General information for g2699.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as ATP-dependent RNA helicase DHX8.
Parent gene
- The parent gene g2699 is located on chr_3: 19771563..19772689 (- 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 | g2699 | g2699.t1 | isoform | g2699.t1 | 19767776 | 19771563 |
| chr_3 | g2699 | g2699.t1 | exon | g2699.t1.exon1 | 19767776 | 19769288 |
| chr_3 | g2699 | g2699.t1 | cds | g2699.t1.CDS1 | 19767776 | 19769288 |
| chr_3 | g2699 | g2699.t1 | exon | g2699.t1.exon2 | 19769361 | 19769742 |
| chr_3 | g2699 | g2699.t1 | cds | g2699.t1.CDS2 | 19769361 | 19769742 |
| chr_3 | g2699 | g2699.t1 | exon | g2699.t1.exon3 | 19769802 | 19771409 |
| chr_3 | g2699 | g2699.t1 | cds | g2699.t1.CDS3 | 19769802 | 19771409 |
| chr_3 | g2699 | g2699.t1 | exon | g2699.t1.exon4 | 19771470 | 19771563 |
| chr_3 | g2699 | g2699.t1 | cds | g2699.t1.CDS4 | 19771470 | 19771563 |
| chr_3 | g2699 | g2699.t1 | TSS | g2699.t1 | NA | NA |
| chr_3 | g2699 | g2699.t1 | TTS | g2699.t1 | NA | NA |
Sequences
>g2699.t1 Gene=g2699 Length=3597
ATGGATGAATTAGAACAACTAGAACATCTTTCTTTAGTTTCAAAGATTTGCACAGAATTG
GAAAATCATTTATCTATAAACGACAAAGATTTGGCTGAATTTATAATTCATCTTGCCGAG
CAAAATCCTAATTTAGATGACTTTAGAAAGGCACTTGCACAAAATGGTGCAGAATTTAGT
GATTCATTTACTTCAAATCTTTTGCGTATTATATGTCTGATGAAACCATCAGTAAAAAAG
AAGTCGAATCAAACAATCACAATAGAAGGCGACTCATCAAAAAGTGCTCTTGCACTTAAA
TTTCCAGGACTAGCTATTCCAAATAAGAAAATAGACGATGATAGTGATGAGGACAATGAT
AAAAAGAAAACATCCGATAATATTGTTGATGATATGATGGCAGAATTAGAAGCAATGGCT
GCACCTCCATCGTCAAGTAAAACAATTGACGAAAAAAAAGAAAGAAAACGAAGCCGTTCT
CGTGAAATAAAAGAGAGAAAAAGGAGTCGTTCAAGAGAAAAGAGAAGAAGATCACGTTCA
AGAAGTCGTGATAGAAAAAAACGTTCAAGAAGCCGTGATAGAGCTAAAAAGAGCAGAAGA
AGTCGCTCAAGAAGTCATAGCAGAAAAGATAGAAGACATCGTTCTAAATCAAGAGATCGA
GATCGATATCACAATCGTCGGAGTCGTTCGCGTGAAGAAAGAAAGAAAATTGAAATCAAA
GATGATCCAGAACCAGGAAAAATTTATGATGGAAAAGTTGCAAACATTGTGAATTTCGGA
TGTTTTGTGCAGCTTTTTGGTTTGAGAAAGAAATGGGAAGGTTTAGTACACATTTCACAA
TTGAGATCAGAGGGACGAGTGTCAGACGTTAGTGAAGTCGTGTCACGGGGAAGTTCAGTA
AAAGTCAAAGTAATTTCAATTACAGGACAAAAGGTATCGCTTTCAATGAAAGAAGTTGAT
CAATTGACTGGAAAAGATTTAAATCCGTTGTCACATAAAGCAGCCGATGATGATATGGGT
CCAAGAAATCCAGATAGACCAATTGATAGAATTTCAATGTTAGCTCTTCCCGGTAATGTT
GATGACGATGTTGTGGAAACTGGTAAACGCGTCACAAGAATCTCAAGTCCAGAGCGATGG
GAAATTCAGCAAATGATTTCATCAGGTGTAATTGATCGAAGTGAAATGCCAGATTATGAT
GAAGAGACTGGATTATTACAAAAAGATGAAGAGGACGAAGAAGATATTGAAATTGAAATT
GTTGAAGACGAACCACCATTTTTACAAGGTCATGGAAGAGCACTACATGATTTATCACCA
GTTAGAATCATTAAAAATCCTGATGGCTCTTTAGCACAAGCTGCCATGATGCAATCAGCA
TTGCAAAAAGAAAGACGTGAACAGAAAATGTTGCAGCGTGAACAAGAAATGGATTCAAAA
CCATCAACTTTTGGTAAAGACTGGATGGATCCATTAAGAGAAGATGAAGACCGTAATGAT
GGTTCAAAAAGTTTCAATGCAGCACTTCAAGATATGCCTGAATGGAAGAAACATATTATA
GGTGGTAAAAAAACATCTTATGGACGAAAAACAGATATGACAATGATTGAACAACGTCAA
TCACTACCAATATATAAGTTAAAAGATGATTTGATAAAAGCAGTCACAGATAATCAAATT
TTAATTGTTGTTGGTGAAACAGGAAGTGGTAAAACAACACAAATGACTCAATATCTTGCA
GAAGCAGGATTTATTAGTCGTGGAAGAATTGGGTGCACACAACCAAGAAGAGTAGCTGCA
ATGAGTGTTGCAAAGCGTGTTGCTGAAGAATATGGTTGTCGTTTAGGTCAAGAAGTCGGA
TACACAATTCGTTTTGAAGATTGTACAAGTTCTGAGACACTTATAAAATACATGACTGAC
GGTATGATGTTGCGTGAATGTTTAATGGATTTAGATTTAAAAGGATATTCAGTTATTATG
CTGGATGAAGCTCATGAAAGAACCATTCATACTGATGTACTTTTTGGATTATTGAAGCAA
GCTGTAAAACGACGACCAGAATTGAAACTTATTGTAACATCAGCCACACTTGATGCTGTC
AAGTTCTCACAATATTTCTTCGAAGCTCCAATTTTTACAATTCCCGGTCGTACTTTTCCA
GTAGAAATTCTTTATACTAAAGAACCAGAAACTGATTATCTAGATGCATCGCTTATCACT
GTTATGCAAATTCATTTGCGAGAACCTCCAGGCGATATACTTCTTTTTCTTACTGGTCAA
GAAGAGATTGATACAGCTTGTGAAATACTCTATGAAAGAATGAAATCTTTAGGACCAGAT
GTTCCTGAACTTATAATTTTACCTGTCTATTCAGCTTTACCATCAGAAATGCAAACAAGA
ATTTTCGATCCAGCACCAGCTGGCAGCAGAAAAGTTGTAATTGCTACAAACATAGCAGAA
ACAAGTTTAACAATAGATGGAATTTATTATGTCGTTGATCCTGGTTTTGTAAAACAAAAA
GTTTACAATTCAAAAACTGGCATGGACTCACTTGTTGTCACACCAATTTCACAAGCAGCT
GCAAAACAACGTGCAGGAAGAGCAGGAAGAACAGGTCCTGGCAAATGCTATCGATTGTAC
ACTGAACGTGCTTATCGTGATGAAATGTTGCCAACACCTGTGCCTGAAATTCAAAGAACT
AATTTAGCTACAACTGTATTACAATTGAAGACTATGGGCATAAATGATTTGCTTAATTTT
GATTTTATGGATTCTCCACCAGTTGAATCGCTTGTAATGGCTCTCGAACAACTTCATTCG
TTGAGTGCTTTAGATGATGAAGGACTTTTAACAAGGCTTGGACGACGTATGGCAGAATTT
CCATTAGAGCCTAATTTATCGAAAATTCTCATCATGTCTGTCGCTCTTCAATGCTCTGAT
GAAATTCTCACAATTGTTTCAATGCTTAGCGTTCAAAATGTCTTTTATCGTCCAAAAGAT
AAGCAAGCATTAGCTGATCAGAAGAAAGCGAAATTCAATCAAGTTGAGGGTGATCATTTA
ACATTATTGGCAGTTTATAATAGTTGGAAAAATAATAAATTTTCAAATGCATGGTGTTAT
GAAAATTTTGTTCAAGTTAGAACATTGAAGCGTGCACAAGATGTAAGGAAACAATTGCTT
GGAATTATGGATAGACATAAACTTGACGTTGTATCGGCTGGTAAAAATTCTGTAAGAATT
CAAAAGACAATTTGCTCTGGTTTCTTTAGAAATGCAGCAAAAAAAGATCCACAAGAGGGA
TATAGAACATTAGTTGATTCTCAAGTCGTATATATTCATCCTTCAAGTGCATTATTCAAC
AGACAACCAGAATGGGTGATTTATCATGAATTAGTTCAAACGACAAAAGAATACATGCGT
GAAGTTACAACAATTGATCCTAAATGGCTTGTAGAGTTTGCATCATCGTTCTTTAAATTT
TCTGACCCAACAAAATTGAGTAAATTCAAGAAAAATCAACGACTTGAACCACTTTATAAT
AAATATGAAGAAGCCAACTCATGGAGAATTAGTCGTGTTCGTAAACGAAGAAATTAA
>g2699.t1 Gene=g2699 Length=1198
MDELEQLEHLSLVSKICTELENHLSINDKDLAEFIIHLAEQNPNLDDFRKALAQNGAEFS
DSFTSNLLRIICLMKPSVKKKSNQTITIEGDSSKSALALKFPGLAIPNKKIDDDSDEDND
KKKTSDNIVDDMMAELEAMAAPPSSSKTIDEKKERKRSRSREIKERKRSRSREKRRRSRS
RSRDRKKRSRSRDRAKKSRRSRSRSHSRKDRRHRSKSRDRDRYHNRRSRSREERKKIEIK
DDPEPGKIYDGKVANIVNFGCFVQLFGLRKKWEGLVHISQLRSEGRVSDVSEVVSRGSSV
KVKVISITGQKVSLSMKEVDQLTGKDLNPLSHKAADDDMGPRNPDRPIDRISMLALPGNV
DDDVVETGKRVTRISSPERWEIQQMISSGVIDRSEMPDYDEETGLLQKDEEDEEDIEIEI
VEDEPPFLQGHGRALHDLSPVRIIKNPDGSLAQAAMMQSALQKERREQKMLQREQEMDSK
PSTFGKDWMDPLREDEDRNDGSKSFNAALQDMPEWKKHIIGGKKTSYGRKTDMTMIEQRQ
SLPIYKLKDDLIKAVTDNQILIVVGETGSGKTTQMTQYLAEAGFISRGRIGCTQPRRVAA
MSVAKRVAEEYGCRLGQEVGYTIRFEDCTSSETLIKYMTDGMMLRECLMDLDLKGYSVIM
LDEAHERTIHTDVLFGLLKQAVKRRPELKLIVTSATLDAVKFSQYFFEAPIFTIPGRTFP
VEILYTKEPETDYLDASLITVMQIHLREPPGDILLFLTGQEEIDTACEILYERMKSLGPD
VPELIILPVYSALPSEMQTRIFDPAPAGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQK
VYNSKTGMDSLVVTPISQAAAKQRAGRAGRTGPGKCYRLYTERAYRDEMLPTPVPEIQRT
NLATTVLQLKTMGINDLLNFDFMDSPPVESLVMALEQLHSLSALDDEGLLTRLGRRMAEF
PLEPNLSKILIMSVALQCSDEILTIVSMLSVQNVFYRPKDKQALADQKKAKFNQVEGDHL
TLLAVYNSWKNNKFSNAWCYENFVQVRTLKRAQDVRKQLLGIMDRHKLDVVSAGKNSVRI
QKTICSGFFRNAAKKDPQEGYRTLVDSQVVYIHPSSALFNRQPEWVIYHELVQTTKEYMR
EVTTIDPKWLVEFASSFFKFSDPTKLSKFKKNQRLEPLYNKYEEANSWRISRVRKRRN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g2699.t1 | CDD | cd05684 | S1_DHX8_helicase | 246 | 324 | 1.00743E-41 |
| 15 | g2699.t1 | CDD | cd17971 | DEXHc_DHX8 | 537 | 715 | 1.62717E-123 |
| 17 | g2699.t1 | CDD | cd18791 | SF2_C_RHA | 719 | 880 | 1.14761E-85 |
| 14 | g2699.t1 | Coils | Coil | Coil | 454 | 474 | - |
| 13 | g2699.t1 | Gene3D | G3DSA:2.40.50.140 | - | 240 | 328 | 3.8E-30 |
| 9 | g2699.t1 | Gene3D | G3DSA:3.40.50.300 | - | 492 | 717 | 1.1E-87 |
| 10 | g2699.t1 | Gene3D | G3DSA:3.40.50.300 | - | 718 | 891 | 2.1E-72 |
| 12 | g2699.t1 | Gene3D | G3DSA:1.20.120.1080 | - | 916 | 1020 | 5.4E-33 |
| 11 | g2699.t1 | Gene3D | G3DSA:1.20.120.1080 | - | 1021 | 1074 | 7.0E-8 |
| 23 | g2699.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 138 | 239 | - |
| 25 | g2699.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 159 | 224 | - |
| 24 | g2699.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 225 | 239 | - |
| 5 | g2699.t1 | PANTHER | PTHR18934 | ATP-DEPENDENT RNA HELICASE | 110 | 1194 | 0.0 |
| 6 | g2699.t1 | PANTHER | PTHR18934:SF230 | - | 110 | 1194 | 0.0 |
| 2 | g2699.t1 | Pfam | PF00575 | S1 RNA binding domain | 243 | 315 | 9.6E-12 |
| 3 | g2699.t1 | Pfam | PF00271 | Helicase conserved C-terminal domain | 744 | 872 | 1.3E-12 |
| 4 | g2699.t1 | Pfam | PF04408 | Helicase associated domain (HA2) | 934 | 1022 | 1.1E-23 |
| 1 | g2699.t1 | Pfam | PF07717 | Oligonucleotide/oligosaccharide-binding (OB)-fold | 1080 | 1156 | 4.3E-25 |
| 22 | g2699.t1 | ProSitePatterns | PS00690 | DEAH-box subfamily ATP-dependent helicases signature. | 657 | 666 | - |
| 28 | g2699.t1 | ProSiteProfiles | PS50126 | S1 domain profile. | 246 | 317 | 17.884 |
| 27 | g2699.t1 | ProSiteProfiles | PS51192 | Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. | 552 | 715 | 17.928 |
| 26 | g2699.t1 | ProSiteProfiles | PS51194 | Superfamilies 1 and 2 helicase C-terminal domain profile. | 733 | 913 | 17.381 |
| 18 | g2699.t1 | SMART | SM00316 | S1_6 | 244 | 317 | 4.0E-18 |
| 20 | g2699.t1 | SMART | SM00487 | ultradead3 | 540 | 724 | 6.2E-30 |
| 19 | g2699.t1 | SMART | SM00490 | helicmild6 | 768 | 872 | 7.0E-21 |
| 21 | g2699.t1 | SMART | SM00847 | ha2_5 | 933 | 1023 | 4.9E-38 |
| 8 | g2699.t1 | SUPERFAMILY | SSF50249 | Nucleic acid-binding proteins | 234 | 319 | 4.4E-16 |
| 7 | g2699.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 537 | 1156 | 4.07E-136 |
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:0004386 | helicase activity | MF |
| GO:0003676 | nucleic acid binding | MF |
KEGG
Orthology
- This transcript has been annotated with K12818 (ATP-dependent RNA helicase DHX8/PRP22)
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.
