General information for g1885.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as THO complex subunit 1.
Parent gene
- The parent gene g1885 is located on chr_3: 13653643..13655723 (- 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 | g1885 | g1885.t1 | TTS | g1885.t1 | 13653544 | 13653544 |
| chr_3 | g1885 | g1885.t1 | isoform | g1885.t1 | 13653643 | 13655723 |
| chr_3 | g1885 | g1885.t1 | exon | g1885.t1.exon1 | 13653643 | 13654429 |
| chr_3 | g1885 | g1885.t1 | cds | g1885.t1.CDS1 | 13653643 | 13654429 |
| chr_3 | g1885 | g1885.t1 | exon | g1885.t1.exon2 | 13654491 | 13655626 |
| chr_3 | g1885 | g1885.t1 | cds | g1885.t1.CDS2 | 13654491 | 13655626 |
| chr_3 | g1885 | g1885.t1 | exon | g1885.t1.exon3 | 13655682 | 13655723 |
| chr_3 | g1885 | g1885.t1 | cds | g1885.t1.CDS3 | 13655682 | 13655723 |
| chr_3 | g1885 | g1885.t1 | TSS | g1885.t1 | 13655800 | 13655800 |
Sequences
>g1885.t1 Gene=g1885 Length=1965
ATGGTGGAAGGAAATAGTTCTATCTTACAACAAAAAGTTTTAGACATTCTTAAAAATGCC
GACAATTCTGAAATATTAGCGTTGATAAAGAAACAATTCAATAATGCCGAATTGGCGCTA
GAAATCAATGACAAAAGATCAACAATTGAGCATGCACTTCGAGAAGTGCTAATAGAGCAA
TGCATTGGTGAAATAGAGAGTGTCGAAAGAATGATAAAACTATCAATAGATTTATCGCGA
CAGGAAATTATTTCACCATTTTCTCCCGTTTCATTATTAGTCGATGTCTTTGATGTATCA
ACATTGGATTTCTGTGAACGTCTATTCAAATTTGTAGAGAGCAACGTCAATGTATTCAAA
GAAGCTCATTTTTTTACACCATGTAAGAATTCATTATTGAGAATGTGCAATGATCTTTTA
AGACGACTTTCACGTTCACAAAATACTGTCTTTTGTGGTCGTATTCTCATGTTCTTGGCA
AAATTCTTTCCATTTTCTGAGCGTTCAGGATTGAACATTGTATCAGAATTCAACATTGAA
AATGTGACTGAATTTGAATTTACTTCTGCAATTGATAGCAACAGTAATAATGAAGATGCT
TTTAGAACAAGTGAAACTAATGTCATAACAGAAGATGCTTCAATGAAAATAGATCAGCAT
TTGTATCTCAAATTTTGGGCTTTGCAAGAATTTTTCCGATGCCCTTATATATGTTACGAC
AAAGAAAAGTTTAAAAAGTTCTCAGGATATACAAAAGATGTGCTCACTGCATTCAAAAGT
TTTAAGCTTGAAGAAACTGCAACATCATCAACTAAAGGAATCAAGTCTGCAAATGAAATT
ATCACGAGTCGTGATGATTCAGAACATTTCTTTGCGAAATTTCTAACAAATCCTAAGCTA
TTAGCACTTCAGATGGGTGACTCGAATTTTAGACGGACGATTTTAGTTCAATATTTAATT
TTATTTCAATATCTTGTATCAACTGTAAAGTTTAAAAGTGAAAATGACAAACTTACCACC
GCTCAACAAGAGTATGTTAGTGAAACTGAAGAGCTTGTGTATAAACTGTTAAACGAAACA
CCACCAAAAAGTAATGAATTCGCAGAAGCCATAAAGCATATTTTAGCTAGAGAAGAAATG
TGGAATTCTTGGAAAAACGAAGGCTGTAGAGAGATCAAGCGTCCTGAAGGTCACGAAAAA
GAAATTCCAGAGCCGAAAAAGAGAAAATTTCTTGGTGATGACATTTTAAATGCAACAAAG
CAGGGGAAATTTGATTTAGGCAACTCAGAATTATCACGATTGTGGAACCTTTGTCCAGAT
AATTTGCAAGCATGTAAAAATTCTGATCGAAACTTTTTGCCCTCTCTCGATACATATTTA
GATATTAAGGATTCAGAAAATAAAGAAAAAACTGATCCTACATATGAATGGAGAGCACTT
CGTTTAGTTTCAAGGCAGAGTTCACACTTTTTCACATTATTAGCACCTCCAAATGAAAAG
GTAGAAAAAATATCAGACTATTTAAAATTATTCAATCAAAAGATACAAAAAGATAAAGTT
GAAGTTAAGGCAGAAACTGGTACAGTAGAAATTGAGTCACAACCAGAAACTTTAATTGAG
GATAATGAAGCATCTGAAAATATTGAAGATGACACTCCAGAGGATGAAAATCAACATAAA
GATACAGCTGCAACACCAGAACAAATTATTGAAATTTCAAAAGTAATTGGAGAGGGCTGG
CAAAAGCTTGGTACGAAATTGGGAATAGAAAAAGATGTTCTTGAATTTTACAAAGAAAAA
AATCCGACTTCACCATGTGAGTTGATGTTGACTGCATGGTTCAACGATGATGAAGATGCA
AATTTGGAAAATTTAGCATACACACTTGAAGGACTTGAGTTTACAAAAGCTGTAACATTG
ATAAAGAAAATTATTGATTCCGATGAAACCATGCAAGTTGATTAA
>g1885.t1 Gene=g1885 Length=654
MVEGNSSILQQKVLDILKNADNSEILALIKKQFNNAELALEINDKRSTIEHALREVLIEQ
CIGEIESVERMIKLSIDLSRQEIISPFSPVSLLVDVFDVSTLDFCERLFKFVESNVNVFK
EAHFFTPCKNSLLRMCNDLLRRLSRSQNTVFCGRILMFLAKFFPFSERSGLNIVSEFNIE
NVTEFEFTSAIDSNSNNEDAFRTSETNVITEDASMKIDQHLYLKFWALQEFFRCPYICYD
KEKFKKFSGYTKDVLTAFKSFKLEETATSSTKGIKSANEIITSRDDSEHFFAKFLTNPKL
LALQMGDSNFRRTILVQYLILFQYLVSTVKFKSENDKLTTAQQEYVSETEELVYKLLNET
PPKSNEFAEAIKHILAREEMWNSWKNEGCREIKRPEGHEKEIPEPKKRKFLGDDILNATK
QGKFDLGNSELSRLWNLCPDNLQACKNSDRNFLPSLDTYLDIKDSENKEKTDPTYEWRAL
RLVSRQSSHFFTLLAPPNEKVEKISDYLKLFNQKIQKDKVEVKAETGTVEIESQPETLIE
DNEASENIEDDTPEDENQHKDTAATPEQIIEISKVIGEGWQKLGTKLGIEKDVLEFYKEK
NPTSPCELMLTAWFNDDEDANLENLAYTLEGLEFTKAVTLIKKIIDSDETMQVD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g1885.t1 | CDD | cd01670 | Death | 568 | 642 | 2.66383E-7 |
| 7 | g1885.t1 | Coils | Coil | Coil | 35 | 55 | - |
| 6 | g1885.t1 | Gene3D | G3DSA:1.10.533.10 | Death Domain | 555 | 646 | 1.1E-8 |
| 10 | g1885.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 524 | 566 | - |
| 11 | g1885.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 536 | 552 | - |
| 3 | g1885.t1 | PANTHER | PTHR13265 | THO COMPLEX SUBUNIT 1 | 31 | 630 | 2.2E-136 |
| 4 | g1885.t1 | PANTHER | PTHR13265:SF2 | THO COMPLEX SUBUNIT 1 | 31 | 630 | 2.2E-136 |
| 2 | g1885.t1 | Pfam | PF11957 | THO complex subunit 1 transcription elongation factor | 70 | 526 | 1.0E-124 |
| 1 | g1885.t1 | Pfam | PF00531 | Death domain | 568 | 644 | 3.6E-11 |
| 12 | g1885.t1 | ProSiteProfiles | PS50017 | Death domain profile. | 572 | 645 | 14.028 |
| 9 | g1885.t1 | SMART | SM00005 | DEATH_4 | 555 | 645 | 0.0016 |
| 5 | g1885.t1 | SUPERFAMILY | SSF47986 | DEATH domain | 559 | 648 | 1.62E-10 |
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:0007165 | signal transduction | BP |
| GO:0005515 | protein binding | MF |
KEGG
Orthology
- This transcript has been annotated with K12878 (THO complex subunit 1)
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.
