General information for g1898.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g1898 is located on chr_3: 13739381..13740628 (- 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 | g1898 | g1898.t2 | TTS | g1898.t2 | 13739139 | 13739139 |
| chr_3 | g1898 | g1898.t2 | isoform | g1898.t2 | 13739140 | 13740026 |
| chr_3 | g1898 | g1898.t2 | exon | g1898.t2.exon1 | 13739140 | 13740026 |
| chr_3 | g1898 | g1898.t2 | cds | g1898.t2.CDS1 | 13739381 | 13739548 |
| chr_3 | g1898 | g1898.t2 | TSS | g1898.t2 | 13740814 | 13740814 |
Sequences
>g1898.t2 Gene=g1898 Length=887
AGTTAGTGGATCATTCTCTCCAGAAGAATTGCAAGCTTTAAAAGAGGAATTTCAACATCA
TGAAGAAAAAGTCGATTTTTACTTCAGTTTACTTGAAAATTTAGATAAAGTGAAGGACAA
AAAAGATGATTTTCATCACAAGAATGCAGTAAATGAAGATGAGCTCGATGAAGCAAATGA
AATTGCATTGAATGATGATGAAGACAAAAATGACATCGTTCAAGAGCAGAAACGAAATAA
ACATGAGGAATACATTGGTAAAGCAAATGAAGTTCGAGAAAAGCACAGAGAAATACGCGA
TAATATTGATCGTTTGGAAAGAAAAGTATCTCGTGGATCAAATTCCAGTGATTTTATTGA
ACCAAAAGTTCAAGGATTATGGAGAATCGCACAAGAGAGTGATTTTAATGCCGAACAGCT
TGCATCGATTAAAGTAGAACTACATCATTTTGAATCAAGATTTTTAAAACTTAGACACAT
GCATGCTGAACATGCCCTTACAATGGAAAAATATAAGAATGCAAAACCTGGTGATAAGCA
TCATGATAAAGTCAGTGAAATGGAAGCAAAGATTCAAAAGCAGTCAAGAAAAGTAGAAAA
ATTACAAGAAGATATAGAAAAGAAATTGAGGAAAACAGAATTGTAGTGAGTAGAGAGCAA
CAATTTATAAGTACTTCTGATGCCAAAAAATCTCATTTTTTCTCAAATTGTGCAACTGTC
CACTGATGAAATTGTCTCTCGTTAGAATATATTATTAAAATGAGCTATTTTAAAACAATG
TGTAGAAAGATTAGATGCCTTAATGTCTGTTCGTATAGTACTACATATTTTATTTTTGTG
AATTTTTCTTTTTCTTAATAAACGTGAATATTTTTATATACCTACCA
>g1898.t2 Gene=g1898 Length=55
MHAEHALTMEKYKNAKPGDKHHDKVSEMEAKIQKQSRKVEKLQEDIEKKLRKTEL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 3 | g1898.t2 | Coils | Coil | Coil | 25 | 52 | - |
| 2 | g1898.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 55 | - |
| 1 | g1898.t2 | Pfam | PF06401 | Alpha-2-macroglobulin RAP, C-terminal domain | 1 | 52 | 4.1E-7 |
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:0005783 | endoplasmic reticulum | CC |
| GO:0008201 | heparin binding | MF |
| GO:0050750 | low-density lipoprotein particle receptor 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.
