General information for g11211.t60
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.t60 | TTS | g11211.t60 | 14598503 | 14598503 |
| chr_1 | g11211 | g11211.t60 | isoform | g11211.t60 | 14598609 | 14601436 |
| chr_1 | g11211 | g11211.t60 | exon | g11211.t60.exon1 | 14598609 | 14598730 |
| chr_1 | g11211 | g11211.t60 | exon | g11211.t60.exon2 | 14598786 | 14599139 |
| chr_1 | g11211 | g11211.t60 | exon | g11211.t60.exon3 | 14599200 | 14599314 |
| chr_1 | g11211 | g11211.t60 | cds | g11211.t60.CDS1 | 14599304 | 14599314 |
| chr_1 | g11211 | g11211.t60 | exon | g11211.t60.exon4 | 14599565 | 14599751 |
| chr_1 | g11211 | g11211.t60 | cds | g11211.t60.CDS2 | 14599565 | 14599751 |
| chr_1 | g11211 | g11211.t60 | exon | g11211.t60.exon5 | 14599808 | 14600000 |
| chr_1 | g11211 | g11211.t60 | cds | g11211.t60.CDS3 | 14599808 | 14600000 |
| chr_1 | g11211 | g11211.t60 | exon | g11211.t60.exon6 | 14600059 | 14600578 |
| chr_1 | g11211 | g11211.t60 | cds | g11211.t60.CDS4 | 14600059 | 14600578 |
| chr_1 | g11211 | g11211.t60 | exon | g11211.t60.exon7 | 14600645 | 14601436 |
| chr_1 | g11211 | g11211.t60 | cds | g11211.t60.CDS5 | 14600645 | 14600984 |
| chr_1 | g11211 | g11211.t60 | TSS | g11211.t60 | 14601549 | 14601549 |
Sequences
>g11211.t60 Gene=g11211 Length=2283
ATGTCAAAACGAAGAATAGAAGTACTGGACCCATTTATCAAGAAACGAAGGTAAAATATC
AAAAAAGTCAATTTTTATAATTTGTTTTCACAAAACGTTTTTTTTTGTTTTCTAGAGAAG
AAAAAGGAATTCCTGTTGATAGTGGCTCATCTTCATCATCAGTCGTAATTACAACAACAC
CAGTTATGTCTGGATCGATAAATCCACTCACAGGCGCACTTTATTCTGCAAATTATCATG
CTCTATATAAAAAGCGTGTTTTGTTGCCTGTATTTGAATATCGTGCTGATTTCATGCGAT
TACTAGCAGAACATCAATGCATTGTATTAGTCGGCGAAACTGGATCAGGTTAGTATTATT
TATATATGAATCAATATTGTTATCATGAATTTTCATATATTTAAGGAAAAACAACACAAA
TTCCACAATGGGCAGTAGATTACGCGCGAAGTATGAGTAGTAAAGGAGTTGCATGTACAC
AGCCAAGAAGAGTAGCAGCAATGTCAGTTGCTCAGCGTGTTTCTGAAGAAATGGACGTTC
TTTTGGGACAAGAAGTCGGATATTCAATTCGTTTTGAAGATTGCTCTTCACCAAAAACTG
TGTTAAAGTACTTGACCGATGGTATGTTACTGAGAGAAGCAATGTCTGATCCAATGCTTG
AAGCATATCAAGTTATTTTGCTCGACGAAGCGCATGAAAGGACATTAGCCACAGATTTGT
TGATGGGAGTTTTGAAAGAAGTGATTAAACAACGTTCTGATTTGAAATTAGTTATTATGT
CTGCCACATTAGATGCTGGAAAATTTCAAAATTATTTCGATAACGCACCATTGATGAATG
TTCCTGGTCGCACACATCCAGTAGAAATCTTTTATACTCCTGAGCCGGAACGCGACTATT
TGGAGGCTGCAATTAGAACTGTTATTCAAATTCACATGTGTGAAGAAGTCGAAGGTGATA
TCTTGATGTTCTTAACTGGTCAAGAGGAAATCGAAGAAGCATGTAAACGCGTAAAGCGTG
AAATTGATAATTTAGGACCCGATGTCGGTGAACTGAGATGTATTCCCTTGTATTCAACCT
TACCGCCAGCAGCTCAACAGAAAATTTTTGAGCCAGCACCACCAAAAAGAGCGAATGGTG
CTATTGGTCGAAAAGTTGTCATTAGTACAAATATTGCTGAAACATCTCTTACAATTGATG
GAGTTGTGTTTGTAATTGATCCTGGTTTTGCTAAGCAAAAGGTTTATAATCCACGTATTC
GTGTCGAGAGTTTATTAGTTTCGCCTATCAGTAAAGCATCCGCACAGCAACGTGCTGGTC
GTGCTGGACGTACACGTCCTGGAAAATGTTTCAGACTTTATACTGAAAAAGCTTACAAAA
ATGAAATGCAGGATAATACATATCCAGAAATTTTACGTTCAAATTTGGGAACTGTTGTTC
TTCAACTAAAGAAACTTGGCATTGATGATTTAGTTCATTTTGATTTTATGGATCCGCCTG
CACCAGAAACTCTTATGCGTGCTTTGGAGTTATTAAATTATTTGGCAGCACTTGATGACG
ATGGAAACTTGACTGATCTTGGATCTGTTTGTTCTGAATTTCCTCTTGATCCACAATTAG
CAAAAATGTTGATTGCTTCATGTTCACACAACTGCTCTAATGAGATTCTCTCAATTACTG
CAATGTTATCGGGCTTTTGTTAGACCTAATGAAATGAAGAAGCAAGCAGACGATGCCAAG
ATGAGATTTGCACACATCGATGGTGATCATTTGACACTTCTCAATGTATTTCATGCTTTC
AAGCAGAATAATGAAGATCCACAATGGTGTTATGAGAATTTCATCAATTATCGTTCGCTG
AAATCAGCTGATAATGTTCGTCAACAATTGGCTCGTATCATGGACAGATTTAATTTGAAG
CGCACGAGTACAGAGTTCACAAGCAAGGATTATTATGTTAATATTCGTAAAGCACTTGTT
GAAGGATTCTTCATGCAAGTCGCACATTTGGAACGCACTGGTCACTACTTAACAATCAAG
GATAATCAGATTGTTCAATTACATCCATCCACATGCTTAGATCATAAACCAGATTGGGTC
ATTTATAATGAGTTTGTATTAACAACAAAGAATTATATTAGGACAGTAACCGATATTAAA
CCCGAATGGTTATTGAAGCTTGCACCACAATATTACGATCTCAACAATTTCCCAGCATGT
GAGGCAAAGAGACAGTTAGAAAACTTACAAGCAAGGCTAGAGAGTCGTCAATATCAATAT
TAA
>g11211.t60 Gene=g11211 Length=416
MSSKGVACTQPRRVAAMSVAQRVSEEMDVLLGQEVGYSIRFEDCSSPKTVLKYLTDGMLL
REAMSDPMLEAYQVILLDEAHERTLATDLLMGVLKEVIKQRSDLKLVIMSATLDAGKFQN
YFDNAPLMNVPGRTHPVEIFYTPEPERDYLEAAIRTVIQIHMCEEVEGDILMFLTGQEEI
EEACKRVKREIDNLGPDVGELRCIPLYSTLPPAAQQKIFEPAPPKRANGAIGRKVVISTN
IAETSLTIDGVVFVIDPGFAKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRTRPGKCF
RLYTEKAYKNEMQDNTYPEILRSNLGTVVLQLKKLGIDDLVHFDFMDPPAPETLMRALEL
LNYLAALDDDGNLTDLGSVCSEFPLDPQLAKMLIASCSHNCSNEILSITAMLSGFC
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g11211.t60 | CDD | cd18791 | SF2_C_RHA | 135 | 303 | 0.000 |
| 9 | g11211.t60 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 133 | 0.000 |
| 8 | g11211.t60 | Gene3D | G3DSA:3.40.50.300 | - | 134 | 316 | 0.000 |
| 10 | g11211.t60 | Gene3D | G3DSA:1.20.120.1080 | - | 339 | 414 | 0.000 |
| 3 | g11211.t60 | PANTHER | PTHR18934:SF95 | PRE-MRNA-SPLICING FACTOR ATP-DEPENDENT RNA HELICASE DHX15 | 4 | 414 | 0.000 |
| 4 | g11211.t60 | PANTHER | PTHR18934 | ATP-DEPENDENT RNA HELICASE | 4 | 414 | 0.000 |
| 1 | g11211.t60 | Pfam | PF00271 | Helicase conserved C-terminal domain | 156 | 294 | 0.000 |
| 2 | g11211.t60 | Pfam | PF04408 | Helicase associated domain (HA2) | 357 | 413 | 0.000 |
| 12 | g11211.t60 | ProSiteProfiles | PS51192 | Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. | 1 | 131 | 15.602 |
| 11 | g11211.t60 | ProSiteProfiles | PS51194 | Superfamilies 1 and 2 helicase C-terminal domain profile. | 156 | 336 | 16.519 |
| 6 | g11211.t60 | SMART | SM00490 | helicmild6 | 178 | 295 | 0.000 |
| 7 | g11211.t60 | SMART | SM00847 | ha2_5 | 356 | 416 | 0.000 |
| 5 | g11211.t60 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 9 | 413 | 0.000 |
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.
