General information for g5682.t1
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.t1 | TSS | g5682.t1 | 11237947 | 11237947 |
| chr_2 | g5682 | g5682.t1 | isoform | g5682.t1 | 11238583 | 11241318 |
| chr_2 | g5682 | g5682.t1 | exon | g5682.t1.exon1 | 11238583 | 11238595 |
| chr_2 | g5682 | g5682.t1 | cds | g5682.t1.CDS1 | 11238583 | 11238595 |
| chr_2 | g5682 | g5682.t1 | exon | g5682.t1.exon2 | 11238743 | 11239498 |
| chr_2 | g5682 | g5682.t1 | cds | g5682.t1.CDS2 | 11238743 | 11239498 |
| chr_2 | g5682 | g5682.t1 | exon | g5682.t1.exon3 | 11239560 | 11239955 |
| chr_2 | g5682 | g5682.t1 | cds | g5682.t1.CDS3 | 11239560 | 11239955 |
| chr_2 | g5682 | g5682.t1 | exon | g5682.t1.exon4 | 11240051 | 11241318 |
| chr_2 | g5682 | g5682.t1 | cds | g5682.t1.CDS4 | 11240051 | 11241318 |
| chr_2 | g5682 | g5682.t1 | TTS | g5682.t1 | 11241528 | 11241528 |
Sequences
>g5682.t1 Gene=g5682 Length=2433
ATGGAATCAAACGGTCTAACAGTAAAACAAAAGGAGGATGCTCTTAATTATTGTTTGAAA
ATGGTACCTAATGTAGATTCAATGGATGTTCAGGATGCTTTATTGCGTTGCGACTGGAAC
AAAGAGAAAGCTGTTGAACATCTTAAAAATTTACCACCTAGAGGTAATAAAAGAACTTAT
TTTCAACATCGCGCAACGAATGAGAATAGCCATAATAATCATGTTGTCAAAAAACAACGC
AGAAATAATGATGAGGATGACGAAGAAACCGCTTCAGAAGATGAACACGAATTTGGTAAA
ACTGCTGTTTTTGACAGTGATTCTGAAAATGATGGCAATTATGCACCAGAAATGACATTG
CAGCGAAAAGAAGTTTTTGATTTCTTCAATAATGCTAATGTTGGAGAATTGACTTGTATT
AAAGCGTGTTCATTGAAAAAGGCCGAAATTCTTATTGAAAATCGTCCATATAGAAATTGG
GAAGAGCTTGTTGCAAAATGCAGAGAAAAACCACTTCAAACTGATCTTCTTAACAATGCT
CAAGAATTTATCGATAAAAGAAATAATCTCAAGAAGCTAATAAAAAAATGCAAGGCTATT
GTATTAAAATTAGAGAAAGCTGTTGAAGAAGGTGCTGGAATTTCAGAACAACCATATATA
CTTAATGAAGAATTCAAGCTCTCTGATTATCAACTTGTTGGACTTAATTGGCTAGCAGTG
CTTCATCAAAATGGAACCAATGGAATTCTTGCTGATGAAATGGGTTTAGGTAAAACAATT
CAAATTATTGCATTCCTTGCTTATTTGAAAGAAACTCAACAACAATTAGCAACTCATGTT
GTTTGCGTTCCATCAAGCACTTTAGACAATTGGGCTAATGAGTTGAGTAAATGGTGTCCA
TCTTTAAATGTCGCAAAATATTATGGCTCGCAAGAAGAGCGACGAATGATGCGTTTTAAG
TGGCTTAAAGAAGGTTTTGATGACACTGACGTAATTTTGACAACATATCATGTTATTGGA
AGTTCTAATGAAGACAAGAAAATGTTTCGCGTTACACCATTTCATTATGTTATATTTGAT
GAAGCACACATGCTGAAAAACATGATGACTCAACGGTACACAACATTATTGAGAATCAAT
GCACAAAGACGAATTCTTTTAACTGGTACTCCATTGCAAAATTCTTTACTGGAATTGATG
AGTCTTTTGTGTTTTGTGATGCCTAAACTTTTTGCCAACAAACAGGAAGACATTAAAGCT
TTATTCTCAAAGAAAGCACCAAAAATGGATGATGGTTCAGAACAAACAAATGATTTCGAA
CAATCACAAATTCAGCGTGCTAAAAACATAATGAAACCATTCATTTTGCGACGTTTAAAA
AAGGATGTACTTTCATTCTTGCCGAAAAAGACAGAAGTTACTGAAAAAGTAAAAATGTTA
CCAGATCAAAGCAAAAAGTATCAACATTTAATTGATGAATATAAAAATATTGATCCAACA
AGCGATAATATTATCGGTCGAGGCACATCGATAATGATGGATATGAGAAAGCTTGCAAAT
CATCCTTTATTATTGCGATATTTCTTCACTGATGAGCGTCTTCGTGAAATTTCCAAAGTA
TTAGCACGTGATTCAGTCTATAAGAATAATAATCCAAAAGAAATTTTCGAAGACATTGCT
CCAATGTCTGATTTCAAAATTCATCAACTTGCTGAAAAATATCCTTCGATAACGAATTTA
GTAAAAATTCCTGATAATGTTGTGTTGAATTCGGGTAAATTTAAGTATCTTGATAATTTG
TTGCCGAAACTCAAGGCTGATGGACATCGTGTTCTCATCTTTTCACAATTTGTAATGATG
CTCGATGTGATTGAAAAGTATCTTTCGATACGTGGTATGAAATTTGTGCGCCTTGATGGT
AGCACTGCAGTTACAGATCGCCAAGATTTGATTGAGGAATATACTGCAAACCCAGAGATC
TTTATTTTTCTTTTAAGTACAAAAGCTGGAGGATTAGGCATCAATCTTACCAGTGCTGAT
CGTGCAATCATTCACGATATTGATTTTAATCCTTACAATGATAAACAAGCTGAAGATAGA
TGTCATCGAATTGGACAAACGAAGGAGGTAGTAATTTATAAACTAATTTCTGATGGAACT
ATCGAAGAAGGTATGAATATCATAGCAAAGGAAAAACTTAATCTCGAACGTGAAGTGACT
TCAAATGATAGCGCAATGGACTCTGCAGAAGAACATAAGTGTCTTGTGCGTTTGATGAAA
ATGTCTTTGGGTTTTAATGAAAAAGTAGCTGAAGTATTTCTATCACCTACAAAGCAAGCT
AATGGAGCAACAGCTTCAACTTCGCAAGGTGAAAATGAAGAAGAAATAATATACGAGGAT
GTTGAATATTTAATTGATGAACATGGCGAATAA
>g5682.t1 Gene=g5682 Length=810
MESNGLTVKQKEDALNYCLKMVPNVDSMDVQDALLRCDWNKEKAVEHLKNLPPRGNKRTY
FQHRATNENSHNNHVVKKQRRNNDEDDEETASEDEHEFGKTAVFDSDSENDGNYAPEMTL
QRKEVFDFFNNANVGELTCIKACSLKKAEILIENRPYRNWEELVAKCREKPLQTDLLNNA
QEFIDKRNNLKKLIKKCKAIVLKLEKAVEEGAGISEQPYILNEEFKLSDYQLVGLNWLAV
LHQNGTNGILADEMGLGKTIQIIAFLAYLKETQQQLATHVVCVPSSTLDNWANELSKWCP
SLNVAKYYGSQEERRMMRFKWLKEGFDDTDVILTTYHVIGSSNEDKKMFRVTPFHYVIFD
EAHMLKNMMTQRYTTLLRINAQRRILLTGTPLQNSLLELMSLLCFVMPKLFANKQEDIKA
LFSKKAPKMDDGSEQTNDFEQSQIQRAKNIMKPFILRRLKKDVLSFLPKKTEVTEKVKML
PDQSKKYQHLIDEYKNIDPTSDNIIGRGTSIMMDMRKLANHPLLLRYFFTDERLREISKV
LARDSVYKNNNPKEIFEDIAPMSDFKIHQLAEKYPSITNLVKIPDNVVLNSGKFKYLDNL
LPKLKADGHRVLIFSQFVMMLDVIEKYLSIRGMKFVRLDGSTAVTDRQDLIEEYTANPEI
FIFLLSTKAGGLGINLTSADRAIIHDIDFNPYNDKQAEDRCHRIGQTKEVVIYKLISDGT
IEEGMNIIAKEKLNLEREVTSNDSAMDSAEEHKCLVRLMKMSLGFNEKVAEVFLSPTKQA
NGATASTSQGENEEEIIYEDVEYLIDEHGE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g5682.t1 | CDD | cd18793 | SF2_C_SNF | 591 | 716 | 7.04807E-61 |
| 9 | g5682.t1 | Coils | Coil | Coil | 190 | 210 | - |
| 7 | g5682.t1 | Gene3D | G3DSA:3.40.50.10810 | - | 193 | 483 | 2.8E-84 |
| 8 | g5682.t1 | Gene3D | G3DSA:3.40.50.300 | - | 568 | 782 | 2.4E-62 |
| 14 | g5682.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 65 | 111 | - |
| 13 | g5682.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 70 | 86 | - |
| 3 | g5682.t1 | PANTHER | PTHR10799:SF964 | SWI/SNF-RELATED MATRIX-ASSOCIATED ACTIN-DEPENDENT REGULATOR OF CHROMATIN SUBFAMILY A CONTAINING DEAD/H BOX 1 | 66 | 760 | 1.9E-211 |
| 4 | g5682.t1 | PANTHER | PTHR10799 | SNF2/RAD54 HELICASE FAMILY | 66 | 760 | 1.9E-211 |
| 2 | g5682.t1 | Pfam | PF00176 | SNF2 family N-terminal domain | 240 | 492 | 3.0E-55 |
| 1 | g5682.t1 | Pfam | PF00271 | Helicase conserved C-terminal domain | 593 | 705 | 6.5E-16 |
| 16 | g5682.t1 | ProSiteProfiles | PS51192 | Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. | 239 | 409 | 25.838 |
| 15 | g5682.t1 | ProSiteProfiles | PS51194 | Superfamilies 1 and 2 helicase C-terminal domain profile. | 596 | 762 | 15.628 |
| 12 | g5682.t1 | SMART | SM00487 | ultradead3 | 223 | 421 | 2.0E-33 |
| 11 | g5682.t1 | SMART | SM00490 | helicmild6 | 622 | 705 | 1.4E-18 |
| 6 | g5682.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 211 | 458 | 3.66E-53 |
| 5 | g5682.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 460 | 761 | 3.78E-59 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5682/g5682.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5682.t1.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 transcript has been annotated with K14439 (SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 [EC:5.6.2.-])
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.
