Gene loci information

Transcript annotation

  • This transcript has been annotated as ATP-dependent DNA helicase Q1.

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_3 g1195 g1195.t1 isoform g1195.t1 8695836 8698054
chr_3 g1195 g1195.t1 exon g1195.t1.exon1 8695836 8696830
chr_3 g1195 g1195.t1 cds g1195.t1.CDS1 8695836 8696830
chr_3 g1195 g1195.t1 exon g1195.t1.exon2 8696907 8697830
chr_3 g1195 g1195.t1 cds g1195.t1.CDS2 8696907 8697830
chr_3 g1195 g1195.t1 exon g1195.t1.exon3 8697886 8698054
chr_3 g1195 g1195.t1 cds g1195.t1.CDS3 8697886 8698054
chr_3 g1195 g1195.t1 TSS g1195.t1 NA NA
chr_3 g1195 g1195.t1 TTS g1195.t1 NA NA

Sequences

>g1195.t1 Gene=g1195 Length=2088
ATGTCTGAAAATCAAATTCAACTAATTGAGAATCGCGTTAAAGAAATAGATGAACAAATT
GATAAATTGCAGTCAATTAAAAGAAAGTTATTATTACAAAGAGAAAAATTAACAGATAGG
AAAAATTTTGAGAAATCCGAAGAGCTCGCCAAAAATCAATGGAATCAAGAAATATATCCA
TGGTCTAAAATGTTGCGAGAGAAAATGAAAGATACCTTTGGTATAAAAGAGTTTCGAAGT
CAACAACTTGAAGCTATAAATGCAACAATGTCAAAACATGATTTGATATTAATAGCACCT
ACAAGTGCAGGCAAAAGCTTATGCTTTCAATTACCTGCATTATGCGATAAAGGCATAACT
CTTGTTATATCACCTTTAATTTCATTAATTGAAGATCAAATATATTCACTTGAAAAGAAA
AACATACCAGCTCAAGCACTTTCATCAAATAGTACAAAGGAACATGTTAAGCATATTATC
AAAATCTTACAAGATCCAAGCATGTCAACAGGAAAAGAATTAAAGTTATTATATGTAACA
CCTGAACGATTAGCAAAGCACAAGACATTGATGCAAGCTCTTCAAAAGTGTTATACTAAC
AAAAAATTGGATAGAATAGCTATTGATGAGGTACATTGTTGCTCTGTATTAGGCCACGAC
TTTCGTCCAGAATACAAGTTTTTGAACACAATGAAAACTCTTTTTCCCGAAACTCCAATC
ATTGGTGTGACAGCAACTGCATCAAGAAAAATTTTAATTGATGTACAAAAACTCTTGAAT
ATTCGTGGTTGTATTATTTTCAATTCACCATTCAATCGACCAAATCTTTATTATCACGTT
TATGAGAAACCAGACTCGCAAGAAGATTGTCTTGATTTATTAGCGGATTTGTTGTTGAAA
AGGTACAATAAACAGACTGGAATTATCTATACATTTTCAATTAAAGATACTGAAACTATC
ACAACTGAACTATTAAAAAGAGATTGCAAAGTAAGGCCTTATCATGCTCAGCTTGATCAA
CTTCAACGAACAAAAATATATCATCAATGGATGAAAGGCGACATTCAAGCAGTTGTAGCA
ACAATTGCATTTGGAATGGGCGTTGACAATCAAAACACACGATTTGTAATACATCACACT
ATTTCAAAATCAATGGAAAACTTTTATCAAGAATCTGGCAGATGTGGCCGAGATGGAAAA
TTTGCAGAATGCATATTGTTATATAGACTACAAGACATGTTTAAAATTTCAACACTAACA
TTTTCGGAAGTAAATGGTATAAAGAACACATATTCTATGGTAGAATATGCCATTAATTCA
AAAATATGTAGACGTGATCAGTTTTCCAAGTATTTTACTGAAGTATGGAATGAAGAAAAT
TGTGGAAAAATGTGTGACTCTTGCTATTACAAGAACAACACTAGATTAATCACACCAGCA
AAGATTAATATTTTGCCACATTATCAATCAATTTTGAAAATTCTTGATAATGCATCGTCA
AGTGATACAAAAATGACTGCTAATAAATTAATCGATGCGTGGTTTCAAAAAGGTGCTAAG
AATTTAAGAATCAAAGACTCATCTGCACCAGATATTGATAAATCATATGCAGAGCAAATT
CTTGCTTTTCTAATAGTGAACGATTATTTGAGAGAAGATTTCCACTATACTGCATATAAT
ACTTACTCATACATTATCAAAGGTCCACGAATTATACAGGATGAAGAAATTGAATTTCAA
CCAGCTCGCAACTTTGATCTGCCAGATATTGAAGAATTAAAGAAATTCCATGAAATTACA
TCACAAAAACCAAAAATTGAAAATGAAAATAAAAGAAATGCTCCCAATACGTCAAGTAAC
TGTTCATCGCCTTCTAAAAAACGAAAAACAAGCGATGATACAATTGTAGTTAGCAGTTCT
AATTTGGAAAAACTTATTACAAGTAAGATTCAAAAAGTTCTATCAGCAAGTCTAAAGGCA
TCAGTATCATTAGAAAATAATTCAGATGATGAAGACGATGGTGGTGATGATGATGATGTT
ATGATAGTTGAACCAAAAACTGAAGATGATGTAATTAATTTAGACTAA

>g1195.t1 Gene=g1195 Length=695
MSENQIQLIENRVKEIDEQIDKLQSIKRKLLLQREKLTDRKNFEKSEELAKNQWNQEIYP
WSKMLREKMKDTFGIKEFRSQQLEAINATMSKHDLILIAPTSAGKSLCFQLPALCDKGIT
LVISPLISLIEDQIYSLEKKNIPAQALSSNSTKEHVKHIIKILQDPSMSTGKELKLLYVT
PERLAKHKTLMQALQKCYTNKKLDRIAIDEVHCCSVLGHDFRPEYKFLNTMKTLFPETPI
IGVTATASRKILIDVQKLLNIRGCIIFNSPFNRPNLYYHVYEKPDSQEDCLDLLADLLLK
RYNKQTGIIYTFSIKDTETITTELLKRDCKVRPYHAQLDQLQRTKIYHQWMKGDIQAVVA
TIAFGMGVDNQNTRFVIHHTISKSMENFYQESGRCGRDGKFAECILLYRLQDMFKISTLT
FSEVNGIKNTYSMVEYAINSKICRRDQFSKYFTEVWNEENCGKMCDSCYYKNNTRLITPA
KINILPHYQSILKILDNASSSDTKMTANKLIDAWFQKGAKNLRIKDSSAPDIDKSYAEQI
LAFLIVNDYLREDFHYTAYNTYSYIIKGPRIIQDEEIEFQPARNFDLPDIEELKKFHEIT
SQKPKIENENKRNAPNTSSNCSSPSKKRKTSDDTIVVSSSNLEKLITSKIQKVLSASLKA
SVSLENNSDDEDDGGDDDDVMIVEPKTEDDVINLD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g1195.t1 Coils Coil Coil 6 40 -
7 g1195.t1 Gene3D G3DSA:3.40.50.300 - 35 272 1.0E-81
8 g1195.t1 Gene3D G3DSA:3.40.50.300 - 273 470 3.1E-59
9 g1195.t1 Gene3D G3DSA:1.10.10.10 winged helix repressor DNA binding domain 479 580 2.4E-31
16 g1195.t1 MobiDBLite mobidb-lite consensus disorder prediction 598 634 -
13 g1195.t1 MobiDBLite mobidb-lite consensus disorder prediction 611 625 -
15 g1195.t1 MobiDBLite mobidb-lite consensus disorder prediction 664 695 -
14 g1195.t1 MobiDBLite mobidb-lite consensus disorder prediction 667 684 -
4 g1195.t1 PANTHER PTHR13710 DNA HELICASE RECQ FAMILY MEMBER 4 657 4.1E-177
5 g1195.t1 PANTHER PTHR13710:SF72 ATP-DEPENDENT DNA HELICASE Q1 4 657 4.1E-177
2 g1195.t1 Pfam PF00270 DEAD/DEAH box helicase 81 250 1.7E-15
3 g1195.t1 Pfam PF00271 Helicase conserved C-terminal domain 292 398 5.1E-14
1 g1195.t1 Pfam PF16124 RecQ zinc-binding 426 468 7.2E-8
19 g1195.t1 ProSiteProfiles PS51192 Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. 86 265 21.625
18 g1195.t1 ProSiteProfiles PS51194 Superfamilies 1 and 2 helicase C-terminal domain profile. 298 442 15.897
12 g1195.t1 SMART SM00487 ultradead3 74 281 5.7E-27
11 g1195.t1 SMART SM00490 helicmild6 318 399 1.2E-18
6 g1195.t1 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 117 414 1.13E-48
17 g1195.t1 TIGRFAM TIGR00614 recQ_fam: ATP-dependent DNA helicase, RecQ family 69 527 2.5E-140

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:0004386 helicase activity MF
GO:0006310 DNA recombination BP
GO:0003676 nucleic acid binding MF

KEGG

Orthology

Pathway

This gene does not belong to any 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