General information for g3940.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g3940 is located on chr_3: 29050555..29051805 (- 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 | g3940 | g3940.t1 | isoform | g3940.t1 | 29050555 | 29051805 |
| chr_3 | g3940 | g3940.t1 | exon | g3940.t1.exon1 | 29050555 | 29051138 |
| chr_3 | g3940 | g3940.t1 | cds | g3940.t1.CDS1 | 29050672 | 29051138 |
| chr_3 | g3940 | g3940.t1 | exon | g3940.t1.exon2 | 29051208 | 29051805 |
| chr_3 | g3940 | g3940.t1 | cds | g3940.t1.CDS2 | 29051208 | 29051805 |
| chr_3 | g3940 | g3940.t1 | TSS | g3940.t1 | NA | NA |
| chr_3 | g3940 | g3940.t1 | TTS | g3940.t1 | NA | NA |
Sequences
>g3940.t1 Gene=g3940 Length=1182
ATGAAGAGAGAAAATCGAAAGACTCAGAACGAGCGTCCGGCTCAAAACATTGCGCCAGAG
CTGAGAAATTATAGAATTCCCAGACTCAGCGAACGTGAAAATAACAATTCAACTCGCCAC
AGCTCTCCTAACAGAGACTCAGCACACTCTTCACGTTCTCGCCATCGCGCTCATTCGTCT
CATCGCAGAAGACAATCTAGTCCTTCGCCTCGACGCCCAAGTCGTGATATCTCTCTAGCA
AGAGTTCGTCGCCGTGCGGAATTACGCCGCAGACCTTCACCTCAAGTGCAATTTCGAGAA
CACATCGAATTCATTCCTCGCCCATCATCACCTCATCATCACGATCGTCCCAGAAGCAGT
CGCCATCGCTCACCATCCAGACGACGCTACTCTTTGGACCGACGTCATCAACCAATTCGT
CGCCAATCAACCGAAGCTCGACGTCCAATCGCTGAACGCTTGGGGCCCAACCCAGGAAAT
AATCCTTTGGTTCGTGTTGTCCATCAACACCGCACCCAAGTGCTTAAGTTTGCAAAAGTT
CCACGAGATGTGAGCCTTATCAGAGTTTCTCAAACTCTTAAGTCGTTGGATGACAGGATG
ATTCAAGAAGAAATAGACGCAGCAGTCAATCGAGAACTTGAATTCAACTTTAGCAGCGGA
ATGATGTCAATAAAACCTTCACTTCAATCAGCCACAATTATGTCCGTAATGATTGCAGAC
GCAGAAGGAGAAGGAATTTCTCTAGTACCAACTTTAATGCTACGTAATTTAATTCCAATT
ACCACTCGACAAGCAATCGCAGGAGTAATTGATGCAGTTGATACAGTGGCTAATGAAGGA
ACTATTGTGACACATGTGCGAGTACCAACAAAAGACTCTGGTTTACACAAAACAGCAGCA
ATCGCATTTGTTGGTATATCATCTGATGCACAACTTTTTTCACTTGATGGTTTTTTATGT
GAACGATTAGTCAAGAACATTCCTTTGGACAAGAGCCTCCAAGCTCCAGTTCTCATCCCA
ACAGCGATGTCTCGTCAGCCACATGACAAGGAATGGGCTAAACAANNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNATTCACACTATTAA
>g3940.t1 Gene=g3940 Length=355
MKRENRKTQNERPAQNIAPELRNYRIPRLSERENNNSTRHSSPNRDSAHSSRSRHRAHSS
HRRRQSSPSPRRPSRDISLARVRRRAELRRRPSPQVQFREHIEFIPRPSSPHHHDRPRSS
RHRSPSRRRYSLDRRHQPIRRQSTEARRPIAERLGPNPGNNPLVRVVHQHRTQVLKFAKV
PRDVSLIRVSQTLKSLDDRMIQEEIDAAVNRELEFNFSSGMMSIKPSLQSATIMSVMIAD
AEGEGISLVPTLMLRNLIPITTRQAIAGVIDAVDTVANEGTIVTHVRVPTKDSGLHKTAA
IAFVGISSDAQLFSLDGFLCERLVKNIPLDKSLQAPVLIPTAMSRQPHDKEWAKQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g3940.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 152 | - |
| 1 | g3940.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 25 | 50 | - |
| 3 | g3940.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 51 | 68 | - |
| 5 | g3940.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 76 | 97 | - |
| 2 | g3940.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 114 | 135 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
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. There were no conditions that were differentially expressed