 | g9085.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 19 | 30 | - |
| 22 | g9085.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 31 | 36 | - |
| 17 | g9085.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 37 | 251 | - |
| 21 | g9085.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 252 | 276 | - |
| 16 | g9085.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 277 | 312 | - |
| 15 | g9085.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 36 | - |
| 5 | g9085.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 19 | 36 | - |
| 4 | g9085.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 251 | 273 | - |
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 |
| GO:0007411 | axon guidance | BP |
KEGG
Orthology
- This transcript has been annotated with K16336 (syndecan 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.
