General information for g3816.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative U5 small nuclear ribonucleoprotein 200 kDa helicase.
Parent gene
- The parent gene g3816 is located on chr_3: 28173423..28174346 (- 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 | g3816 | g3816.t4 | isoform | g3816.t4 | 28172986 | 28174346 |
| chr_3 | g3816 | g3816.t4 | exon | g3816.t4.exon1 | 28172986 | 28173978 |
| chr_3 | g3816 | g3816.t4 | cds | g3816.t4.CDS1 | 28172988 | 28173978 |
| chr_3 | g3816 | g3816.t4 | exon | g3816.t4.exon2 | 28174040 | 28174346 |
| chr_3 | g3816 | g3816.t4 | cds | g3816.t4.CDS2 | 28174040 | 28174095 |
| chr_3 | g3816 | g3816.t4 | TSS | g3816.t4 | 28175133 | 28175133 |
| chr_3 | g3816 | g3816.t4 | TTS | g3816.t4 | NA | NA |
Sequences
>g3816.t4 Gene=g3816 Length=1300
ATGGCTGACGCTGCTGCACGTCAACTACAATACGAGTACAAGGCTGTAAGTATTAATAGT
TTTATTTTTCTTAGAAAACGTCTATAAACGTAAATTTCCGTTTGCTCTAATTTTTCTCTA
ACATCACAAAATGTTTATTTCAGAACTCAAATTTAGTTTTACAAGCTGATGTTAGATTAA
TTGAACGACCTAGAAGAGATGAAGCGACTGGTGAAGTACTTTCTTTGGTTGGAAAACTCG
AAGGCACAAAAATGGGAGATCGAGCTCAACGCTCAAAACCGGAAAAAGCTGAAGAGAAAA
AAGCAATGCGTCGTAAACGTGATGAACAACAATATGATTTTAATAGTATGAGAGGTGCTA
CATTATTATCTGAAGGAATCGATGATATGGTTGGAATTATTTATCGACCAAAAACTCAAG
AAACCCGTCAAACATACGAAGTTCTTCTCAGTTTCATCCAAGAGGCGCTTGGTGATCAAC
CTAGAGATATTTTGTGTGGTGCTGCAGATGAAATTCTTGCTGTTCTCAAAAACGACAAAT
TGAAAGACCGTGAACGGAAAAAGGAAATTGATGGTCTGCTAGGCACAGTTGCGGAAGAAA
GATTTGCATTACTTGTTAATCTTGGCAAGAAAATCACAGATTTTGGTAGTGATTCACTTA
ATATTGCAGCACTCGGCATTAATGAAGATCAACAAATTGATGAGACATATGGTATAAATG
TTCAATTTGAAGAATCGTCAGATGAAAGTGTTGACGATGATTTCGGAGAAATTCGAGATG
ATGGTGATCAAGATGAAGGCGAAGAAGCAGTTGGTGATGGCGTTATTCATTCAGAAAACT
TGGGAGCTTCAGAAGGCGATAAAAAAGAGAAAGCTCTTCATCCATTAGATATTGATGCTT
ATTGGTTGCAACGTCGTTTAAGAGACTATTTTCAAGATCCTTTAGTATCTCAATCAAAGG
CTGATGAAGTTTTAAGTATTTTAAAAAATTCCAATGATGATCGAGATTGTGAAAATCAAA
TGGTATTGCTTTTGGGATATGATTGTTTTGATTTCATCAAAATTTTAAAAAAGAATCGTC
AAATGATTCTTTATTGTACGCTTTTAGCAAAAGCACAAACCGAAAATGAACGACAAAGGA
TTAGAGAGGACATGAAAAATGATGCATTTCTTTTAAAAGTTTTAAGACAATTGGATACTG
GAAAAGGTGAAGATAATGTTGAATATGAAGAGAAAAACAAAGCAAAAAAACGTCGCATGA
ATGATGATGAGGAAGATATGATGATCGAAGATGGAGCTGG
>g3816.t4 Gene=g3816 Length=349
MGDRAQRSKPEKAEEKKAMRRKRDEQQYDFNSMRGATLLSEGIDDMVGIIYRPKTQETRQ
TYEVLLSFIQEALGDQPRDILCGAADEILAVLKNDKLKDRERKKEIDGLLGTVAEERFAL
LVNLGKKITDFGSDSLNIAALGINEDQQIDETYGINVQFEESSDESVDDDFGEIRDDGDQ
DEGEEAVGDGVIHSENLGASEGDKKEKALHPLDIDAYWLQRRLRDYFQDPLVSQSKADEV
LSILKNSNDDRDCENQMVLLLGYDCFDFIKILKKNRQMILYCTLLAKAQTENERQRIRED
MKNDAFLLKVLRQLDTGKGEDNVEYEEKNKAKKRRMNDDEEDMMIEDGA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g3816.t4 | Coils | Coil | Coil | 322 | 342 | - |
| 5 | g3816.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 26 | - |
| 4 | g3816.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 320 | 341 | - |
| 6 | g3816.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 320 | 349 | - |
| 2 | g3816.t4 | PANTHER | PTHR24075 | SEC63 DOMAIN-CONTAINING | 1 | 348 | 8.3E-84 |
| 3 | g3816.t4 | PANTHER | PTHR24075:SF13 | U5 SMALL NUCLEAR RIBONUCLEOPROTEIN 200 KDA HELICASE | 1 | 348 | 8.3E-84 |
| 1 | g3816.t4 | Pfam | PF18149 | N-terminal helicase PWI domain | 206 | 314 | 3.8E-38 |
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