Gene loci information

Transcript annotation

  • This transcript has been annotated as Transcription termination factor 2.

Parent gene

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_1 g10052 g10052.t1 TSS g10052.t1 7084134 7084134
chr_1 g10052 g10052.t1 isoform g10052.t1 7084612 7087772
chr_1 g10052 g10052.t1 exon g10052.t1.exon1 7084612 7084666
chr_1 g10052 g10052.t1 cds g10052.t1.CDS1 7084612 7084666
chr_1 g10052 g10052.t1 exon g10052.t1.exon2 7084730 7086494
chr_1 g10052 g10052.t1 cds g10052.t1.CDS2 7084730 7086494
chr_1 g10052 g10052.t1 exon g10052.t1.exon3 7086553 7087566
chr_1 g10052 g10052.t1 cds g10052.t1.CDS3 7086553 7087566
chr_1 g10052 g10052.t1 exon g10052.t1.exon4 7087625 7087772
chr_1 g10052 g10052.t1 cds g10052.t1.CDS4 7087625 7087772
chr_1 g10052 g10052.t1 TTS g10052.t1 7087863 7087863

Sequences

>g10052.t1 Gene=g10052 Length=2982
ATGAAGGTAAATAACCACATAAGCAGCGACAGTGATGAATCTGAATATGAAAACAGTGAA
GATAACAATAATACGACTGCAGAATCAAGCATTATAATAAATGAATCTATTAACGATAGT
AATATATCATCAAATATAGACGAAATAAGTAACAAAAACGCTTCAAGCGAGCATGTAGAA
ATTTCTGAAACAGATGAAGATGATGAAAGTAAAATAGAGGTATCGCAAAATTCTTTTATT
GATCAAAATGCTGAAGCTATAAAATCAGAAAGTGAAAACGACAGTGATTCTGAGAATGAA
GATGATGATGTTCCTTTAAAGCGTAAAGCTACAACAGCTGTTAATAGAATTGTTGATTCT
GATTCGAGTGATGAAGAAGTGATTGAAAAAAGGAAATCAATATATGCTCTTGAACCAGAA
GGTGATTTATCAATACATATTGAAGATGCTGCCTATTCGAAATCAACTCGTAGAAGCATT
CATGGATTTGAAATAAAACAAGAAAAACATTCAATCAAAGAAGAACCTTTTTCTGAAAAT
GAAGAGAGTGACGATGAATCTGATATCATTATCAGTAGTGATGATGATGATGTAGAAGAA
GGTAATGAAAGCGAGGATAAAGAAAATTTAGATTATTCTGGTATGATTGAAAAGAAATTA
TCTTCTACTATTCGTTCACCGATGAAAGAAAACTTCAAAAGTGAACTGATAGAAACAGAA
ACAAGTTTTAATCAAACAAGTGATCATGAATCATCCATTAAAAAAGTATCTCGTGCCTCG
TACGATCGTATTGTTGCAGAAAAGTATGCTCTTGCGAATCGAATTTCATCAATGAAAAAG
CTTTTAGAAATGAATGCAGGCTTGCCAGATGGCGGAAAGAAATTGCAAGACGCTATAGTT
AAGTTAGAACATGAATTAATAGAAAAAGAAACAGCTATTAAATTTCTTTTAATCGATGAA
AATGAGAGTATAAAAAATTCAATTAAAAGATCTTTTATGTCAGAGAGTGAAGTTAGTGAC
ACATCGTACTCAGTTAAAGAGTCATCTGCTAATGATGATTATATAGAAGTGAAAGATGTT
CAACCAAAATATACTGGCAAAATTGGTCTCAAACATTTTGAACAGCAAAAAGCGTTAACG
GTAGAGAAATTACAAGACATTTATGCTTCATTAGACGAACGTCCAGGAGAGGACGTTGTT
TCAACTCCACCAAAATACCTAAAAATAGATTTGATGCGTCATCAATTGCATGCAATTGCA
TTTATGATTTGGAGAGAGACTAAGCAAAAGCCACGAGGTGGTATTTTAGCTGATGATATG
GGCTTAGGCAAAACATTAACAGTAATTTCTCTCATAATGAAACAATTACAAGTTTATGAA
GACAGAGAAGAGGATGAAGAAGATACAGATACTGATGACGATGAAAAAGTTGAAGAAAAT
GCTTGGATTGCACGTGGTCATAAAAACTTGCGAGCTGGAGGTACTTTAGTAATTTGCCCA
GCATCGTTAATTAATCAATGGGAGCAAGAAATCAAAACTAAAATTAAAAAAGGAGCTCTT
GATGTAAATGTATTCCATGGTCCCAAGCGAGAAACTCATGCAAGAACACTTGCAAAATAT
GATGTTGTTATAACGACATATCAAATTGTTGTGAGTGAACATAAAAATGAAGGATGCCTT
TTTGGAATTAAATGGGATCGTATTGTACTTGATGAAGGACATGTAATTCGAAATTATCGT
TCAAAACAATCGGAAGCTGTTTGTGCTTTACTTGGAAAAAAGCGTTGGGTCCTTACAGGA
ACACCAATCCAAAATAAAGAATTTGATATCTATGCAGCAATTAAATTTCTTCGATGTAAT
CCATTCGATGATCTTCGCTATTGGCGTACATGGATTGAAACAAAAGGTGGTTCTTCACCA
CGGTTGCAAGCTCTTCTTAAATCTATTTTACTACGAAGAACTAAACAACAATTGCAAGAG
TCTGGCGAAATACAATCACTTCCTCAAAAACATTTTGAGCAAATATACGTTACATTAAAT
CGAGAGGAAAGGGCTGTATACAATCGTATTATGGCGTTATCTAAACAAATTTTTGCACAA
TTTCTTGATCAACATCACCAAAAACACAACAACTACACATATGATAACAAAAATTTGGGA
AAATTGCATCAAAAATTTGCTAAAATGCATCAAGTTGATCGTGAAATTCAAGCTCATGAG
ATTTTAACTTTGTTATTACGTTTGCGACAAGTATGTTGTCATCCTGGTCTTGTTAAATCT
ATGATAGAAAATAGCGATATTGACAAAGATCTATTGGATAAAGATTTAAGTGGCTCAGGG
AACGATTCAGATCTCGACATTCTTAACAAGCTCCAAAATCTGAAAATTGGAGATTCTAAT
GATATTGAAGAACTTAACATAGCCAAAAATAGCGAAGTTTTCAATTTTGATATTCCAAGC
TCAAAAATTGAAAAATTAATGAGCATTATTCGTGAAAAATTGATTGAAACGGACGATAAA
GCTATAATTGTCAGTCAATGGGTTACATATTTAAACATTATCAAAGCTATGCTCGAGGTT
GAGGGAATTGATTATTGCGAATTGAATGGAACGATTCCTGTGAAAAATCGAAATGATATC
GTTGTGGATTTTAATGACGCATCTTCAAACAAAAAGGTCATGTTGTTATCTATAACTGCA
GGTGGTGTAGGTTTGAATCTCGTTGGTGCCAATCAACTTTACGTAATGGATCCTCATTGG
AATCCACAAATTGAACAACAAGCACAAGACAGAATTTATCGTTTTGGTCAAAAGAAAGAT
GTGAAAATTATTAAGTTCATATGTGATGACACAATCGAGGAGAACATTTTGAAGAAACAA
CAAGAGAAGTTAGAATTAGCTTTAAGCACACTTACTGGTGCCAAGCGTAATGCTACTAAA
TTAACTATAGATGATTTAAAAGATATTTTTGGTATGAAATAA

>g10052.t1 Gene=g10052 Length=993
MKVNNHISSDSDESEYENSEDNNNTTAESSIIINESINDSNISSNIDEISNKNASSEHVE
ISETDEDDESKIEVSQNSFIDQNAEAIKSESENDSDSENEDDDVPLKRKATTAVNRIVDS
DSSDEEVIEKRKSIYALEPEGDLSIHIEDAAYSKSTRRSIHGFEIKQEKHSIKEEPFSEN
EESDDESDIIISSDDDDVEEGNESEDKENLDYSGMIEKKLSSTIRSPMKENFKSELIETE
TSFNQTSDHESSIKKVSRASYDRIVAEKYALANRISSMKKLLEMNAGLPDGGKKLQDAIV
KLEHELIEKETAIKFLLIDENESIKNSIKRSFMSESEVSDTSYSVKESSANDDYIEVKDV
QPKYTGKIGLKHFEQQKALTVEKLQDIYASLDERPGEDVVSTPPKYLKIDLMRHQLHAIA
FMIWRETKQKPRGGILADDMGLGKTLTVISLIMKQLQVYEDREEDEEDTDTDDDEKVEEN
AWIARGHKNLRAGGTLVICPASLINQWEQEIKTKIKKGALDVNVFHGPKRETHARTLAKY
DVVITTYQIVVSEHKNEGCLFGIKWDRIVLDEGHVIRNYRSKQSEAVCALLGKKRWVLTG
TPIQNKEFDIYAAIKFLRCNPFDDLRYWRTWIETKGGSSPRLQALLKSILLRRTKQQLQE
SGEIQSLPQKHFEQIYVTLNREERAVYNRIMALSKQIFAQFLDQHHQKHNNYTYDNKNLG
KLHQKFAKMHQVDREIQAHEILTLLLRLRQVCCHPGLVKSMIENSDIDKDLLDKDLSGSG
NDSDLDILNKLQNLKIGDSNDIEELNIAKNSEVFNFDIPSSKIEKLMSIIREKLIETDDK
AIIVSQWVTYLNIIKAMLEVEGIDYCELNGTIPVKNRNDIVVDFNDASSNKKVMLLSITA
GGVGLNLVGANQLYVMDPHWNPQIEQQAQDRIYRFGQKKDVKIIKFICDDTIEENILKKQ
QEKLELALSTLTGAKRNATKLTIDDLKDIFGMK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g10052.t1 CDD cd18793 SF2_C_SNF 820 947 5.94219E-48
8 g10052.t1 Coils Coil Coil 957 977 -
7 g10052.t1 Gene3D G3DSA:3.40.50.10810 - 381 671 1.2E-59
14 g10052.t1 MobiDBLite mobidb-lite consensus disorder prediction 1 32 -
15 g10052.t1 MobiDBLite mobidb-lite consensus disorder prediction 51 128 -
13 g10052.t1 MobiDBLite mobidb-lite consensus disorder prediction 163 208 -
16 g10052.t1 MobiDBLite mobidb-lite consensus disorder prediction 163 177 -
12 g10052.t1 MobiDBLite mobidb-lite consensus disorder prediction 178 206 -
3 g10052.t1 PANTHER PTHR45626:SF17 TRANSCRIPTION TERMINATION FACTOR 2 17 987 1.8E-161
4 g10052.t1 PANTHER PTHR45626 TRANSCRIPTION TERMINATION FACTOR 2-RELATED 17 987 1.8E-161
2 g10052.t1 Pfam PF00176 SNF2 family N-terminal domain 426 758 1.7E-75
1 g10052.t1 Pfam PF00271 Helicase conserved C-terminal domain 822 936 2.7E-14
18 g10052.t1 ProSiteProfiles PS51192 Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. 425 620 17.802
17 g10052.t1 ProSiteProfiles PS51194 Superfamilies 1 and 2 helicase C-terminal domain profile. 822 987 14.642
11 g10052.t1 SMART SM00487 ultradead3 407 632 8.8E-32
10 g10052.t1 SMART SM00490 helicmild6 852 936 3.6E-14
6 g10052.t1 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 393 653 1.34E-49
5 g10052.t1 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 665 992 1.02E-55

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:0005524 ATP binding MF
GO:0070615 NA NA

KEGG

Orthology

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.

Raw TPM values