General information for g1845.t4
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.t4 | TSS | g1845.t4 | 13280231 | 13280231 |
| chr_3 | g1845 | g1845.t4 | isoform | g1845.t4 | 13280601 | 13281881 |
| chr_3 | g1845 | g1845.t4 | exon | g1845.t4.exon1 | 13280601 | 13280731 |
| chr_3 | g1845 | g1845.t4 | cds | g1845.t4.CDS1 | 13280642 | 13280731 |
| chr_3 | g1845 | g1845.t4 | exon | g1845.t4.exon2 | 13280784 | 13281881 |
| chr_3 | g1845 | g1845.t4 | cds | g1845.t4.CDS2 | 13280784 | 13281881 |
| chr_3 | g1845 | g1845.t4 | TTS | g1845.t4 | 13281961 | 13281961 |
Sequences
>g1845.t4 Gene=g1845 Length=1229
AGGCGGCCGGAATTGTAGTAGATCTCATAAAAACGAAAAAGATGGCAGGGAGAGCATTGC
TTTTAGCGGGCCCACCTGCTACCGGTAAAACAGCTATTGCTATGGCAATCGCTCATGAAC
TTGGAAACAAAGTTCCTTTCTGTCCAATGGTTGGTTCTGAAGTATTTTCAAGTGAAATAA
AAAAAACGGAGGTTCTTATGGAAAATTTCCGTCGTTCAATTGGTTTACGAATTCGTGAGA
CAAAAGAAGTTTATGAGGGTGAAGTGACTGAGCTAACGCCCGTTGAAACAGAAAATCCAA
TGGGAGGATTTGGAAGAACAATTAGTAATGTTGTTATTGGATTGAAAACAGCAAAAGGAA
CAAAACAACTTAAACTTGATCCTAGCATTTATGAATCATTACAGAAAGAAAAAGTTGAAG
TTGGTGATGTGATTTATATTGAAGCCAACAGTGGAGCAGTGAAGAGGCAAGGTAGAAGTG
ATACATTTGCAACAGAGTTTGATTTGGAAACAGAGGAATATGTTCCTTTGCCAAAAGGAG
ATGTTCATAAGAAGAAAGAAGTTGTTCAAGATGTTACATTACATGACCTTGATGCTGCAA
ATGCTCGACCACAAGGCGGACAAGATGTCATGTCACTTCTCGGACATTTAGTAAAGCCCA
AGAAAACAGAAATTACTGACAAATTAAGATTAGAGATCAACAAAGTAGTTAATAGATATA
TTGATCAAGGAATAGCTGAACTTGTTCCAGGAGTGTTGTTTATCGATGAAGTACATATGC
TTGATCTTGAGACTTTTACTTATCTTCATAAATCTCTTGAATCTCCCATCGCTCCAATTG
TCATTTTTGCTACTAATCGTGGCCGTTGTGTTATTCGTGGAACAGACGATATCGTTTCTC
CTCATGGAATTCCACTCGATTTGCTGGATCGTCTCATGATTATTCGTACATCTCCGTACA
GTATTTCTGAAATGGAGCAAATTATCAAATTGAGAGCACAAACAGAAGGACTTTCGATTG
AAGATGAAGCAATTACAGAATTGAGTGATATAGGCAGTAAATCGACATTAAGATATGCTG
TGCAACTCATGACTCCTGCATTCCAATCAGCCAAAGTAAATGGACGATCACAAATTACAA
AAGATGACATTACAGAAGTTAATTCTCTATTCCTCGATGCCAAGAGAAGTGTTAAATTCT
TGTCAGAAGGCAGTAAATTCATGAAGTAA
>g1845.t4 Gene=g1845 Length=395
MAGRALLLAGPPATGKTAIAMAIAHELGNKVPFCPMVGSEVFSSEIKKTEVLMENFRRSI
GLRIRETKEVYEGEVTELTPVETENPMGGFGRTISNVVIGLKTAKGTKQLKLDPSIYESL
QKEKVEVGDVIYIEANSGAVKRQGRSDTFATEFDLETEEYVPLPKGDVHKKKEVVQDVTL
HDLDAANARPQGGQDVMSLLGHLVKPKKTEITDKLRLEINKVVNRYIDQGIAELVPGVLF
IDEVHMLDLETFTYLHKSLESPIAPIVIFATNRGRCVIRGTDDIVSPHGIPLDLLDRLMI
IRTSPYSISEMEQIIKLRAQTEGLSIEDEAITELSDIGSKSTLRYAVQLMTPAFQSAKVN
GRSQITKDDITEVNSLFLDAKRSVKFLSEGSKFMK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g1845.t4 | CDD | cd00009 | AAA | 3 | 63 | 1.34512E-5 |
| 7 | g1845.t4 | Gene3D | G3DSA:1.10.8.60 | - | 306 | 395 | 4.4E-31 |
| 3 | g1845.t4 | PANTHER | PTHR11093:SF6 | RUVB-LIKE 1 | 1 | 390 | 8.4E-212 |
| 4 | g1845.t4 | PANTHER | PTHR11093 | RUVB-RELATED REPTIN AND PONTIN | 1 | 390 | 8.4E-212 |
| 2 | g1845.t4 | Pfam | PF06068 | TIP49 P-loop domain | 1 | 307 | 2.0E-142 |
| 1 | g1845.t4 | Pfam | PF17856 | TIP49 AAA-lid domain | 314 | 379 | 1.6E-21 |
| 9 | g1845.t4 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 24 | - |
| 10 | g1845.t4 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 4 | - |
| 11 | g1845.t4 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 5 | 15 | - |
| 12 | g1845.t4 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 16 | 24 | - |
| 8 | g1845.t4 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 25 | 395 | - |
| 6 | g1845.t4 | SMART | SM00382 | AAA_5 | 2 | 305 | 1.7E-6 |
| 5 | g1845.t4 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 3 | 374 | 3.92E-31 |
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 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.
