General information for g5818.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g5818 is located on chr_2: 12060583..12061792 (+ 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 | g5818 | g5818.t1 | TSS | g5818.t1 | 12057847 | 12057847 |
| chr_2 | g5818 | g5818.t1 | isoform | g5818.t1 | 12058322 | 12060583 |
| chr_2 | g5818 | g5818.t1 | exon | g5818.t1.exon1 | 12058322 | 12058529 |
| chr_2 | g5818 | g5818.t1 | cds | g5818.t1.CDS1 | 12058322 | 12058529 |
| chr_2 | g5818 | g5818.t1 | TTS | g5818.t1 | 12058394 | 12058394 |
| chr_2 | g5818 | g5818.t1 | exon | g5818.t1.exon2 | 12058723 | 12059013 |
| chr_2 | g5818 | g5818.t1 | cds | g5818.t1.CDS2 | 12058723 | 12059013 |
| chr_2 | g5818 | g5818.t1 | exon | g5818.t1.exon3 | 12059083 | 12059096 |
| chr_2 | g5818 | g5818.t1 | cds | g5818.t1.CDS3 | 12059083 | 12059096 |
| chr_2 | g5818 | g5818.t1 | exon | g5818.t1.exon4 | 12060506 | 12060583 |
| chr_2 | g5818 | g5818.t1 | cds | g5818.t1.CDS4 | 12060506 | 12060583 |
Sequences
>g5818.t1 Gene=g5818 Length=591
ATGAAAATAATTAAAAAATCAATTGTGATAATATGCATCGTCCTGATGCTTTTAAGCATT
AGCGATGCAGCTGAAAAAAAGAAGAAAAAATCTAGAAAATCCAAAACTGTACAAACACCT
GTCATAAGACCACAAAGACAACAACCAGATTATTCAGATATTGAAAATATTGACACAAAT
TTCGACTATGATCAAAATGGAAATGAAGGTTCTGATAGAGTATCATCACAGCCCAATGAA
AATCAATGGCAAAATGCACCATATACTTGTCAATACAATGGTCGATGGTACAGAGAACGT
GAAGAATTTAAATCTGGTCCAAATGATTGTATGACTTGTGTTTGTATTGATACTGAAGTT
GCTTGTGATGACAGAGAATGTCAAATTTCAACAACTGAATATCCACAATTTACTGATTTT
GCTCGTGGTCCACCAAGATTTCCTCAATCTAGACAAGAACAATTTGGTTCAAGAGCACAA
TCACAACAAACTCAAGGAGCTCAAACACAACGTCAATCATTAGCTCAAAAGCATGATCGA
TTAATCAGCTTGTCTAGTTTGATTGCTAATGATGAAGATGATTTTTTTTAA
>g5818.t1 Gene=g5818 Length=196
MKIIKKSIVIICIVLMLLSISDAAEKKKKKSRKSKTVQTPVIRPQRQQPDYSDIENIDTN
FDYDQNGNEGSDRVSSQPNENQWQNAPYTCQYNGRWYREREEFKSGPNDCMTCVCIDTEV
ACDDRECQISTTEYPQFTDFARGPPRFPQSRQEQFGSRAQSQQTQGAQTQRQSLAQKHDR
LISLSSLIANDEDDFF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g5818.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 28 | 55 | - |
| 7 | g5818.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 37 | 55 | - |
| 6 | g5818.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 147 | 176 | - |
| 5 | g5818.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 150 | 176 | - |
| 1 | g5818.t1 | Pfam | PF00093 | von Willebrand factor type C domain | 90 | 132 | 1.0E-6 |
| 11 | g5818.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 23 | - |
| 12 | g5818.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 6 | - |
| 13 | g5818.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 7 | 18 | - |
| 14 | g5818.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 19 | 23 | - |
| 10 | g5818.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 24 | 196 | - |
| 3 | g5818.t1 | SUPERFAMILY | SSF57603 | FnI-like domain | 88 | 135 | 1.46E-8 |
| 9 | g5818.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 23 | - |
| 8 | g5818.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 23 | - |
| 2 | g5818.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 7 | 24 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5818/g5818.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5818.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005515 | protein binding | MF |
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. There were no conditions that were differentially expressed