General information for g4502.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g4502 is located on chr_2: 2920023..2924003 (- 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 | g4502 | g4502.t1 | TTS | g4502.t1 | 2918931 | 2918931 |
| chr_2 | g4502 | g4502.t1 | isoform | g4502.t1 | 2919012 | 2920023 |
| chr_2 | g4502 | g4502.t1 | exon | g4502.t1.exon1 | 2919012 | 2919146 |
| chr_2 | g4502 | g4502.t1 | cds | g4502.t1.CDS1 | 2919012 | 2919146 |
| chr_2 | g4502 | g4502.t1 | exon | g4502.t1.exon2 | 2919239 | 2919674 |
| chr_2 | g4502 | g4502.t1 | cds | g4502.t1.CDS2 | 2919239 | 2919674 |
| chr_2 | g4502 | g4502.t1 | exon | g4502.t1.exon3 | 2919733 | 2919929 |
| chr_2 | g4502 | g4502.t1 | cds | g4502.t1.CDS3 | 2919733 | 2919929 |
| chr_2 | g4502 | g4502.t1 | exon | g4502.t1.exon4 | 2919991 | 2920023 |
| chr_2 | g4502 | g4502.t1 | cds | g4502.t1.CDS4 | 2919991 | 2920023 |
| chr_2 | g4502 | g4502.t1 | TSS | g4502.t1 | 2920096 | 2920096 |
Sequences
>g4502.t1 Gene=g4502 Length=801
ATGGACTGTGATAGCATACAAGAAGAAGGAGAAATCATTGATTTTGATGATGAAGAAGAA
AATAAACAAGTGCAAGAAGAGGAGGAAACAGCAGCATATAATCCAATAATTCGACCAGAA
ACTCAAAGATCTGTACAATTTCAGCAATTGCAACATTCTGATACTAGCTCGAATGAATCA
GATGATGAAGAAGAAAATATTAAAAAAATACCACCATCACAAAAGCCAAAATTTAGTAAT
AAAAGTGGAAATTTATGGGCGCAAATGCTTCAAGAAGAAGATCTCATGGATAATTTAAAA
TCTTGCGAAGTAAATAGAAAGAGAAAGTATGAAGTTGATAGAGGAGTAGAGACTTACAAA
CTAGAAGATCCAGTTAATTATAAGAAACAACGAACTGATACAGCTTCTTCTGCTGATGAA
CCAAGCATTATTCGGAAATATGCTAAAGGGAAAATTAAATCTCTTCATAAACCCAAAAAA
CTTGAAGACCTTGTTGTAGCAGACAATTATAATGATGAAGATTATGGTATTGAAGTAGCG
AAAAAATTAAGTGAACAAAATGTTGATTTGATACACAAAGTAGTAGCGACAATAGGAAGA
GAGAAAGTTAATGATTTGTATGAAAAAACACGAAACATTGAACGAAAAGGAGGAATGCTT
ATTGTGAACAAATCACGTCGTAGAACTTCTGGTGGAATTTTTTTATTTCTTTTAAAGACT
TCCAATGTTATAGATGAAGCTCAAAAAAAAGAGATTTTTGATGATGGAAAAGAAGAAGCA
ACAAAAGAGTTATCTACCTAG
>g4502.t1 Gene=g4502 Length=266
MDCDSIQEEGEIIDFDDEEENKQVQEEEETAAYNPIIRPETQRSVQFQQLQHSDTSSNES
DDEEENIKKIPPSQKPKFSNKSGNLWAQMLQEEDLMDNLKSCEVNRKRKYEVDRGVETYK
LEDPVNYKKQRTDTASSADEPSIIRKYAKGKIKSLHKPKKLEDLVVADNYNDEDYGIEVA
KKLSEQNVDLIHKVVATIGREKVNDLYEKTRNIERKGGMLIVNKSRRRTSGGIFLFLLKT
SNVIDEAQKKEIFDDGKEEATKELST
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g4502.t1 | Gene3D | G3DSA:1.10.10.1440 | - | 166 | 265 | 1.7E-26 |
| 3 | g4502.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 80 | - |
| 4 | g4502.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 25 | - |
| 5 | g4502.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 37 | 55 | - |
| 2 | g4502.t1 | PANTHER | PTHR13135 | CYTOSOLIC RESINIFERATOXIN BINDING PROTEIN RBP-26 | 62 | 260 | 7.5E-32 |
| 1 | g4502.t1 | Pfam | PF10258 | PHAX RNA-binding domain | 178 | 257 | 6.2E-28 |
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:0006408 | snRNA export from nucleus | BP |
KEGG
Orthology
- This transcript has been annotated with K14291 (phosphorylated adapter RNA export protein)
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.
