General information for g5788.t61
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g5788 is located on chr_2: 11943105..11945282 (- 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 | g5788 | g5788.t61 | isoform | g5788.t61 | 11943105 | 11945282 |
| chr_2 | g5788 | g5788.t61 | exon | g5788.t61.exon1 | 11943105 | 11943831 |
| chr_2 | g5788 | g5788.t61 | TSS | g5788.t61 | 11943390 | 11943390 |
| chr_2 | g5788 | g5788.t61 | exon | g5788.t61.exon2 | 11943890 | 11945067 |
| chr_2 | g5788 | g5788.t61 | cds | g5788.t61.CDS1 | 11944120 | 11944500 |
| chr_2 | g5788 | g5788.t61 | exon | g5788.t61.exon3 | 11945156 | 11945282 |
| chr_2 | g5788 | g5788.t61 | TTS | g5788.t61 | NA | NA |
Sequences
>g5788.t61 Gene=g5788 Length=2032
TTGTAAGAATAGGCCATCAGGAAAACGTACTCTAATAACCGAGTATTTGAATTTTTTAAC
AAATCTTTCTTGCTCTTTTTCACGCATTGCCTTTGTTTTTAAAACCATAGCATCTTCAAC
GGCTGAATACTTATTTGTTTGTTCTCTCTTAAGTTCTTCTGCGGTAAGCTTGAAAAAATC
TTGAGATAGCGAAGGCTGATTATTTTGCGAAGGTAGCAAAACTTGAATGTTACGATCAAG
TTCTAGTTGAATTGGTTCGCATTCATTTAAATATTCGATTTGTTTTAAAAGATGTTCTAT
TGATGTTTCTGGCGACCAAACAAGGAAACTTTCACCATCAATGACCTGCTCACTAAAGCC
AGCATTTTTTAAAAATTCCGATGAGCCTTCAACGTTGGCGACTTTATCACAAAAAATTCT
GTTAGTCATACGAATTTTATGAAATTTAACTTCCGATGGTTCTTGAATAATATTTGAGAG
ATACTTTTTGAGTGTCTCAACGCAATCTTGTGAACGCTCGATAGGATTGCAACTCTTTAT
AATAAGACAAGATGTAATTCCTGGATCAAGATGATCAGTGCTATTGCTTAATGCAAGTTG
AAGTTGCTCATGTAAGAAATCTTTGATTTTTTGTTTCCATTCCTTTTTAGGTAGTATTTC
ATCAGATATAAGAGAACATGTAAAATTTATATCAATGGTGTTCTCGTCTTGTTTCGGTTC
TTCATTTATTTTTAAATTACTCATTTCATTTTCAACTTTTCTTACTTTCTCTTCTTCAAG
CTCTTTTCGAGCTTTTTCTTTTATAGCTTTAAGCGAAAGATCAAAAGATGGTGTATTAGA
AGTTTTATTCATTCTTTCCAATGCTGCATCACGAGCTTTCTTCATTTCATCAGTCAAATC
ATCTCTTTTTATAGGGACATATGCATCTTTATCTTTGGGTTTACTATCTCTGCTACTACT
TCCACCATCATCACCTGTCAATTTTCTTCCAGGTCCCGCTTTAGCAAATTTCGCGTCCGA
CTTTTTCTTAGCAAAAAACTTTTTAACTTTAGCTCCTACCGAACTCATTTTTTAAGGTTT
CTTAAAAATACGCAAATAATTGCTGATTATAATCTTGGTGTGTGTTCTTTTGGTAACTTC
AATTTTTCGACGGATTTTCTGAGTGCTTCAATTTCAATTAATGTAGATGATTTTATGAAA
TTCGAGTAAATCGTATCGCCGTAACAATTCCAAAAGAACAAAATCAGTATTATATTGAAG
AATAATATAATGAGCAGTGAATACAAGATGTTAACTTGGAAATCTATACTTACAGCTTCC
TAACAGAGACTCTCTTAAATCAAAATATATTAAAAAATCCACAAGATCGTCAATCATAAT
CAGTACATAAACACTATATTAATATTTTTTCACAAAATCAAAAAGAAAACAAGAATAATC
ACAAAGATTTTCGAATTCGAAATTTTCCTTTTGAAAAAATTTTCCAAACGAATTGGTCAA
AATCCTTTTTTAGAATTTAATTCAATAATGTACAGCCTAACTTGATTGTCTGTCAAATTA
ATATTCACGAAATTTGCTTAATTCTAGAAATTTTTTAATTTAAAATTTAATAAAATTGAA
AATATTATATTTAACGAGTTTTTTAAAACATAGGTTTGTATTTCCCTATGCGACAAAAAA
CATTCGAAGCATTCCCCTTTTAAATTGCCAACTCATAATTTTCTCAACTCTCTCATTAGC
CAGCTCAGTATTTGGTATAAAACAGCAGAGCAGAAAAGCCGGTGGATCATTTTTGTCATT
CTCTGAATTTAAATTAAAGTGCTAAAGTATCTTAAGTTATAAAAATGAAGTGGATATTAC
TACTTTCAAGTCTTTTAATTCTAAATTTAATTCACGCAAGTGAAATTAAAGAGGAAGAAG
GTGTTTTAGTCTTGACAAAATCAAATTTCAAAGAGGCACTTAAGAATGAATTCATTTTAG
TTGAATTTTGTAAGTATTACATAGACCAATTGTTTATTATCTACATTATTAC
>g5788.t61 Gene=g5788 Length=126
MVFSSCFGSSFIFKLLISFSTFLTFSSSSSFRAFSFIALSERSKDGVLEVLFILSNAASR
AFFISSVKSSLFIGTYASLSLGLLSLLLLPPSSPVNFLPGPALANFASDFFLAKNFLTLA
PTELIF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g5788.t61 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 11 | - |
| 8 | g5788.t61 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 12 | 34 | - |
| 5 | g5788.t61 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 35 | 45 | - |
| 10 | g5788.t61 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 46 | 65 | - |
| 7 | g5788.t61 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 66 | 70 | - |
| 9 | g5788.t61 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 71 | 89 | - |
| 4 | g5788.t61 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 90 | 126 | - |
| 2 | g5788.t61 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 7 | 26 | - |
| 3 | g5788.t61 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 46 | 63 | - |
| 1 | g5788.t61 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 70 | 89 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5788/g5788.t61; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5788.t61.fa.iupred3.txt does not exist
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
