Gene loci information

Transcript annotation

  • This transcript has been annotated as General transcription and DNA repair factor IIH helicase subunit XPB.

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_2 g6546 g6546.t1 isoform g6546.t1 17575870 17578240
chr_2 g6546 g6546.t1 exon g6546.t1.exon1 17575870 17578035
chr_2 g6546 g6546.t1 cds g6546.t1.CDS1 17575870 17578035
chr_2 g6546 g6546.t1 TTS g6546.t1 17577515 17577515
chr_2 g6546 g6546.t1 exon g6546.t1.exon2 17578094 17578240
chr_2 g6546 g6546.t1 cds g6546.t1.CDS2 17578094 17578240
chr_2 g6546 g6546.t1 TSS g6546.t1 17578297 17578297

Sequences

>g6546.t1 Gene=g6546 Length=2313
ATGTCTAAAAGTAAGGGAAGAAAGCGAAAGAATGAAGATGAATACGACTTACAAACGATT
TTAGAGGATGATATATCGAATGATGGTACAACTGAAGCTGCAGTTCCGCAAGCTAGCGGT
AGAAATGCCGAAAAAAATGATGATGGGATACAAGAAGATGAATATGGAGCAAAGGATTAT
CGAATGCACCTTGAGCTTAAAACAGATCATTCATCACGACCACTGTATGTTGCTCCAAAT
GGTCATATTTTCTTAGAAACGTTTTCGCCGGTTTATAAAAATGCACACGATTTTTTGATT
GCAATTTCTGAGCCTGTTTGTCGACCAGAACATATTCATGAATATAAGTTGACAGCTTAT
AGCTTATATGCTGCCGTTTCAGTTGGTTTACAAACTCATGATATTATTGAATACCTTCGA
AGATTATGCAAAACTTCCATTCCAAAAGGTATAGAAGAATTCATTAAACTATGTACGCTT
TCATATGGCAAAGTCAAACTAGTTTTAAAACACAATCGATACTTCATTGAAAGTCCTCAT
CCGGAGATATTGCAAAAACTATTGAAAGATCCAGTGATTCAACAGTGTCGATTGAAACGA
ACTGAAGAGAATATGGGTGAAGAATTTATAAAAAGTCAACAGAATATGAAAGGTGTAACA
TTCGGACAAAAAACTACAGTCGAAGAACCAGAAGGAAATAACGAAAAAAATCAAGTTCCG
GAGGATCTTCAAAAGCTAATTGATAATGAAGAAGAAGAGGAAGAAGTTAATTTAGAGACA
GTATCTTTTGAAGTTGATCAAGAGAAAATTGAAATTATTCAAAAACGTTGCATTGAAATT
GATCATCCTTTGCTAGCCGAATATGATTTTAGAAATGATACAATTAATAAGGACATAAAT
ATTGATTTGAAACCAGCTGCAGTTCTTCGTCCTTATCAAGAAAAAAGTTTGAGAAAAATG
TTTGGAAATGGTCGAGCCAGATCAGGTGTAATCGTTTTACCTTGTGGTGCTGGAAAATCT
CTTGTGGGTGTTACTGCTTGTTGTACAGTTCGAAAGAGAGCATTAGTTTTATGTAACAGT
GGTGTTAGTGTTGAACAATGGAAACAACAATTCAAGATGTGGTCGACAGCCGATGACTCA
ATGATATGTAGATTTACTTCAGAAGCAAAAGATAAACCAATGGGTTGTGGAATTTTAATT
ACAACTTATTCTATGATAACTCACACTCAAAAACGTTCATGGGAAGCGGAACAGACAATG
AAATGGCTTCAAGAACAAGAATGGGGTATTATGGTGCTAGATGAAGTACACACTATTCCA
GCAAAAATGTTTCGACGTGTACTCACAATCGTTCAGAGTCATTGTAAATTGGGTTTGACT
GCAACATTACTACGGGAAGATGATAAAATCGCTGATTTAAACTTTCTGATTGGACCAAAA
TTATATGAAGCAAACTGGTTAGAATTACAGAAAAATGGCTATATTGCTCGAGTTGCGTGT
GCAGAAGTATGGTGCCCTATGACAGCTGAATTTTATCGTGAATATCTTATTGCAAAAGTA
TCAAAGAGAATGCTTCTTTATGTTATGAATCCAAATAAATTTCGCATGTGTCAATATTTG
ATTCAGTATCATGAAAGAAGAGGCGACAAAATAATTGTTTTCAGTGATAATGTGTTTGCA
TTGAAGCATTATGCAAAAAAGATGAACAAACCTTATATTTATGGTCCTACACTGCAAAAT
GAAAGAATTCAAATTCTTCAGAATTTCAAATTCAATCCAAAAGTGAACACAATTTTTGTG
AGTAAAGTTGCCGACACTAGTTTCGATTTGCCAGAAGCAAATGTTTTGATTCAAATATCT
TCACATGGTGGTTCGAGACGTCAAGAAGCTCAACGTTTAGGTCGTATTTTACGTGCAAAG
AAAGGATCTTTTGCAGAAGAATATAATGCATTTTTCTACACTCTTGTTTCACAAGACACA
ATGGAAATGAGTTATTCAAGAAAACGTCAAAGATTTTTGGTTAATCAGGGTTACAGTTAC
AAAGTGATTACTCATTTAAGTGGAATGGACGAAGATCAAAGTCTCTTCTATAAGACACGA
GAAGAGCAAGGACAATTGCTGCAACAAGTTTTAGCAGCATCTGATATAGATTGTGAAGAT
GAAAAAGTTCCTGGTGAAATTGGCGGATCAAGACCAGGTACTTCTAGAAAAACTGGTGGT
TTTAGTTCACTTTCTGGTGCTGACAATGAGGTTTACTTTGAACAAAAGAAGAAAAGTAGT
GTTCAACATCCACTTTTTAAAAGATTCCGTTAA

>g6546.t1 Gene=g6546 Length=770
MSKSKGRKRKNEDEYDLQTILEDDISNDGTTEAAVPQASGRNAEKNDDGIQEDEYGAKDY
RMHLELKTDHSSRPLYVAPNGHIFLETFSPVYKNAHDFLIAISEPVCRPEHIHEYKLTAY
SLYAAVSVGLQTHDIIEYLRRLCKTSIPKGIEEFIKLCTLSYGKVKLVLKHNRYFIESPH
PEILQKLLKDPVIQQCRLKRTEENMGEEFIKSQQNMKGVTFGQKTTVEEPEGNNEKNQVP
EDLQKLIDNEEEEEEVNLETVSFEVDQEKIEIIQKRCIEIDHPLLAEYDFRNDTINKDIN
IDLKPAAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNS
GVSVEQWKQQFKMWSTADDSMICRFTSEAKDKPMGCGILITTYSMITHTQKRSWEAEQTM
KWLQEQEWGIMVLDEVHTIPAKMFRRVLTIVQSHCKLGLTATLLREDDKIADLNFLIGPK
LYEANWLELQKNGYIARVACAEVWCPMTAEFYREYLIAKVSKRMLLYVMNPNKFRMCQYL
IQYHERRGDKIIVFSDNVFALKHYAKKMNKPYIYGPTLQNERIQILQNFKFNPKVNTIFV
SKVADTSFDLPEANVLIQISSHGGSRRQEAQRLGRILRAKKGSFAEEYNAFFYTLVSQDT
MEMSYSRKRQRFLVNQGYSYKVITHLSGMDEDQSLFYKTREEQGQLLQQVLAASDIDCED
EKVPGEIGGSRPGTSRKTGGFSSLSGADNEVYFEQKKKSSVQHPLFKRFR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
23 g6546.t1 CDD cd18029 DEXHc_XPB 301 469 4.31519E-110
22 g6546.t1 CDD cd18789 SF2_C_XPB 500 656 5.37677E-86
21 g6546.t1 Gene3D G3DSA:3.40.50.300 - 299 489 4.8E-35
20 g6546.t1 Gene3D G3DSA:3.40.50.300 - 490 724 4.5E-72
27 g6546.t1 MobiDBLite mobidb-lite consensus disorder prediction 1 16 -
28 g6546.t1 MobiDBLite mobidb-lite consensus disorder prediction 1 51 -
26 g6546.t1 MobiDBLite mobidb-lite consensus disorder prediction 23 37 -
4 g6546.t1 PANTHER PTHR11274 RAD25/XP-B DNA REPAIR HELICASE 49 754 0.0
5 g6546.t1 PANTHER PTHR11274:SF0 GENERAL TRANSCRIPTION AND DNA REPAIR FACTOR IIH HELICASE SUBUNIT XPB 49 754 0.0
16 g6546.t1 PRINTS PR00851 Xeroderma pigmentosum group B protein signature 73 93 3.5E-149
6 g6546.t1 PRINTS PR00851 Xeroderma pigmentosum group B protein signature 159 178 3.5E-149
12 g6546.t1 PRINTS PR00851 Xeroderma pigmentosum group B protein signature 290 316 3.5E-149
15 g6546.t1 PRINTS PR00851 Xeroderma pigmentosum group B protein signature 321 343 3.5E-149
13 g6546.t1 PRINTS PR00851 Xeroderma pigmentosum group B protein signature 427 447 3.5E-149
8 g6546.t1 PRINTS PR00851 Xeroderma pigmentosum group B protein signature 493 515 3.5E-149
17 g6546.t1 PRINTS PR00851 Xeroderma pigmentosum group B protein signature 530 545 3.5E-149
9 g6546.t1 PRINTS PR00851 Xeroderma pigmentosum group B protein signature 549 571 3.5E-149
11 g6546.t1 PRINTS PR00851 Xeroderma pigmentosum group B protein signature 596 614 3.5E-149
10 g6546.t1 PRINTS PR00851 Xeroderma pigmentosum group B protein signature 615 640 3.5E-149
14 g6546.t1 PRINTS PR00851 Xeroderma pigmentosum group B protein signature 646 669 3.5E-149
7 g6546.t1 PRINTS PR00851 Xeroderma pigmentosum group B protein signature 736 755 3.5E-149
2 g6546.t1 Pfam PF13625 Helicase conserved C-terminal domain 75 201 3.2E-36
1 g6546.t1 Pfam PF04851 Type III restriction enzyme, res subunit 309 463 3.9E-17
3 g6546.t1 Pfam PF16203 ERCC3/RAD25/XPB C-terminal helicase 489 727 2.4E-124
31 g6546.t1 ProSiteProfiles PS51192 Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. 320 481 19.299
30 g6546.t1 ProSiteProfiles PS51194 Superfamilies 1 and 2 helicase C-terminal domain profile. 535 674 12.416
25 g6546.t1 SMART SM00487 ultradead3 305 485 1.1E-19
24 g6546.t1 SMART SM00490 helicmild6 562 640 3.7E-7
19 g6546.t1 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 254 483 3.31E-37
18 g6546.t1 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 413 717 3.55E-32
29 g6546.t1 TIGRFAM TIGR00603 rad25: DNA repair helicase rad25 59 768 0.0

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:0003677 DNA binding MF
GO:0016787 hydrolase activity MF
GO:0005524 ATP binding MF
GO:0006367 transcription initiation from RNA polymerase II promoter BP
GO:0003678 DNA helicase activity MF
GO:0006289 nucleotide-excision repair BP

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