General information for g11211.t62
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15.
Parent gene
- The parent gene g11211 is located on chr_1: 14600657..14601436 (- 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 | g11211 | g11211.t62 | TTS | g11211.t62 | 14598503 | 14598503 |
| chr_1 | g11211 | g11211.t62 | isoform | g11211.t62 | 14598609 | 14601436 |
| chr_1 | g11211 | g11211.t62 | exon | g11211.t62.exon1 | 14598609 | 14598730 |
| chr_1 | g11211 | g11211.t62 | exon | g11211.t62.exon2 | 14598786 | 14599139 |
| chr_1 | g11211 | g11211.t62 | exon | g11211.t62.exon3 | 14599200 | 14599464 |
| chr_1 | g11211 | g11211.t62 | cds | g11211.t62.CDS1 | 14599325 | 14599464 |
| chr_1 | g11211 | g11211.t62 | exon | g11211.t62.exon4 | 14599565 | 14599751 |
| chr_1 | g11211 | g11211.t62 | cds | g11211.t62.CDS2 | 14599565 | 14599751 |
| chr_1 | g11211 | g11211.t62 | exon | g11211.t62.exon5 | 14599808 | 14600000 |
| chr_1 | g11211 | g11211.t62 | cds | g11211.t62.CDS3 | 14599808 | 14600000 |
| chr_1 | g11211 | g11211.t62 | exon | g11211.t62.exon6 | 14600059 | 14600578 |
| chr_1 | g11211 | g11211.t62 | cds | g11211.t62.CDS4 | 14600059 | 14600578 |
| chr_1 | g11211 | g11211.t62 | exon | g11211.t62.exon7 | 14600645 | 14601031 |
| chr_1 | g11211 | g11211.t62 | cds | g11211.t62.CDS5 | 14600645 | 14600984 |
| chr_1 | g11211 | g11211.t62 | exon | g11211.t62.exon8 | 14601085 | 14601321 |
| chr_1 | g11211 | g11211.t62 | exon | g11211.t62.exon9 | 14601387 | 14601436 |
| chr_1 | g11211 | g11211.t62 | TSS | g11211.t62 | 14601549 | 14601549 |
Sequences
>g11211.t62 Gene=g11211 Length=2315
ATGTCAAAACGAAGAATAGAAGTACTGGACCCATTTATCAAGAAACGAAGAGAAGAAAAA
GGAATTCCTGTTGATAGTGGCTCATCTTCATCATCAGTCGTAATTACAACAACACCAGTT
ATGTCTGGATCGATAAATCCACTCACAGGCGCACTTTATTCTGCAAATTATCATGCTCTA
TATAAAAAGCGTGTTTTGTTGCCTGTATTTGAATATCGTGCTGATTTCATGCGATTACTA
GCAGAACATCAATGCATTGTATTAGTCGGCGAAACTGGATCAGGTTAGAAAAACAACACA
AATTCCACAATGGGCAGTAGATTACGCGCGAAGTATGAGTAGTAAAGGAGTTGCATGTAC
ACAGCCAAGAAGAGTAGCAGCAATGTCAGTTGCTCAGCGTGTTTCTGAAGAAATGGACGT
TCTTTTGGGACAAGAAGTCGGATATTCAATTCGTTTTGAAGATTGCTCTTCACCAAAAAC
TGTGTTAAAGTACTTGACCGATGGTATGTTACTGAGAGAAGCAATGTCTGATCCAATGCT
TGAAGCATATCAAGTTATTTTGCTCGACGAAGCGCATGAAAGGACATTAGCCACAGATTT
GTTGATGGGAGTTTTGAAAGAAGTGATTAAACAACGTTCTGATTTGAAATTAGTTATTAT
GTCTGCCACATTAGATGCTGGAAAATTTCAAAATTATTTCGATAACGCACCATTGATGAA
TGTTCCTGGTCGCACACATCCAGTAGAAATCTTTTATACTCCTGAGCCGGAACGCGACTA
TTTGGAGGCTGCAATTAGAACTGTTATTCAAATTCACATGTGTGAAGAAGTCGAAGGTGA
TATCTTGATGTTCTTAACTGGTCAAGAGGAAATCGAAGAAGCATGTAAACGCGTAAAGCG
TGAAATTGATAATTTAGGACCCGATGTCGGTGAACTGAGATGTATTCCCTTGTATTCAAC
CTTACCGCCAGCAGCTCAACAGAAAATTTTTGAGCCAGCACCACCAAAAAGAGCGAATGG
TGCTATTGGTCGAAAAGTTGTCATTAGTACAAATATTGCTGAAACATCTCTTACAATTGA
TGGAGTTGTGTTTGTAATTGATCCTGGTTTTGCTAAGCAAAAGGTTTATAATCCACGTAT
TCGTGTCGAGAGTTTATTAGTTTCGCCTATCAGTAAAGCATCCGCACAGCAACGTGCTGG
TCGTGCTGGACGTACACGTCCTGGAAAATGTTTCAGACTTTATACTGAAAAAGCTTACAA
AAATGAAATGCAGGATAATACATATCCAGAAATTTTACGTTCAAATTTGGGAACTGTTGT
TCTTCAACTAAAGAAACTTGGCATTGATGATTTAGTTCATTTTGATTTTATGGATCCGCC
TGCACCAGAAACTCTTATGCGTGCTTTGGAGTTATTAAATTATTTGGCAGCACTTGATGA
CGATGGAAACTTGACTGATCTTGGATCTGTTTGTTCTGAATTTCCTCTTGATCCACAATT
AGCAAAAATGTTGATTGCTTCATGTTCACACAACTGCTCTAATGAGATTCTCTCAATTAC
TGCAATGTTATCGGATGTATCAATTGTTTTTTGGCAATTTTTATTCATTTGTGGACGTGT
GAATGGGCTTTTGGGATTTTTTTTATTAATTCTGATCCCCATTCAAAAAACTGCACATTT
GCTGCGTCCATTTTTTTCTGTTCTTAACTTTTAAAGTGCCCCAGGCTTTTGTTAGACCTA
ATGAAATGAAGAAGCAAGCAGACGATGCCAAGATGAGATTTGCACACATCGATGGTGATC
ATTTGACACTTCTCAATGTATTTCATGCTTTCAAGCAGAATAATGAAGATCCACAATGGT
GTTATGAGAATTTCATCAATTATCGTTCGCTGAAATCAGCTGATAATGTTCGTCAACAAT
TGGCTCGTATCATGGACAGATTTAATTTGAAGCGCACGAGTACAGAGTTCACAAGCAAGG
ATTATTATGTTAATATTCGTAAAGCACTTGTTGAAGGATTCTTCATGCAAGTCGCACATT
TGGAACGCACTGGTCACTACTTAACAATCAAGGATAATCAGATTGTTCAATTACATCCAT
CCACATGCTTAGATCATAAACCAGATTGGGTCATTTATAATGAGTTTGTATTAACAACAA
AGAATTATATTAGGACAGTAACCGATATTAAACCCGAATGGTTATTGAAGCTTGCACCAC
AATATTACGATCTCAACAATTTCCCAGCATGTGAGGCAAAGAGACAGTTAGAAAACTTAC
AAGCAAGGCTAGAGAGTCGTCAATATCAATATTAA
>g11211.t62 Gene=g11211 Length=459
MSSKGVACTQPRRVAAMSVAQRVSEEMDVLLGQEVGYSIRFEDCSSPKTVLKYLTDGMLL
REAMSDPMLEAYQVILLDEAHERTLATDLLMGVLKEVIKQRSDLKLVIMSATLDAGKFQN
YFDNAPLMNVPGRTHPVEIFYTPEPERDYLEAAIRTVIQIHMCEEVEGDILMFLTGQEEI
EEACKRVKREIDNLGPDVGELRCIPLYSTLPPAAQQKIFEPAPPKRANGAIGRKVVISTN
IAETSLTIDGVVFVIDPGFAKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRTRPGKCF
RLYTEKAYKNEMQDNTYPEILRSNLGTVVLQLKKLGIDDLVHFDFMDPPAPETLMRALEL
LNYLAALDDDGNLTDLGSVCSEFPLDPQLAKMLIASCSHNCSNEILSITAMLSDVSIVFW
QFLFICGRVNGLLGFFLLILIPIQKTAHLLRPFFSVLNF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g11211.t62 | CDD | cd18791 | SF2_C_RHA | 135 | 303 | 9.39449E-88 |
| 7 | g11211.t62 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 133 | 2.7E-62 |
| 6 | g11211.t62 | Gene3D | G3DSA:3.40.50.300 | - | 134 | 316 | 5.6E-73 |
| 8 | g11211.t62 | Gene3D | G3DSA:1.20.120.1080 | - | 339 | 422 | 1.1E-27 |
| 3 | g11211.t62 | PANTHER | PTHR18934:SF95 | PRE-MRNA-SPLICING FACTOR ATP-DEPENDENT RNA HELICASE DHX15 | 4 | 415 | 3.4E-262 |
| 4 | g11211.t62 | PANTHER | PTHR18934 | ATP-DEPENDENT RNA HELICASE | 4 | 415 | 3.4E-262 |
| 1 | g11211.t62 | Pfam | PF00271 | Helicase conserved C-terminal domain | 156 | 294 | 3.6E-12 |
| 2 | g11211.t62 | Pfam | PF04408 | Helicase associated domain (HA2) | 357 | 417 | 5.8E-19 |
| 10 | g11211.t62 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 417 | - |
| 11 | g11211.t62 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 418 | 441 | - |
| 9 | g11211.t62 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 442 | 459 | - |
| 17 | g11211.t62 | ProSiteProfiles | PS51192 | Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. | 1 | 131 | 15.602 |
| 16 | g11211.t62 | ProSiteProfiles | PS51194 | Superfamilies 1 and 2 helicase C-terminal domain profile. | 156 | 336 | 16.519 |
| 14 | g11211.t62 | SMART | SM00490 | helicmild6 | 178 | 295 | 9.4E-16 |
| 15 | g11211.t62 | SMART | SM00847 | ha2_5 | 356 | 440 | 1.8E-14 |
| 5 | g11211.t62 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 9 | 413 | 2.8E-101 |
| 13 | g11211.t62 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 419 | 441 | - |
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 |
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.
