General information for g5682.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 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.t2 | TSS | g5682.t2 | 11237947 | 11237947 |
| chr_2 | g5682 | g5682.t2 | isoform | g5682.t2 | 11238583 | 11239480 |
| chr_2 | g5682 | g5682.t2 | exon | g5682.t2.exon1 | 11238583 | 11238599 |
| chr_2 | g5682 | g5682.t2 | exon | g5682.t2.exon2 | 11238743 | 11239480 |
| chr_2 | g5682 | g5682.t2 | cds | g5682.t2.CDS1 | 11238790 | 11239479 |
| chr_2 | g5682 | g5682.t2 | TTS | g5682.t2 | NA | NA |
Sequences
>g5682.t2 Gene=g5682 Length=755
ATGGAATCAAACGGCAAGTCTAACAGTAAAACAAAAGGAGGATGCTCTTAATTATTGTTT
GAAAATGGTACCTAATGTAGATTCAATGGATGTTCAGGATGCTTTATTGCGTTGCGACTG
GAACAAAGAGAAAGCTGTTGAACATCTTAAAAATTTACCACCTAGAGGTAATAAAAGAAC
TTATTTTCAACATCGCGCAACGAATGAGAATAGCCATAATAATCATGTTGTCAAAAAACA
ACGCAGAAATAATGATGAGGATGACGAAGAAACCGCTTCAGAAGATGAACACGAATTTGG
TAAAACTGCTGTTTTTGACAGTGATTCTGAAAATGATGGCAATTATGCACCAGAAATGAC
ATTGCAGCGAAAAGAAGTTTTTGATTTCTTCAATAATGCTAATGTTGGAGAATTGACTTG
TATTAAAGCGTGTTCATTGAAAAAGGCCGAAATTCTTATTGAAAATCGTCCATATAGAAA
TTGGGAAGAGCTTGTTGCAAAATGCAGAGAAAAACCACTTCAAACTGATCTTCTTAACAA
TGCTCAAGAATTTATCGATAAAAGAAATAATCTCAAGAAGCTAATAAAAAAATGCAAGGC
TATTGTATTAAAATTAGAGAAAGCTGTTGAAGAAGGTGCTGGAATTTCAGAACAACCATA
TATACTTAATGAAGAATTCAAGCTCTCTGATTATCAACTTGTTGGACTTAATTGGCTAGC
AGTGCTTCATCAAAATGGAACCAATGGAATTCTTG
>g5682.t2 Gene=g5682 Length=230
MVPNVDSMDVQDALLRCDWNKEKAVEHLKNLPPRGNKRTYFQHRATNENSHNNHVVKKQR
RNNDEDDEETASEDEHEFGKTAVFDSDSENDGNYAPEMTLQRKEVFDFFNNANVGELTCI
KACSLKKAEILIENRPYRNWEELVAKCREKPLQTDLLNNAQEFIDKRNNLKKLIKKCKAI
VLKLEKAVEEGAGISEQPYILNEEFKLSDYQLVGLNWLAVLHQNGTNGIL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g5682.t2 | Coils | Coil | Coil | 170 | 190 | - |
| 5 | g5682.t2 | Gene3D | G3DSA:3.40.50.10810 | - | 154 | 230 | 1.1E-5 |
| 4 | g5682.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 45 | 91 | - |
| 3 | g5682.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 50 | 66 | - |
| 1 | g5682.t2 | PANTHER | PTHR10799:SF964 | SWI/SNF-RELATED MATRIX-ASSOCIATED ACTIN-DEPENDENT REGULATOR OF CHROMATIN SUBFAMILY A CONTAINING DEAD/H BOX 1 | 47 | 230 | 3.3E-13 |
| 2 | g5682.t2 | PANTHER | PTHR10799 | SNF2/RAD54 HELICASE FAMILY | 47 | 230 | 3.3E-13 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5682/g5682.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5682.t2.fa.iupred3.txt does not exist
GO terms from InterProScan
There are no GO annotations for this transcript.
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. There were no conditions that were differentially expressed