General information for g14138.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 PRP16.
Parent gene
- The parent gene g14138 is located on chr_1: 34859209..34863760 (+ 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_1 | g14138 | g14138.t1 | TSS | g14138.t1 | 34855386 | 34855386 |
| chr_1 | g14138 | g14138.t1 | isoform | g14138.t1 | 34855477 | 34859209 |
| chr_1 | g14138 | g14138.t1 | exon | g14138.t1.exon1 | 34855477 | 34856695 |
| chr_1 | g14138 | g14138.t1 | cds | g14138.t1.CDS1 | 34855477 | 34856695 |
| chr_1 | g14138 | g14138.t1 | exon | g14138.t1.exon2 | 34856757 | 34857986 |
| chr_1 | g14138 | g14138.t1 | cds | g14138.t1.CDS2 | 34856757 | 34857986 |
| chr_1 | g14138 | g14138.t1 | exon | g14138.t1.exon3 | 34858053 | 34859209 |
| chr_1 | g14138 | g14138.t1 | cds | g14138.t1.CDS3 | 34858053 | 34859209 |
| chr_1 | g14138 | g14138.t1 | TTS | g14138.t1 | 34859264 | 34859264 |
Sequences
>g14138.t1 Gene=g14138 Length=3606
ATGGACGATGTACATAGACTGGAGGCATCTGAACATCAAGCAGGTGGATTAATCATTAAA
AAGAAAAATTCTGACGAGAAGAAAGATGTTTTTAAAATTCCTCAATCGAAATTTGGTTTA
GATTTGTTAGCAAAGAAATTGAAAAAAGAACGTGAAACAGGATTATTGAGTTCATTTAAA
GATCATGATGACGAAGATGATTCAAGAAAACAATCAAACGATAAAAATGACGATGATGTA
AAATTTAAGAAATCAATAGAGACTAAATCGAAAAACTATCGCTCATCACAACCAGAAACT
CCGAGTTATTCTTCAGCAGTGACAAAATCAGTGAGAGAACATTATAATGAAAGAATAAGT
GACAAATCCAAAGGATTGTACACATCAACAAAGGATAAACAAAGAGATAAACGTGATAAA
GACAGAAGATCGCATAAAAGTTCAAGAGATCGTGACAGAGATTATGACAGAAAAAGATCG
AGACATGATGGTAGCAGTCATCGTAGTCATAGAGATCGTTCTCATAGATATAAAGATGAA
CCAGAAACACCAAGATATTATGAAAGCAAAAGTAACAGTTCAATAGGCAAGAGCTCATGG
GACGATGATGATGAAGATGAGTTCAAATATAAGAAAAAGAAATCATCTTGGGATTTTCCT
ACACCAAATCAATATAAAAGTCGTTCAGATGATTCAGTTCGTTCTAATCGGTCGACAAAA
GCTTTGAGAAAATATGAAGATGATACGCCAAGAGCAACACCCGCACATAAATTCAACAAG
TGGGCAGCAGATAGAAAACATTCTGGTGCAACGCCAAGAGTTGATAAAAATAGTTCAGAT
CCTGAAAAGCCATGGGAAAATGATGAAGATCGTGATTTATGGGAGGAAGAACAAATTCGT
CTTGACAGAGAATGGTACAATATGGATGAAGGATATGATGATGAAAATAATCCTTTTGCT
GGAGCAAGTGCAGACTATTTAAAGAAACGCGAAGAACAGATTGAAATGAGAAAACGCAAA
AGAATAAGTGCTCAACAACGTCAAATTAACAAAGATAATGAGTTGTGGGAGAAAAATCGA
ATGATTACGTCAGGTGTTGTACAGAAAATCAATTTCAATGAAGACTTTGAGGAGGAAACC
ATCGAAAGAGTAAACTTATTAGTTCATCATGCTGTTCCACCATTCTTAGATGGAAGAATT
GTTTTCACAAAAGTCATGGAACCTGTTATTCCCGTGAAAGACCCAACTTCTGATATGGCA
TTAGTTGCACGTAAAGGAAGTGCATTAGTACGTGTTTTTCGTGAGCAAAAAGAGAGAAAA
AAAGCACAGAAGAAACATTGGGAACTTGGAGGAACAAAGTTAGGAAATATCATGGGTGTT
GAAAAGAAAAAAGATGAAGAAGATGCACAATATGATGCTGAAACTGACAGTACAGATTAT
AAAAAAGATCAAAAGTTTGCAGAACATATGATGAAACAAAGTGAAGAAGGAAATTTTAGT
AATAAAAGGAAAAAGATAAGTCAGCAAAGAAGGAGTTTACCAGTTTTTGCTGTTCGTCAA
GATTTACTAAATGTTATTCGAGAAAATAGTGTTGTAATCATAGTCGGTGAGACAGGTAGT
GGTAAAACAACACAGTTAACTCAATATCTTCATGAAGATGGTTATAGCAAATATGGAATG
ATTGGGTGCACACAACCAAGAAGAGTAGCTGCAATGTCAGTTGCTAATCGTGTATCAGAT
GAAATGAACACAAAATTAGGAAATGAAGTGGGTTATGCTATTCGATTTGAGGATTGTACT
TCTGAACATACCATTATTAAATACATGACTGATGGTATTTTATTGCGTGAAAGTTTAAGA
GATGGAGACTTGGACAGTTATTCTGCAATTATTATGGATGAAGCGCATGAGAGAAGTTTA
TCCACTGATGTGCTTTTTGGCTTATTAAGAGATATTGTGGCTAGAAGACGAGATTTAAAA
TTAATTGTAACATCAGCCACAATGGACGCAACTAAGTTTAGTCAATTTTTCGGGAATGTA
CCGACTTTCACAATTCCAGGAAGAACATTTCCTGTTGAACTATTCTTTAGTAAAAATACT
GTTGAAGATTATGTTGATGCTGCAGTTAAACAGACACTTCAAATTCATTTGGGTAATTTA
GAAGGAGATATTTTAATTTTTATGCCTGGTCAAGAAGATATTGAAGTAACGTGCGAAGTT
TTAGCAGAAAGATTATCTCAACTTGATGATGCTCCAGAATTATTAATTTTACCAATTTAT
TCACAACTTCCATCAGACTTACAAGCTAAAATTTTTCAAAAGGCACAAGACGGTTTAAGA
AAATGTGTTGTTGCTACAAATATTGCCGAAACAAGTTTAACTGTCGATGGAATAATGTAT
GTAATAGACAGTGGCTATTGCAAATTAAAAGTATATAATCCAAGAATAGGTATGGACGCA
CTTCAAATTTATCCAATTTCTCAGGCAAATGCAAATCAACGTTCTGGAAGAGCAGGCAGA
ACAGGTCCTGGAATGGCATATCGTTTATACACGGAGAGGCAATATAAAGATGAATTACTT
CCTCTTACGGTTCCTGAAATTCAGAGAACAAATTTAGCCAACACAGTTCTTTTACTCAAA
TCACTTGGTGTAGTTGATTTACTATCATTTCATTTTATGGATCCACCACCTCAAGACAAT
ATTTTGAATTCACTCTATCAGTTATGGATTTTAGGCGCATTAGATCACACTGGTCGATTG
GCGCCTCTTGGACGAGTTATGGCTGAATTTCCTTTAGATCCGCCACAATGTCAAATGCTA
ATCGTTTCATGTGAAATGGAATGTTCAGCAGAAGTTCTTATTATAGTATCAATGCTTTCG
GTGCCATCAATTTTTTACAGACCAAAAGGACGCGAAGAAGAAGCAGATAATGTTAGAGAA
AAATTTCAAGTTCCTGAATCAGATCATTTAACATATTTGAATGTATATCAGCAATGGAAA
ATGAATAATTATTCTTCAAATTGGGCAAACGAGCATTTCATTCATATAAAAGCTCTAAGA
AAAGTGAGAGAAGTGAGGCAACAACTTAAAGATATTCTCATTCAACAGAAATTGGAAGTT
AAATCGTGTGGAACAAATTGGGACATTATTAGAAAATGTATTTGCTCAGCCTATTTCTAT
CAGGCTGCTCGTTTAAAAGGTATTGGTGAATATGTCAATTTGAGAACAGGCATGCCTTGT
CATTTGCATCCAACTTCTGCTCTTTATGGATTGGGAACTTCACCAGAATATGTCGTTTAT
CATGAATTGGTAATGACAGCCAAAGAATATATGCAATGTGCAACAGCTGTTGACGGTTAT
TGGTTGGCTGAATTAGGTCCGATGTTTTTCTCTGTAAAAGAATCAGGAAAAAGTGGTAGA
GATAAAAGAAAGCAAGCAGCTGAACATTTGCATAAAATGGAATCACAAATGCAAGAAGCA
CAAGAAGAAATTGAAAGGGAGAAACAATTGAATGCTCAAAAGCAAGAAGCAATAATGGCA
AAGCAAGAAATTGTTACTCCAGGCACTTCAACACCTAGAAGAACTCCAGCAAGAATTGGA
CTTTGA
>g14138.t1 Gene=g14138 Length=1201
MDDVHRLEASEHQAGGLIIKKKNSDEKKDVFKIPQSKFGLDLLAKKLKKERETGLLSSFK
DHDDEDDSRKQSNDKNDDDVKFKKSIETKSKNYRSSQPETPSYSSAVTKSVREHYNERIS
DKSKGLYTSTKDKQRDKRDKDRRSHKSSRDRDRDYDRKRSRHDGSSHRSHRDRSHRYKDE
PETPRYYESKSNSSIGKSSWDDDDEDEFKYKKKKSSWDFPTPNQYKSRSDDSVRSNRSTK
ALRKYEDDTPRATPAHKFNKWAADRKHSGATPRVDKNSSDPEKPWENDEDRDLWEEEQIR
LDREWYNMDEGYDDENNPFAGASADYLKKREEQIEMRKRKRISAQQRQINKDNELWEKNR
MITSGVVQKINFNEDFEEETIERVNLLVHHAVPPFLDGRIVFTKVMEPVIPVKDPTSDMA
LVARKGSALVRVFREQKERKKAQKKHWELGGTKLGNIMGVEKKKDEEDAQYDAETDSTDY
KKDQKFAEHMMKQSEEGNFSNKRKKISQQRRSLPVFAVRQDLLNVIRENSVVIIVGETGS
GKTTQLTQYLHEDGYSKYGMIGCTQPRRVAAMSVANRVSDEMNTKLGNEVGYAIRFEDCT
SEHTIIKYMTDGILLRESLRDGDLDSYSAIIMDEAHERSLSTDVLFGLLRDIVARRRDLK
LIVTSATMDATKFSQFFGNVPTFTIPGRTFPVELFFSKNTVEDYVDAAVKQTLQIHLGNL
EGDILIFMPGQEDIEVTCEVLAERLSQLDDAPELLILPIYSQLPSDLQAKIFQKAQDGLR
KCVVATNIAETSLTVDGIMYVIDSGYCKLKVYNPRIGMDALQIYPISQANANQRSGRAGR
TGPGMAYRLYTERQYKDELLPLTVPEIQRTNLANTVLLLKSLGVVDLLSFHFMDPPPQDN
ILNSLYQLWILGALDHTGRLAPLGRVMAEFPLDPPQCQMLIVSCEMECSAEVLIIVSMLS
VPSIFYRPKGREEEADNVREKFQVPESDHLTYLNVYQQWKMNNYSSNWANEHFIHIKALR
KVREVRQQLKDILIQQKLEVKSCGTNWDIIRKCICSAYFYQAARLKGIGEYVNLRTGMPC
HLHPTSALYGLGTSPEYVVYHELVMTAKEYMQCATAVDGYWLAELGPMFFSVKESGKSGR
DKRKQAAEHLHKMESQMQEAQEEIEREKQLNAQKQEAIMAKQEIVTPGTSTPRRTPARIG
L
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g14138.t1 | CDD | cd17983 | DEXHc_DHX38 | 513 | 685 | 8.52203E-119 |
| 12 | g14138.t1 | CDD | cd18791 | SF2_C_RHA | 690 | 850 | 3.32407E-76 |
| 11 | g14138.t1 | Coils | Coil | Coil | 1143 | 1177 | - |
| 9 | g14138.t1 | Gene3D | G3DSA:3.40.50.300 | - | 460 | 688 | 1.9E-92 |
| 8 | g14138.t1 | Gene3D | G3DSA:3.40.50.300 | - | 689 | 861 | 2.2E-67 |
| 10 | g14138.t1 | Gene3D | G3DSA:1.20.120.1080 | - | 885 | 991 | 1.4E-27 |
| 23 | g14138.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 26 | - |
| 19 | g14138.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 53 | 291 | - |
| 22 | g14138.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 53 | 90 | - |
| 18 | g14138.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 91 | 110 | - |
| 21 | g14138.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 111 | 162 | - |
| 20 | g14138.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 197 | 216 | - |
| 24 | g14138.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 230 | 291 | - |
| 5 | g14138.t1 | PANTHER | PTHR18934 | ATP-DEPENDENT RNA HELICASE | 337 | 1132 | 0.0 |
| 6 | g14138.t1 | PANTHER | PTHR18934:SF233 | PRE-MRNA-SPLICING FACTOR ATP-DEPENDENT RNA HELICASE PRP16 | 337 | 1132 | 0.0 |
| 2 | g14138.t1 | Pfam | PF00270 | DEAD/DEAH box helicase | 520 | 671 | 2.4E-6 |
| 3 | g14138.t1 | Pfam | PF00271 | Helicase conserved C-terminal domain | 716 | 842 | 2.0E-13 |
| 4 | g14138.t1 | Pfam | PF04408 | Helicase associated domain (HA2) | 905 | 990 | 1.2E-18 |
| 1 | g14138.t1 | Pfam | PF07717 | Oligonucleotide/oligosaccharide-binding (OB)-fold | 1050 | 1127 | 1.3E-14 |
| 17 | g14138.t1 | ProSitePatterns | PS00690 | DEAH-box subfamily ATP-dependent helicases signature. | 628 | 637 | - |
| 26 | g14138.t1 | ProSiteProfiles | PS51192 | Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. | 523 | 686 | 19.412 |
| 25 | g14138.t1 | ProSiteProfiles | PS51194 | Superfamilies 1 and 2 helicase C-terminal domain profile. | 700 | 883 | 16.574 |
| 15 | g14138.t1 | SMART | SM00487 | ultradead3 | 511 | 695 | 4.3E-31 |
| 14 | g14138.t1 | SMART | SM00490 | helicmild6 | 739 | 842 | 5.3E-20 |
| 16 | g14138.t1 | SMART | SM00847 | ha2_5 | 903 | 993 | 3.3E-33 |
| 7 | g14138.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 505 | 1064 | 2.86E-132 |
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:0005524 | ATP binding | MF |
| GO:0004386 | helicase activity | MF |
| GO:0003676 | nucleic acid binding | MF |
KEGG
Orthology
- This transcript has been annotated with K12815 (pre-mRNA-splicing factor ATP-dependent RNA helicase DHX38/PRP16)
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.
