General information for g4343.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t1 | TSS | g4343.t1 | 1422198 | 1422198 |
| chr_2 | g4343 | g4343.t1 | isoform | g4343.t1 | 1422272 | 1424794 |
| chr_2 | g4343 | g4343.t1 | exon | g4343.t1.exon1 | 1422272 | 1422458 |
| chr_2 | g4343 | g4343.t1 | cds | g4343.t1.CDS1 | 1422272 | 1422458 |
| chr_2 | g4343 | g4343.t1 | exon | g4343.t1.exon2 | 1422516 | 1424584 |
| chr_2 | g4343 | g4343.t1 | cds | g4343.t1.CDS2 | 1422516 | 1424584 |
| chr_2 | g4343 | g4343.t1 | TTS | g4343.t1 | 1422757 | 1422757 |
| chr_2 | g4343 | g4343.t1 | exon | g4343.t1.exon3 | 1424648 | 1424794 |
| chr_2 | g4343 | g4343.t1 | cds | g4343.t1.CDS3 | 1424648 | 1424794 |
Sequences
>g4343.t1 Gene=g4343 Length=2403
ATGGGCAAAGAAAAAAAGCATAAAAGAGATAAAGATTTAAGTTCACGACGTAGAAGTCGT
TCAAGATCACGATCAAGAAGTGAAGAATATAAAGAAAAGAAAAGGAGCAAGAAAAATCGT
GAAAAAGACAGAGAGAGAAAACATCGAAGGAGAAGTTCAGATCGTGAAAAATCATATCAC
AGTGACAGTTCAGATGTAGTTGAAGTTCCAATTATACCTGATCCACCAGTTATTTCTTCT
TCTTTTCGAAATGAACCAACACCTTCAAAAACATCAAAGCAAAGAAAAAAGTCTCTTTCA
CCAATTCCTGCTGATGGTGCTGGCGATGTTCTCTCTATTGAAGAAACTAATAAATTAAGA
GCAAAATTAGGACTTAAACCATTAGAAGTTGGTTCATCTGAAGTTCCTCAGAGTAGCAGC
AGTGGCAGCAAAAAAGAAGAAGAAAAAGATAAAGATGGAAATTCTCAAGAATTAAAGAAG
ATAAAAGATGATTGGGGTGAATTTTATCATAAACCAGCTGGTCAATTTAATGAAAAGACT
GAAGTTGAATTGCTTAGAGAAAAAATTCAATCTAAACGTGAAAAAAGAAAGATTGAGGAC
AAATTGGCAAGAATCAAAACACTCGGTGAGTCTGATTCAGATGATGATGCCAATGCTTGG
GTTGATAAAAGTCGTAAAATTGAAGAAGAGAAAAAGAAAGCGCAACTTCGAGCTAAAATG
CTTCAAGAAATGGATGAGAATTTAGATAATGTCACTACAACACATGCACGTCGTCCTGCT
AGACCTCAAAAATCATCACAATTATCGAAAGATCAAGGATATGGCTCAAAAGACCTTCAA
GGACTAAAAGTAGCTCACGATATTGATAGTTTTAAAGAAGAGAGACAAGTTATTTTAACT
CTAGAGGATAAAGACGTATTGGATGAGGATGGTGACACTCTTATGAATGTGAACATGAAA
GATGATGAACGATATAAGAAAAATGTTGAAGTCAAGAAACAAAATCCACAACATTATGGC
TATGATGTATATGAAGATCAATATGATGAGTTTGGTAATTTCATTGGTCGAGGCATTCTA
TCAAAATACGATGAAGAAATTGATGGATCTAAAAAACCTACATTTACAATAGGAGAAAGT
AAAGATTTAATACAAGAGCAACAACGTAAAGCACTAGAAGTAAAAGCAAAATTAGAAAAT
AAACGACTTGAAACCCTTAATTTGGATCCATTAAAAATCGCATCGGATTGCTTTACTGAA
GAAGAATTAACAAAATTCAAAAAACCTAAAAAGAAAGTTAAAAAAATTCGACAAAAACTA
AAAGCTGATGACTTGTTAGAAATTGCTGGTGATTCAAGTTCAAACAAGGATCTTGGAAGT
AGAAAAAGAAAAGACGATGATGAACTGAAAAAAGTTGTTCTTAATATAGATGATCTTCCT
GAATTGCCTGAAGATACATCAAATATCAAAATTGAACCAGAGGATGATGAACTTGAACAT
ATTTTAAGTAAAGCTAGACGGTTAAAGCAAAAAGAGATTATTAAGAAAGAACTGCCAGTT
GATAATATTAAAACAGAGGTGAAAATGGAAACTGAAGATTCTGAGGGCGAGGCAGAAATT
CGTGCTAATAATTTTATTACACTCAATCAAACAGCAGAATTTTGTAGAACTTTGGGTGAT
ATACCTACTTATGGAATGGCTGGAAATCGCGATGAAAATACAGATATGATGGATCTTGAA
GATGAAGTTGAAGAACAAGAGCCTTCAATGGATAAACGCGGTAAATGGAATACTGTTGAT
CCGAATGAAGAACCAAAATTAGCTGAAGGAGTTCCGATTGTTGAGCCCGAAGATGTTGCC
ATTTTAGATGAAGAGCCCGATATTGGTGCAGGCGTAGCAAATGCTTTAAAATTAGCCATG
TCTAAAGGATATCTAGAAAAAGAAGAAACAAATCGTCCAAGTAATTCTAGATTTGCTCAT
TTGCAAGCACAACATTATTCAATTGATGATAAGGCACATGGAGAAGACGATAAATATGGT
AGAAGAGGAGGTGGCGGTGGTGGTTATAATGGTCCACTCTCAGAATTTAGAGAAAAAGCT
GGATATAAACCTAATGTTAAACTTGAATATATTGATGATAATAACATGAAGTTGACACCA
AAAGAAGCTTTCAGATATTTATCTCATAAATTTCATGGAAAAGGTCCAGGGAAGAACAAG
ATTGAGAAGAGGTTAAAGAAATTGGAGCAAGAAGGGCTTATGAAAAAAATGTCATCATCA
GATACTCCTTTAAATACATTAACAATGTTACAACAAAAGCAAAAGGAAACACAAAGTCCA
TTTATTGTGCTCAGTGGAAATAAATCATCGCAATCAACAATGCTAGGAAAAAACAAACGA
TAA
>g4343.t1 Gene=g4343 Length=800
MGKEKKHKRDKDLSSRRRSRSRSRSRSEEYKEKKRSKKNREKDRERKHRRRSSDREKSYH
SDSSDVVEVPIIPDPPVISSSFRNEPTPSKTSKQRKKSLSPIPADGAGDVLSIEETNKLR
AKLGLKPLEVGSSEVPQSSSSGSKKEEEKDKDGNSQELKKIKDDWGEFYHKPAGQFNEKT
EVELLREKIQSKREKRKIEDKLARIKTLGESDSDDDANAWVDKSRKIEEEKKKAQLRAKM
LQEMDENLDNVTTTHARRPARPQKSSQLSKDQGYGSKDLQGLKVAHDIDSFKEERQVILT
LEDKDVLDEDGDTLMNVNMKDDERYKKNVEVKKQNPQHYGYDVYEDQYDEFGNFIGRGIL
SKYDEEIDGSKKPTFTIGESKDLIQEQQRKALEVKAKLENKRLETLNLDPLKIASDCFTE
EELTKFKKPKKKVKKIRQKLKADDLLEIAGDSSSNKDLGSRKRKDDDELKKVVLNIDDLP
ELPEDTSNIKIEPEDDELEHILSKARRLKQKEIIKKELPVDNIKTEVKMETEDSEGEAEI
RANNFITLNQTAEFCRTLGDIPTYGMAGNRDENTDMMDLEDEVEEQEPSMDKRGKWNTVD
PNEEPKLAEGVPIVEPEDVAILDEEPDIGAGVANALKLAMSKGYLEKEETNRPSNSRFAH
LQAQHYSIDDKAHGEDDKYGRRGGGGGGYNGPLSEFREKAGYKPNVKLEYIDDNNMKLTP
KEAFRYLSHKFHGKGPGKNKIEKRLKKLEQEGLMKKMSSSDTPLNTLTMLQQKQKETQSP
FIVLSGNKSSQSTMLGKNKR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 21 | g4343.t1 | Coils | Coil | Coil | 144 | 164 | - |
| 20 | g4343.t1 | Coils | Coil | Coil | 224 | 246 | - |
| 19 | g4343.t1 | Coils | Coil | Coil | 381 | 409 | - |
| 11 | g4343.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 111 | - |
| 6 | g4343.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 22 | 39 | - |
| 8 | g4343.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 47 | 63 | - |
| 7 | g4343.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 80 | 98 | - |
| 5 | g4343.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 124 | 167 | - |
| 17 | g4343.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 141 | 167 | - |
| 18 | g4343.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 189 | 219 | - |
| 13 | g4343.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 240 | 276 | - |
| 16 | g4343.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 246 | 274 | - |
| 4 | g4343.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 581 | 612 | - |
| 15 | g4343.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 586 | 602 | - |
| 14 | g4343.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 663 | 696 | - |
| 9 | g4343.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 664 | 682 | - |
| 12 | g4343.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 754 | 800 | - |
| 10 | g4343.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 755 | 800 | - |
| 2 | g4343.t1 | PANTHER | PTHR14152:SF5 | U4/U6.U5 TRI-SNRNP-ASSOCIATED PROTEIN 1 | 31 | 789 | 1.6E-152 |
| 3 | g4343.t1 | PANTHER | PTHR14152 | SQUAMOUS CELL CARCINOMA ANTIGEN RECOGNISED BY CYTOTOXIC T LYMPHOCYTES | 31 | 789 | 1.6E-152 |
| 1 | g4343.t1 | Pfam | PF03343 | SART-1 family | 111 | 751 | 1.9E-141 |
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 transcript has been annotated with K11984 (U4/U6.U5 tri-snRNP-associated protein 1)
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.
