General information for g4983.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Exosome RNA helicase MTR4.
Parent gene
- The parent gene g4983 is located on chr_2: 6286074..6287738 (+ 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 | g4983 | g4983.t2 | isoform | g4983.t2 | 6286074 | 6287738 |
| chr_2 | g4983 | g4983.t2 | exon | g4983.t2.exon1 | 6286074 | 6287738 |
| chr_2 | g4983 | g4983.t2 | cds | g4983.t2.CDS1 | 6286077 | 6287738 |
| chr_2 | g4983 | g4983.t2 | TTS | g4983.t2 | 6287809 | 6287809 |
| chr_2 | g4983 | g4983.t2 | TSS | g4983.t2 | NA | NA |
Sequences
>g4983.t2 Gene=g4983 Length=1665
GCAATGGGATTAAATATGCCTGCACGAACAGTAGTTTTTACAAGTAGTCAAAAGTTTGAT
GGTAAAAATTTCCGAACACTTGCTAGTGGTGAATACATACAAATGTCAGGAAGAGCAGGA
CGTCGTGGTCTTGATGATAAAGGTATTGTAATTCTTATGGTGGATGAGAAAGTTTCACCT
GCAATCGGTCGTGAAATTGTCCAAGGAAAACCTAATGCTATTAATTCAGCATTTCATCTT
ACTTACAATATGGTTCTCAATTTGTTGCGTGTAGAAGAAATTAATCCTGAATATATGCTT
GAACGTTCATTTTTCCAATTTCAAAATCAATCAACAATTCCTGACCTTTACAAAAAAGTT
CAACAAAAACAAGACGAATTAATAGAATTTGTAGTGAAAGAAGAATCATCAATAAGAACT
TATCATCATATTCGTGAACAATTGGATACATTAACGGAGAAATATCAACAATTTTATACT
AATCCACAATATATAAGACCATTTCTTCAACCTGGACGTCTGTGTAAAATTAAAACTGGA
GAGCATGAGTTTGATTGGGGAATGGTAGTCAATAATAAAATCGAGCATACTGACAATTCA
AAAAATCCACTCAAATCTGATTCTAAATTGATAATTGAAGTTTTACTCCATATTGATGAT
ACACCAGATAAATCAAAAAATCCAATACCTTGTCCGCCTGGTAAAAAAGGATGTGCTGAA
ATTATTCCCATTACATCAAACTTAGTTTCAAAGCTTAGTACATTAAGAATCTACTATCCT
GATGATTTACGGCCAACTGACAGTCGAAGAGCTGTGTTGAAAAGGATTGAAGAAGTGAAA
AAGAAATTTCCAAATGGGGCACCAATTTTGAATCCTGTCGAAGATATGCGAATCAAAGAT
AAAGAATTTTTAAACATTATAACTTTGCTTGAAAAATTTGAAAAACAACTTTATTCTCAT
CCACTTCATTCATCACCTGAGCTAGCTGATATTTATAATTCATATTTAGCAAAATTACAA
TTAGAATCTGAGTTAGTTGAAGCAAAGAAGAAATTGAAAGATGCTAAAAGTTTATTACAA
ATGGACGATTTGAAACATCGTAAAAGAGTTTTGAGACGTCTTGGTTATTGTACAAATTCC
GATGTTATTGAATTCAAAGGTCGAGTTGCATGCGAACTTTCTTCAGGCGATGAACTTTTG
ATTACCGAAATGATTTTTAATGGCACTTTCAACGACTTGCAGCCTGCTCAGTGTGCTGCA
TTATTATCATGCTTTGTCTGTGATGATAGAGCAGGCGAACTTAATATTGATGCTGAGCTT
CAAGCGCCATTCAAACAAATGCAAGATTTTGCTCGTCGTATTGCAAAAGTGTCAAAAGAA
TGCAAAATGGATATTGATGAAGACGATTATGTGGAAAAATTCAAACCAACTCTGATGGAT
GTGGTATTAAAATGGTGTAAGGGTGCATCATTTTCACAAATTTGTCAGATAACAGATGTA
TTTGAAGGTAATATTATTCGATGCATGCGACGACTTGAAGAACTCATGCGACAAATGGTC
CAAGCATCAAAAACAATTGGAAATACTGATTTGGAAAATAAATTTTCTGAAGGTATTCGA
TTATTAAAACGTGATATTGTTTTTGCTGCATCACTTTATCTTTAA
>g4983.t2 Gene=g4983 Length=553
MGLNMPARTVVFTSSQKFDGKNFRTLASGEYIQMSGRAGRRGLDDKGIVILMVDEKVSPA
IGREIVQGKPNAINSAFHLTYNMVLNLLRVEEINPEYMLERSFFQFQNQSTIPDLYKKVQ
QKQDELIEFVVKEESSIRTYHHIREQLDTLTEKYQQFYTNPQYIRPFLQPGRLCKIKTGE
HEFDWGMVVNNKIEHTDNSKNPLKSDSKLIIEVLLHIDDTPDKSKNPIPCPPGKKGCAEI
IPITSNLVSKLSTLRIYYPDDLRPTDSRRAVLKRIEEVKKKFPNGAPILNPVEDMRIKDK
EFLNIITLLEKFEKQLYSHPLHSSPELADIYNSYLAKLQLESELVEAKKKLKDAKSLLQM
DDLKHRKRVLRRLGYCTNSDVIEFKGRVACELSSGDELLITEMIFNGTFNDLQPAQCAAL
LSCFVCDDRAGELNIDAELQAPFKQMQDFARRIAKVSKECKMDIDEDDYVEKFKPTLMDV
VLKWCKGASFSQICQITDVFEGNIIRCMRRLEELMRQMVQASKTIGNTDLENKFSEGIRL
LKRDIVFAASLYL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g4983.t2 | Coils | Coil | Coil | 337 | 357 | - |
| 7 | g4983.t2 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 74 | 4.1E-25 |
| 10 | g4983.t2 | Gene3D | G3DSA:1.10.3380.30 | - | 81 | 544 | 3.1E-172 |
| 8 | g4983.t2 | Gene3D | G3DSA:1.20.1500.20 | - | 103 | 353 | 3.1E-172 |
| 9 | g4983.t2 | Gene3D | G3DSA:2.40.30.300 | - | 169 | 285 | 3.1E-172 |
| 3 | g4983.t2 | PANTHER | PTHR12131:SF7 | EXOSOME RNA HELICASE MTR4 | 1 | 552 | 1.3E-150 |
| 4 | g4983.t2 | PANTHER | PTHR12131 | ATP-DEPENDENT RNA AND DNA HELICASE | 1 | 552 | 1.3E-150 |
| 2 | g4983.t2 | Pfam | PF13234 | rRNA-processing arch domain | 96 | 353 | 4.7E-71 |
| 1 | g4983.t2 | Pfam | PF08148 | DSHCT (NUC185) domain | 380 | 548 | 8.7E-53 |
| 12 | g4983.t2 | ProSiteProfiles | PS51194 | Superfamilies 1 and 2 helicase C-terminal domain profile. | 1 | 91 | 8.701 |
| 6 | g4983.t2 | SMART | SM01142 | DSHCT_2 | 377 | 553 | 4.9E-95 |
| 5 | g4983.t2 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 1 | 104 | 1.22E-14 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
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.
