General information for g5724.t1
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.t1 | TSS | g5724.t1 | 11395257 | 11395257 |
| chr_2 | g5724 | g5724.t1 | isoform | g5724.t1 | 11395345 | 11398068 |
| chr_2 | g5724 | g5724.t1 | exon | g5724.t1.exon1 | 11395345 | 11396785 |
| chr_2 | g5724 | g5724.t1 | cds | g5724.t1.CDS1 | 11395345 | 11396785 |
| chr_2 | g5724 | g5724.t1 | exon | g5724.t1.exon2 | 11396846 | 11398068 |
| chr_2 | g5724 | g5724.t1 | cds | g5724.t1.CDS2 | 11396846 | 11398068 |
| chr_2 | g5724 | g5724.t1 | TTS | g5724.t1 | NA | NA |
Sequences
>g5724.t1 Gene=g5724 Length=2664
ATGAGCCGGAAAAGAGATCCAAGCTCTAGTAGTGAGGAGGTGGATAGTGCTGAAGAAGAA
AGAAAACGAGATTTAAGAGAAAGAGACGAATTTTCGAAACGATTAAAAGAGAAAGATGAA
TCAAAAACTCGTAAAATTGTTGAAGCACAAAATAAGAAAGCATTTGAAGAAGCAGCTAAA
AGACTCAAGCTTGAAAATGAAGATCGTTCGAAGTTGGTTCCACAACTGCGTATACAATCA
CGTCGTGAATATCTTGCTAAAAGAAAAGATGATAAAGTTTCTGAACTTGAAGCTGATATT
ATTGATGATGAGTATTTATTTGATGAATCACAGCTTACAACTAAAGAAAAACGAGATCGT
GAGTATAAGAAGAGAGTGCTTGATATTGCAAAGCAACATGAAAGAGCTCGTGAGCTCGAA
CGAGTTCAACGATATCATATGCCAAAAGATATGAAAAAAGGAGAAAAAGGCGAATATGTT
GAAGTTGATGAGACTGAAAAGTTGCCACATTCAGAACAGAGAAAATGGGAAGCTGAACAG
TTGGCTTCAGCTCGTTTTAAGTTCGGTGCAAAAGATGCAAAGCAACAGCAAGAATATGAA
TTGCTGTTGGAAGATGAAATTGAATTTGTGCAAGTTCTTACAATGGATGGCTCAAAAGAA
AAAGATCGAAAGCCAGAAATAACTGAAGCTCAAAAGATAAAAATGGATATTGAGGAAACA
AAAAAGAGTTTACCTGTTTATCCATTCAGAGATGATCTCATTAGAGCTATTGAAGAACAT
CAAGTGCTTATCATTGAAGGTGAAACTGGCAGTGGTAAAACAACTCAAATTCCACAATAC
CTTTATGAAGCAGGATTCACGAAAGATGGAAAAAAGATTGGTTGTACTCAACCAAGAAGA
GTTGCTGCAATGTCAGTTGCTGCACGTGTGGCTCAAGAAATGGGTGTGAAATTAGGAAAT
GAAGTCGGTTATAGTATTCGTTTTGAAGATTGTACATCCGAACGGACAGTGATAAAGTAT
ATGACTGATGGTACATTGCATAGAGAATTTTTAAGTGAACCCGATTTAGCATCTTATAGT
GTGATGATTATTGATGAAGCTCATGAGAGAACTTTACACACTGATATTCTATTTGGATTA
GTAAAAGACATTGCAAGATTTAGATCAGACTTGAAACTGCTTATTTCTTCAGCTACGCTG
GACGCAGAGAAATTCTCCTCCTTTTTTGACGACGCACCGATTTTTAGAATTCCTGGTAGA
CGATTTCCAGTTGACATTTATTATACAAAAGCACCTGAAGCTGACTATATTGATGCATGT
GTTGTTTCAATTCTACAAATTCATGCAACACAACCATTAGGTGATATTTTAGTTTTTCTT
ACGGGACAAGAAGAAATCGAAACATGTCAAGAAATTCTTACAGACAGAGTGAAACGATTA
GGATCAAAAATAAAAGAACTTCTCATTCTTCCAATCTACGCTAATTTACCTTCTGATATG
CAAGCAAAAATATTTGAGCCCACACCACCAAATGCAAGAAAAGTTGTTCTTGCGACAAAT
ATAGCAGAGACGAGTTTAACAATTGACAACATCATTTATGTTATAGATCCAGGTTTTGCT
AAACAAAATAATTTTAATTCACGAACTGGTATGGAGACACTTATGGTCGTTCCAATTTCA
AAAGCTTCAGCAAATCAACGTGCGGGAAGGGCAGGTCGTGTTGCAGCTGGAAAATGTTTT
AGATTGTATACAGCTTGGGCATATCAACATGAATTAGAAGAGAATACAATACCAGAAATA
ATGCGTATAAATTTAGGAAACGCTGTGTTGATGCTCAAAGCACTTGGAATTAATGATTTA
TTACATTTTGATTTTCTTGATCCTCCACCTTCTGAAACACTTGTATTAGCTTTAGAACAA
CTTTATGCACTTGGAGCTTTAAATCATCATGGTGAATTAACAAAAATGGGGAGACGTATG
GCTGAACTTCCAGTAGAGCCCATGATGTCGAAGATGCTACTTGCTTCAGAAAAATATAAA
TGTTCTGAAGAAATTGTTACAATTGCAGCTATGCTCTCGGTGAACGGTGCTATTTTCTAT
CGACCAAAAGACAAAATAATTCATGCAGACACAGCAAGAAAAAACTTTAATCACATCAAT
GGTGATCACTTGAGTTTATTAAATGTTTATAATCAATGGGTTGAGAGTGATTACAGTACA
CAATGGTGTTACGAGAATTTCATTCAGTATCGATCTATGAAACGAGCACGCGATGTAAGA
GAACAATTAGCTAATTTAATGCAACGAATTGAGATTGATATGGTTTCTGGAATAACAGAA
ACGGTAAATATAAGAAAAGCGATAACAGCAGGATATTTTTATCATATTGCCAAGTTTTCG
AAAGGAGGACACTATAAAACTGCCAAACATAATCAGACTGTCATGATTCATCCAAACTCT
GCACTCTTTGAAGATTTGCCACGATGGGTTTTGTATCATGAATTGGTATTTACAACAAAA
GAATTTATGCGACAAGTAATTGAAATAGATAGCAAATGGCTTCTAGAAGTTGCTCCACAT
TATTATAAACCAAAAGAATTAGAAGATTCAACGAATAAAAAAATGCCGAAAGTTGTAGGT
CGCTCTGGTCCGTCAGATCCATAG
>g5724.t1 Gene=g5724 Length=887
MSRKRDPSSSSEEVDSAEEERKRDLRERDEFSKRLKEKDESKTRKIVEAQNKKAFEEAAK
RLKLENEDRSKLVPQLRIQSRREYLAKRKDDKVSELEADIIDDEYLFDESQLTTKEKRDR
EYKKRVLDIAKQHERARELERVQRYHMPKDMKKGEKGEYVEVDETEKLPHSEQRKWEAEQ
LASARFKFGAKDAKQQQEYELLLEDEIEFVQVLTMDGSKEKDRKPEITEAQKIKMDIEET
KKSLPVYPFRDDLIRAIEEHQVLIIEGETGSGKTTQIPQYLYEAGFTKDGKKIGCTQPRR
VAAMSVAARVAQEMGVKLGNEVGYSIRFEDCTSERTVIKYMTDGTLHREFLSEPDLASYS
VMIIDEAHERTLHTDILFGLVKDIARFRSDLKLLISSATLDAEKFSSFFDDAPIFRIPGR
RFPVDIYYTKAPEADYIDACVVSILQIHATQPLGDILVFLTGQEEIETCQEILTDRVKRL
GSKIKELLILPIYANLPSDMQAKIFEPTPPNARKVVLATNIAETSLTIDNIIYVIDPGFA
KQNNFNSRTGMETLMVVPISKASANQRAGRAGRVAAGKCFRLYTAWAYQHELEENTIPEI
MRINLGNAVLMLKALGINDLLHFDFLDPPPSETLVLALEQLYALGALNHHGELTKMGRRM
AELPVEPMMSKMLLASEKYKCSEEIVTIAAMLSVNGAIFYRPKDKIIHADTARKNFNHIN
GDHLSLLNVYNQWVESDYSTQWCYENFIQYRSMKRARDVREQLANLMQRIEIDMVSGITE
TVNIRKAITAGYFYHIAKFSKGGHYKTAKHNQTVMIHPNSALFEDLPRWVLYHELVFTTK
EFMRQVIEIDSKWLLEVAPHYYKPKELEDSTNKKMPKVVGRSGPSDP
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g5724.t1 | CDD | cd17974 | DEXHc_DHX16 | 244 | 417 | 3.51277E-126 |
| 13 | g5724.t1 | CDD | cd18791 | SF2_C_RHA | 422 | 583 | 1.61415E-81 |
| 11 | g5724.t1 | Coils | Coil | Coil | 14 | 34 | - |
| 12 | g5724.t1 | Coils | Coil | Coil | 753 | 773 | - |
| 9 | g5724.t1 | Gene3D | G3DSA:3.40.50.300 | - | 197 | 420 | 1.2E-89 |
| 8 | g5724.t1 | Gene3D | G3DSA:3.40.50.300 | - | 421 | 596 | 2.0E-69 |
| 10 | g5724.t1 | Gene3D | G3DSA:1.20.120.1080 | - | 620 | 728 | 8.4E-32 |
| 20 | g5724.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 43 | - |
| 19 | g5724.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 866 | 887 | - |
| 5 | g5724.t1 | PANTHER | PTHR18934:SF208 | OS05G0389800 PROTEIN | 3 | 878 | 0.0 |
| 6 | g5724.t1 | PANTHER | PTHR18934 | ATP-DEPENDENT RNA HELICASE | 3 | 878 | 0.0 |
| 2 | g5724.t1 | Pfam | PF00270 | DEAD/DEAH box helicase | 252 | 403 | 1.4E-7 |
| 3 | g5724.t1 | Pfam | PF00271 | Helicase conserved C-terminal domain | 445 | 574 | 5.8E-12 |
| 4 | g5724.t1 | Pfam | PF04408 | Helicase associated domain (HA2) | 637 | 711 | 6.6E-22 |
| 1 | g5724.t1 | Pfam | PF07717 | Oligonucleotide/oligosaccharide-binding (OB)-fold | 784 | 861 | 5.4E-21 |
| 18 | g5724.t1 | ProSitePatterns | PS00690 | DEAH-box subfamily ATP-dependent helicases signature. | 360 | 369 | - |
| 22 | g5724.t1 | ProSiteProfiles | PS51192 | Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. | 254 | 418 | 20.185 |
| 21 | g5724.t1 | ProSiteProfiles | PS51194 | Superfamilies 1 and 2 helicase C-terminal domain profile. | 443 | 616 | 15.702 |
| 16 | g5724.t1 | SMART | SM00487 | ultradead3 | 242 | 427 | 4.6E-35 |
| 15 | g5724.t1 | SMART | SM00490 | helicmild6 | 475 | 575 | 1.3E-16 |
| 17 | g5724.t1 | SMART | SM00847 | ha2_5 | 636 | 727 | 5.1E-34 |
| 7 | g5724.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 228 | 805 | 5.66E-132 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5724/g5724.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5724.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005524 | ATP binding | MF |
| GO:0004386 | helicase activity | MF |
| GO:0003676 | nucleic acid binding | MF |
KEGG
Orthology
- This transcript has been annotated with K12813 (pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16)
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.
