General information for g5724.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16.
Parent gene
- The parent gene g5724 is located on chr_2: 11396846..11398068 (+ 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 | g5724 | g5724.t2 | isoform | g5724.t2 | 11396846 | 11398068 |
| chr_2 | g5724 | g5724.t2 | exon | g5724.t2.exon1 | 11396846 | 11398068 |
| chr_2 | g5724 | g5724.t2 | cds | g5724.t2.CDS1 | 11396902 | 11398068 |
| chr_2 | g5724 | g5724.t2 | TSS | g5724.t2 | NA | NA |
| chr_2 | g5724 | g5724.t2 | TTS | g5724.t2 | NA | NA |
Sequences
>g5724.t2 Gene=g5724 Length=1223
GATCAAAAATAAAAGAACTTCTCATTCTTCCAATCTACGCTAATTTACCTTCTGATATGC
AAGCAAAAATATTTGAGCCCACACCACCAAATGCAAGAAAAGTTGTTCTTGCGACAAATA
TAGCAGAGACGAGTTTAACAATTGACAACATCATTTATGTTATAGATCCAGGTTTTGCTA
AACAAAATAATTTTAATTCACGAACTGGTATGGAGACACTTATGGTCGTTCCAATTTCAA
AAGCTTCAGCAAATCAACGTGCGGGAAGGGCAGGTCGTGTTGCAGCTGGAAAATGTTTTA
GATTGTATACAGCTTGGGCATATCAACATGAATTAGAAGAGAATACAATACCAGAAATAA
TGCGTATAAATTTAGGAAACGCTGTGTTGATGCTCAAAGCACTTGGAATTAATGATTTAT
TACATTTTGATTTTCTTGATCCTCCACCTTCTGAAACACTTGTATTAGCTTTAGAACAAC
TTTATGCACTTGGAGCTTTAAATCATCATGGTGAATTAACAAAAATGGGGAGACGTATGG
CTGAACTTCCAGTAGAGCCCATGATGTCGAAGATGCTACTTGCTTCAGAAAAATATAAAT
GTTCTGAAGAAATTGTTACAATTGCAGCTATGCTCTCGGTGAACGGTGCTATTTTCTATC
GACCAAAAGACAAAATAATTCATGCAGACACAGCAAGAAAAAACTTTAATCACATCAATG
GTGATCACTTGAGTTTATTAAATGTTTATAATCAATGGGTTGAGAGTGATTACAGTACAC
AATGGTGTTACGAGAATTTCATTCAGTATCGATCTATGAAACGAGCACGCGATGTAAGAG
AACAATTAGCTAATTTAATGCAACGAATTGAGATTGATATGGTTTCTGGAATAACAGAAA
CGGTAAATATAAGAAAAGCGATAACAGCAGGATATTTTTATCATATTGCCAAGTTTTCGA
AAGGAGGACACTATAAAACTGCCAAACATAATCAGACTGTCATGATTCATCCAAACTCTG
CACTCTTTGAAGATTTGCCACGATGGGTTTTGTATCATGAATTGGTATTTACAACAAAAG
AATTTATGCGACAAGTAATTGAAATAGATAGCAAATGGCTTCTAGAAGTTGCTCCACATT
ATTATAAACCAAAAGAATTAGAAGATTCAACGAATAAAAAAATGCCGAAAGTTGTAGGTC
GCTCTGGTCCGTCAGATCCATAG
>g5724.t2 Gene=g5724 Length=388
MQAKIFEPTPPNARKVVLATNIAETSLTIDNIIYVIDPGFAKQNNFNSRTGMETLMVVPI
SKASANQRAGRAGRVAAGKCFRLYTAWAYQHELEENTIPEIMRINLGNAVLMLKALGIND
LLHFDFLDPPPSETLVLALEQLYALGALNHHGELTKMGRRMAELPVEPMMSKMLLASEKY
KCSEEIVTIAAMLSVNGAIFYRPKDKIIHADTARKNFNHINGDHLSLLNVYNQWVESDYS
TQWCYENFIQYRSMKRARDVREQLANLMQRIEIDMVSGITETVNIRKAITAGYFYHIAKF
SKGGHYKTAKHNQTVMIHPNSALFEDLPRWVLYHELVFTTKEFMRQVIEIDSKWLLEVAP
HYYKPKELEDSTNKKMPKVVGRSGPSDP
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g5724.t2 | CDD | cd18791 | SF2_C_RHA | 1 | 84 | 2.86404E-53 |
| 9 | g5724.t2 | Coils | Coil | Coil | 254 | 274 | - |
| 7 | g5724.t2 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 97 | 1.3E-41 |
| 8 | g5724.t2 | Gene3D | G3DSA:1.20.120.1080 | - | 120 | 229 | 2.3E-32 |
| 12 | g5724.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 367 | 388 | - |
| 4 | g5724.t2 | PANTHER | PTHR18934:SF208 | OS05G0389800 PROTEIN | 1 | 379 | 2.4E-182 |
| 5 | g5724.t2 | PANTHER | PTHR18934 | ATP-DEPENDENT RNA HELICASE | 1 | 379 | 2.4E-182 |
| 2 | g5724.t2 | Pfam | PF00271 | Helicase conserved C-terminal domain | 3 | 75 | 6.0E-7 |
| 3 | g5724.t2 | Pfam | PF04408 | Helicase associated domain (HA2) | 138 | 212 | 1.9E-22 |
| 1 | g5724.t2 | Pfam | PF07717 | Oligonucleotide/oligosaccharide-binding (OB)-fold | 285 | 362 | 1.6E-21 |
| 13 | g5724.t2 | ProSiteProfiles | PS51194 | Superfamilies 1 and 2 helicase C-terminal domain profile. | 1 | 117 | 12.033 |
| 11 | g5724.t2 | SMART | SM00847 | ha2_5 | 137 | 228 | 5.1E-34 |
| 6 | g5724.t2 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 2 | 307 | 3.49E-61 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5724/g5724.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5724.t2.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0004386 | helicase activity | MF |
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.
