General information for g5682.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1-like protein.
Parent gene
- The parent gene g5682 is located on chr_2: 11238583..11241318 (+ 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_2 | g5682 | g5682.t4 | TSS | g5682.t4 | 11237947 | 11237947 |
| chr_2 | g5682 | g5682.t4 | isoform | g5682.t4 | 11238583 | 11240139 |
| chr_2 | g5682 | g5682.t4 | exon | g5682.t4.exon1 | 11238583 | 11238599 |
| chr_2 | g5682 | g5682.t4 | exon | g5682.t4.exon2 | 11238743 | 11239498 |
| chr_2 | g5682 | g5682.t4 | cds | g5682.t4.CDS1 | 11238790 | 11239498 |
| chr_2 | g5682 | g5682.t4 | exon | g5682.t4.exon3 | 11239560 | 11239955 |
| chr_2 | g5682 | g5682.t4 | cds | g5682.t4.CDS2 | 11239560 | 11239955 |
| chr_2 | g5682 | g5682.t4 | exon | g5682.t4.exon4 | 11240051 | 11240139 |
| chr_2 | g5682 | g5682.t4 | cds | g5682.t4.CDS3 | 11240051 | 11240139 |
| chr_2 | g5682 | g5682.t4 | TTS | g5682.t4 | NA | NA |
Sequences
>g5682.t4 Gene=g5682 Length=1258
ATGGAATCAAACGGCAAGTCTAACAGTAAAACAAAAGGAGGATGCTCTTAATTATTGTTT
GAAAATGGTACCTAATGTAGATTCAATGGATGTTCAGGATGCTTTATTGCGTTGCGACTG
GAACAAAGAGAAAGCTGTTGAACATCTTAAAAATTTACCACCTAGAGGTAATAAAAGAAC
TTATTTTCAACATCGCGCAACGAATGAGAATAGCCATAATAATCATGTTGTCAAAAAACA
ACGCAGAAATAATGATGAGGATGACGAAGAAACCGCTTCAGAAGATGAACACGAATTTGG
TAAAACTGCTGTTTTTGACAGTGATTCTGAAAATGATGGCAATTATGCACCAGAAATGAC
ATTGCAGCGAAAAGAAGTTTTTGATTTCTTCAATAATGCTAATGTTGGAGAATTGACTTG
TATTAAAGCGTGTTCATTGAAAAAGGCCGAAATTCTTATTGAAAATCGTCCATATAGAAA
TTGGGAAGAGCTTGTTGCAAAATGCAGAGAAAAACCACTTCAAACTGATCTTCTTAACAA
TGCTCAAGAATTTATCGATAAAAGAAATAATCTCAAGAAGCTAATAAAAAAATGCAAGGC
TATTGTATTAAAATTAGAGAAAGCTGTTGAAGAAGGTGCTGGAATTTCAGAACAACCATA
TATACTTAATGAAGAATTCAAGCTCTCTGATTATCAACTTGTTGGACTTAATTGGCTAGC
AGTGCTTCATCAAAATGGAACCAATGGAATTCTTGCTGATGAAATGGGTTTAGGTAAAAC
AATTCAAATTATTGCATTCCTTGCTTATTTGAAAGAAACTCAACAACAATTAGCAACTCA
TGTTGTTTGCGTTCCATCAAGCACTTTAGACAATTGGGCTAATGAGTTGAGTAAATGGTG
TCCATCTTTAAATGTCGCAAAATATTATGGCTCGCAAGAAGAGCGACGAATGATGCGTTT
TAAGTGGCTTAAAGAAGGTTTTGATGACACTGACGTAATTTTGACAACATATCATGTTAT
TGGAAGTTCTAATGAAGACAAGAAAATGTTTCGCGTTACACCATTTCATTATGTTATATT
TGATGAAGCACACATGCTGAAAAACATGATGACTCAACGGTACACAACATTATTGAGAAT
CAATGCACAAAGACGAATTCTTTTAACTGGTACTCCATTGCAAAATTCTTTACTGGAATT
GATGAGTCTTTTGTGTTTTGTGATGCCTAAACTTTTTGCCAACAAACAGGAAGACATT
>g5682.t4 Gene=g5682 Length=398
MVPNVDSMDVQDALLRCDWNKEKAVEHLKNLPPRGNKRTYFQHRATNENSHNNHVVKKQR
RNNDEDDEETASEDEHEFGKTAVFDSDSENDGNYAPEMTLQRKEVFDFFNNANVGELTCI
KACSLKKAEILIENRPYRNWEELVAKCREKPLQTDLLNNAQEFIDKRNNLKKLIKKCKAI
VLKLEKAVEEGAGISEQPYILNEEFKLSDYQLVGLNWLAVLHQNGTNGILADEMGLGKTI
QIIAFLAYLKETQQQLATHVVCVPSSTLDNWANELSKWCPSLNVAKYYGSQEERRMMRFK
WLKEGFDDTDVILTTYHVIGSSNEDKKMFRVTPFHYVIFDEAHMLKNMMTQRYTTLLRIN
AQRRILLTGTPLQNSLLELMSLLCFVMPKLFANKQEDI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g5682.t4 | Coils | Coil | Coil | 170 | 190 | - |
| 5 | g5682.t4 | Gene3D | G3DSA:3.40.50.10810 | - | 171 | 398 | 4.2E-74 |
| 9 | g5682.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 45 | 91 | - |
| 8 | g5682.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 50 | 66 | - |
| 2 | g5682.t4 | PANTHER | PTHR10799:SF964 | SWI/SNF-RELATED MATRIX-ASSOCIATED ACTIN-DEPENDENT REGULATOR OF CHROMATIN SUBFAMILY A CONTAINING DEAD/H BOX 1 | 47 | 397 | 8.8E-94 |
| 3 | g5682.t4 | PANTHER | PTHR10799 | SNF2/RAD54 HELICASE FAMILY | 47 | 397 | 8.8E-94 |
| 1 | g5682.t4 | Pfam | PF00176 | SNF2 family N-terminal domain | 220 | 395 | 1.4E-45 |
| 10 | g5682.t4 | ProSiteProfiles | PS51192 | Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. | 219 | 389 | 25.838 |
| 7 | g5682.t4 | SMART | SM00487 | ultradead3 | 203 | 397 | 1.7E-32 |
| 4 | g5682.t4 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 190 | 395 | 3.36E-51 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5682/g5682.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5682.t4.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005524 | ATP binding | MF |
| GO:0070615 | NA | NA |
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.
