General information for g1845.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as RuvB-like helicase 1.
Parent gene
- The parent gene g1845 is located on chr_3: 13281881..13282790 (+ 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 | g1845 | g1845.t2 | TSS | g1845.t2 | 13280231 | 13280231 |
| chr_3 | g1845 | g1845.t2 | isoform | g1845.t2 | 13280397 | 13281881 |
| chr_3 | g1845 | g1845.t2 | exon | g1845.t2.exon1 | 13280397 | 13280553 |
| chr_3 | g1845 | g1845.t2 | cds | g1845.t2.CDS1 | 13280397 | 13280553 |
| chr_3 | g1845 | g1845.t2 | exon | g1845.t2.exon2 | 13280649 | 13280731 |
| chr_3 | g1845 | g1845.t2 | cds | g1845.t2.CDS2 | 13280649 | 13280731 |
| chr_3 | g1845 | g1845.t2 | exon | g1845.t2.exon3 | 13280784 | 13281881 |
| chr_3 | g1845 | g1845.t2 | cds | g1845.t2.CDS3 | 13280784 | 13281881 |
| chr_3 | g1845 | g1845.t2 | TTS | g1845.t2 | 13281961 | 13281961 |
Sequences
>g1845.t2 Gene=g1845 Length=1338
ATGAAAATCGAAGAAGTAAAATCAACAGTCAAAACTCAACGCATTGCAGCTCATTCGCAT
GTAAAAGGTCTTGGTTTAGATGAAAATGGAATCCCTTTACCAATTGCAGCTGGTTTAGTT
GGTCAGAAAAATGCAAGAGAGGTGAATATAAGATATGGGAGAGCATTGCTTTTAGCGGGC
CCACCTGCTACCGGTAAAACAGCTATTGCTATGGCAATCGCTCATGAACTTGGAAACAAA
GTTCCTTTCTGTCCAATGGTTGGTTCTGAAGTATTTTCAAGTGAAATAAAAAAAACGGAG
GTTCTTATGGAAAATTTCCGTCGTTCAATTGGTTTACGAATTCGTGAGACAAAAGAAGTT
TATGAGGGTGAAGTGACTGAGCTAACGCCCGTTGAAACAGAAAATCCAATGGGAGGATTT
GGAAGAACAATTAGTAATGTTGTTATTGGATTGAAAACAGCAAAAGGAACAAAACAACTT
AAACTTGATCCTAGCATTTATGAATCATTACAGAAAGAAAAAGTTGAAGTTGGTGATGTG
ATTTATATTGAAGCCAACAGTGGAGCAGTGAAGAGGCAAGGTAGAAGTGATACATTTGCA
ACAGAGTTTGATTTGGAAACAGAGGAATATGTTCCTTTGCCAAAAGGAGATGTTCATAAG
AAGAAAGAAGTTGTTCAAGATGTTACATTACATGACCTTGATGCTGCAAATGCTCGACCA
CAAGGCGGACAAGATGTCATGTCACTTCTCGGACATTTAGTAAAGCCCAAGAAAACAGAA
ATTACTGACAAATTAAGATTAGAGATCAACAAAGTAGTTAATAGATATATTGATCAAGGA
ATAGCTGAACTTGTTCCAGGAGTGTTGTTTATCGATGAAGTACATATGCTTGATCTTGAG
ACTTTTACTTATCTTCATAAATCTCTTGAATCTCCCATCGCTCCAATTGTCATTTTTGCT
ACTAATCGTGGCCGTTGTGTTATTCGTGGAACAGACGATATCGTTTCTCCTCATGGAATT
CCACTCGATTTGCTGGATCGTCTCATGATTATTCGTACATCTCCGTACAGTATTTCTGAA
ATGGAGCAAATTATCAAATTGAGAGCACAAACAGAAGGACTTTCGATTGAAGATGAAGCA
ATTACAGAATTGAGTGATATAGGCAGTAAATCGACATTAAGATATGCTGTGCAACTCATG
ACTCCTGCATTCCAATCAGCCAAAGTAAATGGACGATCACAAATTACAAAAGATGACATT
ACAGAAGTTAATTCTCTATTCCTCGATGCCAAGAGAAGTGTTAAATTCTTGTCAGAAGGC
AGTAAATTCATGAAGTAA
>g1845.t2 Gene=g1845 Length=445
MKIEEVKSTVKTQRIAAHSHVKGLGLDENGIPLPIAAGLVGQKNAREVNIRYGRALLLAG
PPATGKTAIAMAIAHELGNKVPFCPMVGSEVFSSEIKKTEVLMENFRRSIGLRIRETKEV
YEGEVTELTPVETENPMGGFGRTISNVVIGLKTAKGTKQLKLDPSIYESLQKEKVEVGDV
IYIEANSGAVKRQGRSDTFATEFDLETEEYVPLPKGDVHKKKEVVQDVTLHDLDAANARP
QGGQDVMSLLGHLVKPKKTEITDKLRLEINKVVNRYIDQGIAELVPGVLFIDEVHMLDLE
TFTYLHKSLESPIAPIVIFATNRGRCVIRGTDDIVSPHGIPLDLLDRLMIIRTSPYSISE
MEQIIKLRAQTEGLSIEDEAITELSDIGSKSTLRYAVQLMTPAFQSAKVNGRSQITKDDI
TEVNSLFLDAKRSVKFLSEGSKFMK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g1845.t2 | CDD | cd00009 | AAA | 40 | 113 | 7.9e-06 |
| 7 | g1845.t2 | Gene3D | G3DSA:1.10.8.60 | - | 356 | 445 | 0.0e+00 |
| 3 | g1845.t2 | PANTHER | PTHR11093:SF6 | RUVB-LIKE 1 | 1 | 440 | 0.0e+00 |
| 4 | g1845.t2 | PANTHER | PTHR11093 | RUVB-RELATED REPTIN AND PONTIN | 1 | 440 | 0.0e+00 |
| 2 | g1845.t2 | Pfam | PF06068 | TIP49 P-loop domain | 14 | 357 | 0.0e+00 |
| 1 | g1845.t2 | Pfam | PF17856 | TIP49 AAA-lid domain | 364 | 429 | 0.0e+00 |
| 6 | g1845.t2 | SMART | SM00382 | AAA_5 | 52 | 355 | 3.7e-06 |
| 5 | g1845.t2 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 39 | 424 | 0.0e+00 |
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:0043139 | 5’-3’ DNA helicase activity | MF |
| GO:0035267 | NuA4 histone acetyltransferase complex | CC |
| GO:0005524 | ATP binding | MF |
| GO:0031011 | Ino80 complex | CC |
| GO:0097255 | R2TP complex | CC |
| GO:0003678 | DNA helicase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K04499 (RuvB-like protein 1)
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.
