General information for g3957.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Vang-like protein 2-B.
Parent gene
- The parent gene g3957 is located on chr_3: 29269159..29270864 (+ 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 | g3957 | g3957.t1 | TSS | g3957.t1 | 29268868 | 29268868 |
| chr_3 | g3957 | g3957.t1 | isoform | g3957.t1 | 29269159 | 29270864 |
| chr_3 | g3957 | g3957.t1 | exon | g3957.t1.exon1 | 29269159 | 29269657 |
| chr_3 | g3957 | g3957.t1 | cds | g3957.t1.CDS1 | 29269159 | 29269657 |
| chr_3 | g3957 | g3957.t1 | exon | g3957.t1.exon2 | 29269717 | 29270864 |
| chr_3 | g3957 | g3957.t1 | cds | g3957.t1.CDS2 | 29269717 | 29270864 |
| chr_3 | g3957 | g3957.t1 | TTS | g3957.t1 | 29271397 | 29271397 |
Sequences
>g3957.t1 Gene=g3957 Length=1647
ATGGAAACAGAATCAGTAAAATCAGAAAGAAGCAATAGATCGCACAAGAGCAGGAATTCA
GGGATAAATTCACATCGCTCAAGACATTCGAGTCGAAATCAGTCGAGTGGCAAAGCAGGA
AAGATGGCTCCATTCCAAACAACAGTTAATTTAACGAATGACGATACGCGTGAAGGACAT
GGTCAAGAAATCATTGAAGTACAGATTCTGCCTCAAAACGATGAGACATGGGGCACAGAA
ACGCACATCACGGGAAATACCTCAGAACAAAGTATCTCTATGGAAAATGTCAATTGGCCC
ACTAATGATGGTGGTTCACTTGCATGTCAAAAACATTTTGAACAAATATTATCACTTCTT
CTGTGCATGGCATCATTCTTTAGTCCCATCGCAATGGCCTTACTACCGAAGCTAGGATTT
TTTCCTTCAACTTTTCAAAATGAAGAACTCAATCAATTGACAAAAATTCAATTATTAGAC
TGTAATGCAGAATGTAAAGGATTACTTGTGACATTAACAACAAGACAATTGCTATTAGCT
ATAGCTTTATGGGCTCTTTTCTTTCGTCGACCAATTGCAGTGATGCCACGGATATTTCTC
TTCCGTTCGATAGCACTACTTTTAGTACTCATTTCAACATTTTCGTATTGGCTTTTTTAT
ATTGTTCAAGTAACAGAAAGTATAACCAAAGCAATAGTTGATGGCACAGAAGCTGCCAAT
TACAAGACACTTGTGTCATATGCAATCAATTTTAGTGACACACTCTTATTCATTCACTAT
GTCGCTGTTATTTTGATGGAGATCCGGCATCTTCAACCATTGTATTATGTGAAAGTTGTA
CGATCACCGGATGGCGAATCTCGAAGCTATGCAATTGGACAATTCTCAATACAACGTGCG
TCAGTTTGGATTTTGCAAAAATATTATTCAGATTTCTCTGTTTACAATCCATATCTCGAA
AGAATACCATTGTCAAAGCAACAGAGAAAAGCTCTTTCAACAAGTTTCAAATATTATGAT
GTTGATGGCTCTATTCAAACGACACCACACCAGCAGAGTCAAAGAGCTGTTTTAGCAGCA
CATGCACGTCGTCGAGATTCTTCACACAATGAGAGATTTTATGAAGAACATGAATATGAG
AGACGAGTGAAAAAACGTCGTGCACGTTTAATTACAGCTGCTGAAGAAGCATTTACTCAC
ATTAAACGAGTTCATGATCAATCTACATCAAACACACTCGACCCTAATGAAGCTGCAGCT
TCTATTTTCCCATCATTAGCTCGCGCTTTACAAAAATACCTCAGAGTAACACGCCAGCAA
CCTCGGCATAGTGTAGAATCAATTCTTAAGCATTTATCGCATTGCCTTAAGAATGATCTC
TCGCCACGTGCATTTCTTGAAATGTATCTGATTGAGTCACCAGTGCTGCAGAATGAGAAA
GAACATCACAATCAATCTTGGTCTCTAATTTGTGATGAACTTCTCTCACGACCAATTTTT
GATTCGTGCGTGTTTCAATTAGTACAGAATGATGTCTCCCTCACCGTATCTGTTCATAAA
TTGCCACACTTTAATATTACAGAAAAAGTTGTTGACCCAAAGTGTAACAAGTTTGTATTG
CGTCTCAACTCTGAAACAAGTGTTTGA
>g3957.t1 Gene=g3957 Length=548
METESVKSERSNRSHKSRNSGINSHRSRHSSRNQSSGKAGKMAPFQTTVNLTNDDTREGH
GQEIIEVQILPQNDETWGTETHITGNTSEQSISMENVNWPTNDGGSLACQKHFEQILSLL
LCMASFFSPIAMALLPKLGFFPSTFQNEELNQLTKIQLLDCNAECKGLLVTLTTRQLLLA
IALWALFFRRPIAVMPRIFLFRSIALLLVLISTFSYWLFYIVQVTESITKAIVDGTEAAN
YKTLVSYAINFSDTLLFIHYVAVILMEIRHLQPLYYVKVVRSPDGESRSYAIGQFSIQRA
SVWILQKYYSDFSVYNPYLERIPLSKQQRKALSTSFKYYDVDGSIQTTPHQQSQRAVLAA
HARRRDSSHNERFYEEHEYERRVKKRRARLITAAEEAFTHIKRVHDQSTSNTLDPNEAAA
SIFPSLARALQKYLRVTRQQPRHSVESILKHLSHCLKNDLSPRAFLEMYLIESPVLQNEK
EHHNQSWSLICDELLSRPIFDSCVFQLVQNDVSLTVSVHKLPHFNITEKVVDPKCNKFVL
RLNSETSV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g3957.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 16 | - |
| 8 | g3957.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 55 | - |
| 9 | g3957.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 26 | 55 | - |
| 2 | g3957.t1 | PANTHER | PTHR20886 | VANG-LIKE PROTEIN | 1 | 548 | 2.6E-209 |
| 3 | g3957.t1 | PANTHER | PTHR20886:SF11 | VANG-LIKE PROTEIN | 1 | 548 | 2.6E-209 |
| 19 | g3957.t1 | PIRSF | PIRSF007991 | Vang-like | 1 | 548 | 5.6E-222 |
| 1 | g3957.t1 | Pfam | PF06638 | Strabismus protein | 25 | 548 | 4.3E-216 |
| 11 | g3957.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 115 | - |
| 16 | g3957.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 116 | 135 | - |
| 14 | g3957.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 136 | 167 | - |
| 18 | g3957.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 168 | 187 | - |
| 12 | g3957.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 188 | 198 | - |
| 17 | g3957.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 199 | 219 | - |
| 13 | g3957.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 220 | 243 | - |
| 15 | g3957.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 244 | 266 | - |
| 10 | g3957.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 267 | 548 | - |
| 4 | g3957.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 116 | 135 | - |
| 6 | g3957.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 168 | 187 | - |
| 5 | g3957.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 199 | 221 | - |
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:0007275 | multicellular organism development | BP |
| GO:0016021 | integral component of membrane | CC |
KEGG
Orthology
- This transcript has been annotated with K04510 (vang-like)
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.
