General information for g1885.t2
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.t2 | TTS | g1885.t2 | 13653544 | 13653544 |
| chr_3 | g1885 | g1885.t2 | isoform | g1885.t2 | 13653643 | 13655723 |
| chr_3 | g1885 | g1885.t2 | exon | g1885.t2.exon1 | 13653643 | 13654429 |
| chr_3 | g1885 | g1885.t2 | cds | g1885.t2.CDS1 | 13653643 | 13654429 |
| chr_3 | g1885 | g1885.t2 | exon | g1885.t2.exon2 | 13654491 | 13655723 |
| chr_3 | g1885 | g1885.t2 | cds | g1885.t2.CDS2 | 13654491 | 13655458 |
| chr_3 | g1885 | g1885.t2 | TSS | g1885.t2 | 13655800 | 13655800 |
Sequences
>g1885.t2 Gene=g1885 Length=2020
ATGGTGGAAGGAAATAGTTCTATCTTACAACAAAAAGTTTTAGTAAGTACATAGAGCAAA
AATATAAAGTACAAATTAAAGAGTTTTGAAATTTCAGGACATTCTTAAAAATGCCGACAA
TTCTGAAATATTAGCGTTGATAAAGAAACAATTCAATAATGCCGAATTGGCGCTAGAAAT
CAATGACAAAAGATCAACAATTGAGCATGCACTTCGAGAAGTGCTAATAGAGCAATGCAT
TGGTGAAATAGAGAGTGTCGAAAGAATGATAAAACTATCAATAGATTTATCGCGACAGGA
AATTATTTCACCATTTTCTCCCGTTTCATTATTAGTCGATGTCTTTGATGTATCAACATT
GGATTTCTGTGAACGTCTATTCAAATTTGTAGAGAGCAACGTCAATGTATTCAAAGAAGC
TCATTTTTTTACACCATGTAAGAATTCATTATTGAGAATGTGCAATGATCTTTTAAGACG
ACTTTCACGTTCACAAAATACTGTCTTTTGTGGTCGTATTCTCATGTTCTTGGCAAAATT
CTTTCCATTTTCTGAGCGTTCAGGATTGAACATTGTATCAGAATTCAACATTGAAAATGT
GACTGAATTTGAATTTACTTCTGCAATTGATAGCAACAGTAATAATGAAGATGCTTTTAG
AACAAGTGAAACTAATGTCATAACAGAAGATGCTTCAATGAAAATAGATCAGCATTTGTA
TCTCAAATTTTGGGCTTTGCAAGAATTTTTCCGATGCCCTTATATATGTTACGACAAAGA
AAAGTTTAAAAAGTTCTCAGGATATACAAAAGATGTGCTCACTGCATTCAAAAGTTTTAA
GCTTGAAGAAACTGCAACATCATCAACTAAAGGAATCAAGTCTGCAAATGAAATTATCAC
GAGTCGTGATGATTCAGAACATTTCTTTGCGAAATTTCTAACAAATCCTAAGCTATTAGC
ACTTCAGATGGGTGACTCGAATTTTAGACGGACGATTTTAGTTCAATATTTAATTTTATT
TCAATATCTTGTATCAACTGTAAAGTTTAAAAGTGAAAATGACAAACTTACCACCGCTCA
ACAAGAGTATGTTAGTGAAACTGAAGAGCTTGTGTATAAACTGTTAAACGAAACACCACC
AAAAAGTAATGAATTCGCAGAAGCCATAAAGCATATTTTAGCTAGAGAAGAAATGTGGAA
TTCTTGGAAAAACGAAGGCTGTAGAGAGATCAAGCGTCCTGAAGGTCACGAAAAAGAAAT
TCCAGAGCCGAAAAAGAGAAAATTTCTTGGTGATGACATTTTAAATGCAACAAAGCAGGG
GAAATTTGATTTAGGCAACTCAGAATTATCACGATTGTGGAACCTTTGTCCAGATAATTT
GCAAGCATGTAAAAATTCTGATCGAAACTTTTTGCCCTCTCTCGATACATATTTAGATAT
TAAGGATTCAGAAAATAAAGAAAAAACTGATCCTACATATGAATGGAGAGCACTTCGTTT
AGTTTCAAGGCAGAGTTCACACTTTTTCACATTATTAGCACCTCCAAATGAAAAGGTAGA
AAAAATATCAGACTATTTAAAATTATTCAATCAAAAGATACAAAAAGATAAAGTTGAAGT
TAAGGCAGAAACTGGTACAGTAGAAATTGAGTCACAACCAGAAACTTTAATTGAGGATAA
TGAAGCATCTGAAAATATTGAAGATGACACTCCAGAGGATGAAAATCAACATAAAGATAC
AGCTGCAACACCAGAACAAATTATTGAAATTTCAAAAGTAATTGGAGAGGGCTGGCAAAA
GCTTGGTACGAAATTGGGAATAGAAAAAGATGTTCTTGAATTTTACAAAGAAAAAAATCC
GACTTCACCATGTGAGTTGATGTTGACTGCATGGTTCAACGATGATGAAGATGCAAATTT
GGAAAATTTAGCATACACACTTGAAGGACTTGAGTTTACAAAAGCTGTAACATTGATAAA
GAAAATTATTGATTCCGATGAAACCATGCAAGTTGATTAA
>g1885.t2 Gene=g1885 Length=584
MIKLSIDLSRQEIISPFSPVSLLVDVFDVSTLDFCERLFKFVESNVNVFKEAHFFTPCKN
SLLRMCNDLLRRLSRSQNTVFCGRILMFLAKFFPFSERSGLNIVSEFNIENVTEFEFTSA
IDSNSNNEDAFRTSETNVITEDASMKIDQHLYLKFWALQEFFRCPYICYDKEKFKKFSGY
TKDVLTAFKSFKLEETATSSTKGIKSANEIITSRDDSEHFFAKFLTNPKLLALQMGDSNF
RRTILVQYLILFQYLVSTVKFKSENDKLTTAQQEYVSETEELVYKLLNETPPKSNEFAEA
IKHILAREEMWNSWKNEGCREIKRPEGHEKEIPEPKKRKFLGDDILNATKQGKFDLGNSE
LSRLWNLCPDNLQACKNSDRNFLPSLDTYLDIKDSENKEKTDPTYEWRALRLVSRQSSHF
FTLLAPPNEKVEKISDYLKLFNQKIQKDKVEVKAETGTVEIESQPETLIEDNEASENIED
DTPEDENQHKDTAATPEQIIEISKVIGEGWQKLGTKLGIEKDVLEFYKEKNPTSPCELML
TAWFNDDEDANLENLAYTLEGLEFTKAVTLIKKIIDSDETMQVD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g1885.t2 | CDD | cd01670 | Death | 498 | 572 | 1.46416E-7 |
| 6 | g1885.t2 | Gene3D | G3DSA:1.10.533.10 | Death Domain | 485 | 577 | 9.1E-9 |
| 9 | g1885.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 454 | 496 | - |
| 10 | g1885.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 466 | 482 | - |
| 3 | g1885.t2 | PANTHER | PTHR13265:SF0 | HPR1 | 4 | 525 | 1.2E-132 |
| 4 | g1885.t2 | PANTHER | PTHR13265 | THO COMPLEX SUBUNIT 1 | 4 | 525 | 1.2E-132 |
| 2 | g1885.t2 | Pfam | PF11957 | THO complex subunit 1 transcription elongation factor | 2 | 456 | 1.6E-124 |
| 1 | g1885.t2 | Pfam | PF00531 | Death domain | 498 | 574 | 3.1E-11 |
| 11 | g1885.t2 | ProSiteProfiles | PS50017 | Death domain profile. | 502 | 575 | 14.028 |
| 8 | g1885.t2 | SMART | SM00005 | DEATH_4 | 485 | 575 | 0.0016 |
| 5 | g1885.t2 | SUPERFAMILY | SSF47986 | DEATH domain | 489 | 578 | 1.38E-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.
