General information for g4343.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative U4/U6.U5 tri-snRNP-associated protein 1.
Parent gene
- The parent gene g4343 is located on chr_2: 1423611..1424794 (+ 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 | g4343 | g4343.t4 | isoform | g4343.t4 | 1423611 | 1424584 |
| chr_2 | g4343 | g4343.t4 | exon | g4343.t4.exon1 | 1423611 | 1424584 |
| chr_2 | g4343 | g4343.t4 | cds | g4343.t4.CDS1 | 1423913 | 1424584 |
| chr_2 | g4343 | g4343.t4 | TTS | g4343.t4 | 1424859 | 1424859 |
| chr_2 | g4343 | g4343.t4 | TSS | g4343.t4 | NA | NA |
Sequences
>g4343.t4 Gene=g4343 Length=974
AACCTAAAAAGAAAGTTAAAAAAATTCGACAAAAACTAAAAGCTGATGACTTGTTAGAAA
TTGCTGGTGATTCAAGTTCAAACAAGGATCTTGGAAGTAGAAAAAGAAAAGACGATGATG
AACTGAAAAAAGTTGTTCTTAATATAGATGATCTTCCTGAATTGCCTGAAGATACATCAA
ATATCAAAATTGAACCAGAGGATGATGAACTTGAACATATTTTAAGTAAAGCTAGACGGT
TAAAGCAAAAAGAGATTATTAAGAAAGAACTGCCAGTTGATAATATTAAAACAGAGGTGA
AAATGGAAACTGAAGATTCTGAGGGCGAGGCAGAAATTCGTGCTAATAATTTTATTACAC
TCAATCAAACAGCAGAATTTTGTAGAACTTTGGGTGATATACCTACTTATGGAATGGCTG
GAAATCGCGATGAAAATACAGATATGATGGATCTTGAAGATGAAGTTGAAGAACAAGAGC
CTTCAATGGATAAACGCGGTAAATGGAATACTGTTGATCCGAATGAAGAACCAAAATTAG
CTGAAGGAGTTCCGATTGTTGAGCCCGAAGATGTTGCCATTTTAGATGAAGAGCCCGATA
TTGGTGCAGGCGTAGCAAATGCTTTAAAATTAGCCATGTCTAAAGGATATCTAGAAAAAG
AAGAAACAAATCGTCCAAGTAATTCTAGATTTGCTCATTTGCAAGCACAACATTATTCAA
TTGATGATAAGGCACATGGAGAAGACGATAAATATGGTAGAAGAGGAGGTGGCGGTGGTG
GTTATAATGGTCCACTCTCAGAATTTAGAGAAAAAGCTGGATATAAACCTAATGTTAAAC
TTGAATATATTGATGATAATAACATGAAGTTGACACCAAAAGAAGCTTTCAGATATTTAT
CTCATAAATTTCATGGAAAAGGTCCAGGGAAGAACAAGATTGAGAAGAGGTTAAAGAAAT
TGGAGCAAGAAGGG
>g4343.t4 Gene=g4343 Length=224
METEDSEGEAEIRANNFITLNQTAEFCRTLGDIPTYGMAGNRDENTDMMDLEDEVEEQEP
SMDKRGKWNTVDPNEEPKLAEGVPIVEPEDVAILDEEPDIGAGVANALKLAMSKGYLEKE
ETNRPSNSRFAHLQAQHYSIDDKAHGEDDKYGRRGGGGGGYNGPLSEFREKAGYKPNVKL
EYIDDNNMKLTPKEAFRYLSHKFHGKGPGKNKIEKRLKKLEQEG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g4343.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 53 | 84 | - |
| 4 | g4343.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 58 | 74 | - |
| 7 | g4343.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 135 | 168 | - |
| 6 | g4343.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 136 | 154 | - |
| 2 | g4343.t4 | PANTHER | PTHR14152:SF5 | U4/U6.U5 TRI-SNRNP-ASSOCIATED PROTEIN 1 | 5 | 223 | 4.9E-44 |
| 3 | g4343.t4 | PANTHER | PTHR14152 | SQUAMOUS CELL CARCINOMA ANTIGEN RECOGNISED BY CYTOTOXIC T LYMPHOCYTES | 5 | 223 | 4.9E-44 |
| 1 | g4343.t4 | Pfam | PF03343 | SART-1 family | 10 | 223 | 1.9E-49 |
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:0000398 | mRNA splicing, via spliceosome | BP |
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.
