General information for g1000.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as THO complex subunit 2.
Parent gene
- The parent gene g1000 is located on chr_3: 7390303..7395889 (- 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 | g1000 | g1000.t1 | isoform | g1000.t1 | 7390303 | 7395889 |
| chr_3 | g1000 | g1000.t1 | exon | g1000.t1.exon1 | 7390303 | 7390374 |
| chr_3 | g1000 | g1000.t1 | cds | g1000.t1.CDS1 | 7390303 | 7390374 |
| chr_3 | g1000 | g1000.t1 | exon | g1000.t1.exon2 | 7390438 | 7390554 |
| chr_3 | g1000 | g1000.t1 | cds | g1000.t1.CDS2 | 7390438 | 7390554 |
| chr_3 | g1000 | g1000.t1 | exon | g1000.t1.exon3 | 7390629 | 7390757 |
| chr_3 | g1000 | g1000.t1 | cds | g1000.t1.CDS3 | 7390629 | 7390757 |
| chr_3 | g1000 | g1000.t1 | exon | g1000.t1.exon4 | 7391382 | 7391410 |
| chr_3 | g1000 | g1000.t1 | cds | g1000.t1.CDS4 | 7391382 | 7391410 |
| chr_3 | g1000 | g1000.t1 | exon | g1000.t1.exon5 | 7391474 | 7391818 |
| chr_3 | g1000 | g1000.t1 | cds | g1000.t1.CDS5 | 7391474 | 7391818 |
| chr_3 | g1000 | g1000.t1 | exon | g1000.t1.exon6 | 7391878 | 7392259 |
| chr_3 | g1000 | g1000.t1 | cds | g1000.t1.CDS6 | 7391878 | 7392259 |
| chr_3 | g1000 | g1000.t1 | exon | g1000.t1.exon7 | 7392321 | 7392500 |
| chr_3 | g1000 | g1000.t1 | cds | g1000.t1.CDS7 | 7392321 | 7392500 |
| chr_3 | g1000 | g1000.t1 | exon | g1000.t1.exon8 | 7392566 | 7393891 |
| chr_3 | g1000 | g1000.t1 | cds | g1000.t1.CDS8 | 7392566 | 7393891 |
| chr_3 | g1000 | g1000.t1 | exon | g1000.t1.exon9 | 7393952 | 7395472 |
| chr_3 | g1000 | g1000.t1 | cds | g1000.t1.CDS9 | 7393952 | 7395472 |
| chr_3 | g1000 | g1000.t1 | exon | g1000.t1.exon10 | 7395534 | 7395696 |
| chr_3 | g1000 | g1000.t1 | cds | g1000.t1.CDS10 | 7395534 | 7395696 |
| chr_3 | g1000 | g1000.t1 | exon | g1000.t1.exon11 | 7395837 | 7395889 |
| chr_3 | g1000 | g1000.t1 | cds | g1000.t1.CDS11 | 7395837 | 7395889 |
| chr_3 | g1000 | g1000.t1 | TSS | g1000.t1 | 7395920 | 7395920 |
| chr_3 | g1000 | g1000.t1 | TTS | g1000.t1 | NA | NA |
Sequences
>g1000.t1 Gene=g1000 Length=4317
ATGGATATTCAAAATTTTATTAAAAATTGGGATTCTAAAGGAAAAACAGAATTTTTTAAG
CAAGTAAAAGCAGTGTTAAAAGAGGATGAGAGTTTGTTACTAACGAAAAAAGCAAAAGGA
CCTGATATTAGTCGCGTTATTTACGATTTAATTATTGGCGGCATCAAATCAGAAATAAAG
AAAGATGTTGTCTTATCAATTCTCGCGGAACTTTCCTATATGCATAAAGACATTGCATCA
ATCACGACAGACATCTTTCAAGTGATAGACACAGAAACAAATCTACCAAATGGCGAATAT
ACAGCTAAAGAAAGAAGCATGTTTGGAAGTTTAGTTCGAGATTCTGAGAAAATTTTCTCT
GAAAAACTATTAAAAGAACGTCTTGAAACAGAAACATTACAGGAATTTGGTATCGTGAAT
AAAAATTTCTATAGCAAATTCATTAAAATCAAAACAAAGCTGTATTATAAACAACGTCGA
TTTAATTTGTTTCGGGAAGAAAATGAAGGATATGCAAAGCTATTAACAGAACTTAACAAA
GAATATGTAGATGAAGTCAACGATAAAAATTCATTAGAAATCGTTAAATCTCTTATTGGT
TGCTTCAATGTCGATCCAAATCGAGTTCTGGATGTTATACTTGAGTCGTTTGAAATTCGT
CCAGAACGAAAAGAGCTCTATATTCCTTTACTTCAATCATACATGCCTGATTCGAATATA
ATCAGCGAAGTTCTTGGATATAAATATCGAAATTATAGTGAAGAGAAAACACCATCGTCA
CTATATAAAGTTACTGCCATTTTACTTCAACATGAAATCATTGAGCTTGACGACATTTAT
TCTTGGCTTTCTCCTGTTGATGAGAAATTATTTGCTGTTTGGCAAGCAGAAATTGAAGAT
GCAAAGGAATATGTTCGTAAATTAAAAATAATTTCAACAAACAAGGATAAACAAGAAGAT
GAAAAGGAGCAAGAATCAGATAACAAAGATGAAAAGAATGAAAATAATCAAAAGTTTGGA
TTATGTGAAGCTCTTTTAAATATTGGTGATTGGCTTAATGCTAGCAGATTAATATCAAAA
TTGCCTGAGAAATGTGCAACATCAAATGAATTTTTGGCACGATCGCTATGTAATTTAATT
CACATTATTATCGAGCCGGTTTATCGACTTAAATGTGCTGTGCCTCTCAATTTAAAAGGA
ACTGAAATTAAACCTCATCCAAATCGAAAAGCACCACCTCAAGTACACAACTTTTTAGAT
TTGCGTCAAAATGTTTTTGCAATGTTTCACACTCTCGGTCCATCACTTCATTTTGATCCT
GTATTGTTACAAAAACTCATAAGAATTATGAGAGTTATTCTCGAAAACGAGTTAAATGTT
GATGCTTCAACACCTTCACCGAGTCAAACAGATGAAAAGACTATTCTTTATTATGATATA
ATTTCATTACTTGATAGTTGTGTACTGCCATCTTTATCTTACATGTCTTGCAATTGCTGT
GTTGCTGAAGAAATATGGACTGTTGTGAAACTTTTTCCATATAACATAAGATATGCATTG
TACAATGGATGGAAAAATGAGTCATATTTGTTGCATCCTAAACTGATAAGACTTCGCGGC
GAAGCTGAACAAGATATTAAAGCATTGATGAAACGCGTGAGCAAAGAGAATGTGAAACCT
GTTGGAAGGAGAATTGGAAAATTAACTCATAGCTCGCCTGGATTTTTATTTGATTACGTT
CTTGGTCAAATTCAGTTGTATGACAATTTAATTGCTCCTGTAGTTGATGCACTTAGATTT
CTCACATCTCTTTCATATGATGTACTCGGTTATTGTGTCATTGAAGCTCTTGTCTCAACT
GGTCGTGAACGATTTAAATATGGTGTTTTGTCAGATTGGTTGCAGAGTTTAGCAAATTTC
TGTGGAGCTATTTACAAAAAATATTCTATTGAACTCAGTGGACTTCTTCAATATATTTGT
AATCAATTGAAAGCACAAAAGAGTCTCGATCTTCTGATTCTCAAGGAAATTGTACAAAAG
ATGGTTGGCATTGAAGCAGTTGAAGAAATGACAAATGAACAATTAAGCGCAATGAGCGGT
GGAGAATTGCTAAAAGGAGAAGCTGGTTACTTTAGTCAAGTTCGAAATACTAAAAAATCC
TCGCAACGTTTGAAAGATGCATTGGCGAGCAATGATCTTTCAGTAGCATTGTGTTTGCTA
ATAGCTCAACAGAAAAATTGTGTAATTTATCACGAAACATCAAAAAGTCATCCAAAATTA
GTTGGAAAACTTTATGATCAATGTCAAGATACGCTTGTTCAATTTGGAAATTTCTTAGGA
TCAACATATACAGTTGAAGAATATGTTGAGCGATTGCCATCAATTCATAGCATGCTACAA
GAATATCACATTCATTCTGATGTTGCATTCTTTTTGGCTCGTCCAATGTTTACTCATGCC
ATCACTCAAAAGTATGATCAATTGCGAAAAAATGATACAAGCTTGAAGAAACTGACTAGT
ACACAAAAAATGGAAAAATATTTGGAGGCAACGAATTTGGTTATGAATCCAGTCATTGAT
TCTGTGCGTCCATTGCATCCATTAAAAGTTTGGGAAGATATCAGTCCGCAATTTCTAGTA
ACTTTTTGGTCTTTATCAATGTATGATCTTCAGACACCTAATGAAAGTTATCAGCGTGAA
ATTAATAAATTAAAACTACAAATTGCATCGCTTAATTCGAACGAACTTGGCAGCGCAACC
TCTAAAATAAAGAAAGAGTTGGAAAGAATTCAGACATTTTCTGAAAAACTGCAAGAAGAG
AAGAAGAAACAACAAGAGCATGTTGAAAAAATCATGGGAAGACTTAATAGTGAGAAGGAC
AATTGGTTTCCAGCAAGGGCTGCTAAGGGAGCAAAAAATGAAACAATTCCTCAATTTTTA
CAACTATGTTTGTTTCCTCGATGTACATTCACTGCTCTCGATGCAATATATTGTGCTAAA
TTTGTTAATATCATTCATAACTTGAAAACACCAAATTTTTCAACTCTTTTGTGTTATGAT
AGAATCTTGTGTGATATTACATGCAGCATAACAACTTGTACTGAAAATGAAGCCAATAGA
TATGGACGATTTTTAAATGCGATGCTAGAGACAGTCATGAGATGGCATTCTGATCAAGCT
ACTTTCAATAAAGAATGTGCTAATTATCCAGGTTTTGTAACTAAATTCAGAATTAGTAAT
CAGTGCACCGACAAAAATGATCATGTTGGATATGAAAACTTCCGTCATGTGTGTCATAAA
TGGCATTTTAAAATAACAAGATCGATTGTCACATGTCTTAGTTCAAAGGATTACATACAA
ATTCGAAATGCTTTCATTATTCTTATGCATATTCAAAATCATTTCCCTGTAGTTATGAAG
ACTGAACAGGTTATTCATAAGCGTGTAGAGAAGGTTCGAGATGAAGAAAAGACAAAACGT
CAAGATCTTCATGTGCTTGCATCATCTTATTTGGGCATTTTAAAGCAAAAACATGGTCAG
TTAATGACAGAGCAAGATTTTCATCAGGTTAGCGAATCAGCGAGTAATGATCAATCAAAA
TCTGTAAATGGAGACTCTAAGAGTGATAAAAAACCAATAAAAGAAGAACGCAAACCAACA
AGAACAGTAGATCGTGAATCATCCAAGGCAACCGTTGAACGCGATGTAAAGATTACACCA
GCTCGAGAAGCGTCAAAGGACAAACGTGAACCAACACCTCGCGAAAAATCAACAAAGAAA
GAAGAGCGACACGATCGAGAAACGAAAGAACGTGATGATGAATACACTCGAAAGCGTGAC
AAGGAAAAGAAAAGAGAGAAACGGCCATCCTCACCTGTTGAATTTGAAGGCGATCTTAGC
TCGGTTTCTAACTCAAGTACTGGCTCAATACAACATAATGCTGAAGTAATCAATATTGAT
GAACCTCGAGAACCAAAGCGACGCAAAGTAGAATCGAAGAAGCGTATTGAAGATGATGAT
ATTGTCGAAGTTAGTAAAAAGGATCGAGCTATTAAAAAAGAAAAACGAGAAAAGCAAACC
GATGAAGAGAAAGAATTGCGAAAAGAAAAGAAATTGATAAAGAAGAGAGATCGTGAAGAA
ATACAACAAGTTGAAAAGAGAAGAAAAGATGAGGAGAAGACGAATAAAATATCGCATCAC
AATGGAGAAGAAGATAATATGAGAGAAAGACATAATAGAAATCAGGACGTATATTCACGT
GAAGATAGACATGAGAAAAGTCATTATCAGAAGACAAGTAGATCAAGTCGTTATTAA
>g1000.t1 Gene=g1000 Length=1438
MDIQNFIKNWDSKGKTEFFKQVKAVLKEDESLLLTKKAKGPDISRVIYDLIIGGIKSEIK
KDVVLSILAELSYMHKDIASITTDIFQVIDTETNLPNGEYTAKERSMFGSLVRDSEKIFS
EKLLKERLETETLQEFGIVNKNFYSKFIKIKTKLYYKQRRFNLFREENEGYAKLLTELNK
EYVDEVNDKNSLEIVKSLIGCFNVDPNRVLDVILESFEIRPERKELYIPLLQSYMPDSNI
ISEVLGYKYRNYSEEKTPSSLYKVTAILLQHEIIELDDIYSWLSPVDEKLFAVWQAEIED
AKEYVRKLKIISTNKDKQEDEKEQESDNKDEKNENNQKFGLCEALLNIGDWLNASRLISK
LPEKCATSNEFLARSLCNLIHIIIEPVYRLKCAVPLNLKGTEIKPHPNRKAPPQVHNFLD
LRQNVFAMFHTLGPSLHFDPVLLQKLIRIMRVILENELNVDASTPSPSQTDEKTILYYDI
ISLLDSCVLPSLSYMSCNCCVAEEIWTVVKLFPYNIRYALYNGWKNESYLLHPKLIRLRG
EAEQDIKALMKRVSKENVKPVGRRIGKLTHSSPGFLFDYVLGQIQLYDNLIAPVVDALRF
LTSLSYDVLGYCVIEALVSTGRERFKYGVLSDWLQSLANFCGAIYKKYSIELSGLLQYIC
NQLKAQKSLDLLILKEIVQKMVGIEAVEEMTNEQLSAMSGGELLKGEAGYFSQVRNTKKS
SQRLKDALASNDLSVALCLLIAQQKNCVIYHETSKSHPKLVGKLYDQCQDTLVQFGNFLG
STYTVEEYVERLPSIHSMLQEYHIHSDVAFFLARPMFTHAITQKYDQLRKNDTSLKKLTS
TQKMEKYLEATNLVMNPVIDSVRPLHPLKVWEDISPQFLVTFWSLSMYDLQTPNESYQRE
INKLKLQIASLNSNELGSATSKIKKELERIQTFSEKLQEEKKKQQEHVEKIMGRLNSEKD
NWFPARAAKGAKNETIPQFLQLCLFPRCTFTALDAIYCAKFVNIIHNLKTPNFSTLLCYD
RILCDITCSITTCTENEANRYGRFLNAMLETVMRWHSDQATFNKECANYPGFVTKFRISN
QCTDKNDHVGYENFRHVCHKWHFKITRSIVTCLSSKDYIQIRNAFIILMHIQNHFPVVMK
TEQVIHKRVEKVRDEEKTKRQDLHVLASSYLGILKQKHGQLMTEQDFHQVSESASNDQSK
SVNGDSKSDKKPIKEERKPTRTVDRESSKATVERDVKITPAREASKDKREPTPREKSTKK
EERHDRETKERDDEYTRKRDKEKKREKRPSSPVEFEGDLSSVSNSSTGSIQHNAEVINID
EPREPKRRKVESKKRIEDDDIVEVSKKDRAIKKEKREKQTDEEKELRKEKKLIKKRDREE
IQQVEKRRKDEEKTNKISHHNGEEDNMRERHNRNQDVYSREDRHEKSHYQKTSRSSRY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g1000.t1 | Coils | Coil | Coil | 301 | 335 | - |
| 16 | g1000.t1 | Coils | Coil | Coil | 894 | 914 | - |
| 14 | g1000.t1 | Coils | Coil | Coil | 923 | 954 | - |
| 13 | g1000.t1 | Coils | Coil | Coil | 1349 | 1394 | - |
| 12 | g1000.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 315 | 334 | - |
| 7 | g1000.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1188 | 1202 | - |
| 10 | g1000.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1188 | 1438 | - |
| 11 | g1000.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1203 | 1293 | - |
| 9 | g1000.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1296 | 1314 | - |
| 8 | g1000.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1317 | 1432 | - |
| 5 | g1000.t1 | PANTHER | PTHR21597 | THO2 PROTEIN | 23 | 1431 | 0.0 |
| 4 | g1000.t1 | Pfam | PF16134 | THO complex subunit 2 N-terminus | 4 | 397 | 1.7E-48 |
| 3 | g1000.t1 | Pfam | PF16134 | THO complex subunit 2 N-terminus | 413 | 563 | 4.0E-23 |
| 2 | g1000.t1 | Pfam | PF11732 | Transcription- and export-related complex subunit | 565 | 638 | 1.1E-26 |
| 1 | g1000.t1 | Pfam | PF11262 | Transcription factor/nuclear export subunit protein 2 | 871 | 1172 | 4.9E-102 |
| 6 | g1000.t1 | SUPERFAMILY | SSF52283 | Formate/glycerate dehydrogenase catalytic domain-like | 756 | 842 | 2.72E-5 |
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:0006406 | mRNA export from nucleus | BP |
| GO:0006397 | mRNA processing | BP |
| GO:0000347 | THO complex | CC |
KEGG
Orthology
- This transcript has been annotated with K12879 (THO complex subunit 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.
