Gene loci information

Transcript annotation

  • This transcript has been annotated as Helicase SKI2W.

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 g8095 g8095.t1 isoform g8095.t1 28553104 28556879
chr_2 g8095 g8095.t1 exon g8095.t1.exon1 28553104 28553328
chr_2 g8095 g8095.t1 cds g8095.t1.CDS1 28553104 28553328
chr_2 g8095 g8095.t1 exon g8095.t1.exon2 28553383 28554907
chr_2 g8095 g8095.t1 cds g8095.t1.CDS2 28553383 28554907
chr_2 g8095 g8095.t1 exon g8095.t1.exon3 28554968 28556799
chr_2 g8095 g8095.t1 cds g8095.t1.CDS3 28554968 28556799
chr_2 g8095 g8095.t1 exon g8095.t1.exon4 28556874 28556879
chr_2 g8095 g8095.t1 cds g8095.t1.CDS4 28556874 28556879
chr_2 g8095 g8095.t1 TSS g8095.t1 28556912 28556912
chr_2 g8095 g8095.t1 TTS g8095.t1 NA NA

Sequences

>g8095.t1 Gene=g8095 Length=3588
ATGAAAGACGATGATATAGTAGAAAGTTCGGAAAAACTTTTAGAAAAGTATGTAAAAAAT
CCAAATTTACCAAAATTGCATGATCCAAAAGCTAATTATACAACACGTCAACTAAATTCA
TATGAGAAATTACTGCACATACCTTCATGTCCTCAAAACACTCGTATTGTAGCAAAACGT
AATGAAGAAAGTGGAAAAATTGAGAAATTTATAGAAGTTCAAATCGAAAATGCCGGTTCG
AATGCAAAAACTAGTTTTTCTCTTGATAGAGCTCCTAATCAGCAACAAGCGACTAGAGGA
TCTGCTTCTAATTTCATGTTTTGGCCAGGTGGATTCGATTTACCACCAAATGAAGAAATT
GAAAAATTAGAACTTAATGATGATTATAATTTCTATGAAAAACTTTTGAATGTAGCACCC
GGATTTACTAATGGCATTGATTTCAGTCATCTTGTAAAAAACCATAATGAAAAGACTGTT
GAAAGTGATTCAAACACAATTGATCTGCTTGCAGCAATTGATAATGAAGATATTTTTAAA
ATTGATAAAGAAAATGTAACAAAAACTGTTGAAACAAATCTTAAGAAACCACTTCTTTTA
AGTGAAAATGTTAAAATTGAAGATTCTCTGTTGGAAGTCAAAAACAGAAACGTTTTACAA
ATCAAAGATACAAAGAATCACACTCAAAGTTCAGAGTGGGCTGAGTTGATTGACATATCG
CAGCCAGTAAAAAATTTTTATGATCGTGTTGCAGATATGGCTCATCAATTTCCGTTTGAA
TTGGATAATTTTCAAAAGCAAGCGATACTTAAACTTGAGTCACATGATCATGTTTTTGTT
GCAGCACACACAAGCGCTGGAAAAACTGTTGTAGCAGAATATTGCATTGCTCTCTCTATG
AAGCATATGACAAAATCAATCTATACCAGTCCAATAAAAGCTTTGAGTAATCAAAAATAT
AGAGATTTCAAGCAAACATTTGGTGATGTTGGTCTAATTACTGGAGACATTCAAATTAAT
CAAACAGCTAGTTGCTTAATTATGACAACTGAAATTCTTCGTTCAATGTTGTATTGTGGT
AGTGATGTTACTAGAGATTTGGAATATGTCATTTTCGATGAAATTCACTATCTTTCAGAT
GGTGAAAGAGGTCATGTATGGGAAGAAGCTTTAATTCTTCTTCCATCTCACGTTACAATA
GTTATGCTATCAGCAACTGTTCCAAATTATCTTGAATTTGCTAATTGGGTTGGAAAAACA
AAAAGAAAGAAGGTTTATGTAATCAGCACTCTCAAACGTCCTGTGCCTCTTCAACATTTT
CTTTATACTGGCAATGGCGGGAAATCGAGAGATGATATTTTTCTCTTAGTAGATGAGAAT
GGAAAATTTCTTACTGAAGGATATGAAAAAGCAAAAAATTGCAAAGCAGCACGACAAAAA
GAATTTCAAAAAAATTTCGGATCTAAACAATCCAACTTTTTAAATCCTAAACAAGAAAAA
ACAATGTGGGAAGGTCTCATTGGTCATTTGAAAAAGAATGATCGACTACCCGTTGTTGCT
TTTACTTTGTCGCGAAATCGTTGTGATACAAATGCAGAAGCTCTTAAATCTTGTGATTTA
ACCACTGCCCGAGAAAAATTCAAAATCTCCTCCTTCTTCAAAGCATGCATTCAAAAATTA
AAAACTGAAGATCGTGAACTTCCACAAGTACTTACTATTCAAGATTGTCTTGAGCGTGGT
ATTGGCATACATCATTCTGGAATTTTACCAATTCTCAAAGAGATTGTAGAAATGTGTTTC
CAATCAGGATTAGTCAAATTATTATTTGCTACAGAAACTTTTGCGATGGGTGTAAACATG
CCTGCGAGAACTGTTATTTTTGATTCCATCACTAAATTTGATGGTAAGAATTCACGTAAT
CTCGAATCAGCAGAATATACGCAAATGGCTGGTAGGGCTGGAAGGAGAGGGCTAGATTCG
ACAGGCACTGTAATTATTCTCTGCAAGACATCTGAAATACCTCATCCTGATGTTCTTAAA
AGAATGATTTTAGGTCGACCTATACAATTAGAGTCGAAATTCAAATTGACATATGCTATG
ATATTGTCATTATTGAGAGTCGAGCGAGTATCTGTTGAAGATATGATGCAGCATAGTTTT
AGAGAATTTGGAAAGCAATTAAAAGTGCCAGAAAATAAGAAACAACTTGAACTTGCTGAA
AAAAAATTGGCAGAATTAACTGAGATTTCAGAGCATTTGACACCTTTGTGCAATTTCTAT
ACGGCTTGCAAGGCATTTTTGGATTTTCATGAAGAAATCATGCCAAAGTTTATTGCACAA
CAAAAAGTCTCAAATGAATTGAAAGCAGGGAGAGTGTTAATAGTAACCTCAGAAAATCAT
TATAACAAATATGGTATTTTACTGAAAGCTGACTTACAAAGCATGACATTTAAAGTTTTA
ATAATGAATAGTCATAATCATTTTGAAGAAATTTATCAAAAGAAAAGTGTTTTATGGCAC
AAAATAATTGCCTTATCACAAAACTATAATAATTTGTCTAACGACAATGGCGATCACACA
ATTCTTACTCTCAAAGCATCAGATATTATGGAAATAACTCGTACTATATTTAAATGTGAT
GCAGAGAAAATCATTTTGAATTGGGAACAACGACAAATTCCACGTTTTAAGGATAGTCCA
GCGGGTCCTAGTGTTGTACAAGCTATAAACGATTTAAATGCGCTTATTAAATCTAATACA
AAGCTTGAATGCTTATCTTTGACAAGTCAAAATATTGAACTATTTGAACAACTTAAGCAG
CTCGTAGAATTAAAAGAGAATATTGCGATATATCAACCATACACCAATGTTCCAAATTTC
TTAGAAAAATTTTCCCAAGTCTTTGATCGTAAAATTCTTGAAGACCGAAAAGAGACTTTA
ATGTTTCAATTATCTAATAAAAATTTATCACTTTATCCTGATTATTGCAATAAGCTGCTT
GTACTTCAAGAATTGAAATATATAGATGAGTTGAATCAAGTGGCATTAAAAGGACGTGTT
GCTTGTGAGATGGGTCAGAATGAACTTATCATAACAGAATTAGTTTTGCGAAATGTACTC
ACAAACCTTGAACCTGCTGAAATTGCTGCCTTACTCTCATCTCTTGTATTTCAAGCAAAA
ACAGACGTAGAACCTAGTGTGTCAGAAAAGATGAAGTCACTTATACAAAAAGTTACTGAA
GTGGAAGAGTCAATACGTGAAGTTGAAATGAAATACAATGTTGGAAAATCTGATGAAACT
GTAGAAAGAGATCGCCTTAATTTTGGTCTAATTGAGGTTGTTTATGAATGGGCCAGAAAT
AAGCCATTTTCAGAGATTATACAATTAACAGACATAAAAGAAGGTGTCATCGTAAGATGT
ATTCAACAGTTGCATGAAACACTTAGTGATGTTAAAGATGCTGCAAGAATCATTGGTGAT
CCTGTGCTTCATTCAAAAATGGAAGAGGCTTCAAACGCGATCAAACGTGATATCGTTTTT
GCTGCATCTCTCTATACATCAAATGATACAATAACTATTACTGCTTAG

>g8095.t1 Gene=g8095 Length=1195
MKDDDIVESSEKLLEKYVKNPNLPKLHDPKANYTTRQLNSYEKLLHIPSCPQNTRIVAKR
NEESGKIEKFIEVQIENAGSNAKTSFSLDRAPNQQQATRGSASNFMFWPGGFDLPPNEEI
EKLELNDDYNFYEKLLNVAPGFTNGIDFSHLVKNHNEKTVESDSNTIDLLAAIDNEDIFK
IDKENVTKTVETNLKKPLLLSENVKIEDSLLEVKNRNVLQIKDTKNHTQSSEWAELIDIS
QPVKNFYDRVADMAHQFPFELDNFQKQAILKLESHDHVFVAAHTSAGKTVVAEYCIALSM
KHMTKSIYTSPIKALSNQKYRDFKQTFGDVGLITGDIQINQTASCLIMTTEILRSMLYCG
SDVTRDLEYVIFDEIHYLSDGERGHVWEEALILLPSHVTIVMLSATVPNYLEFANWVGKT
KRKKVYVISTLKRPVPLQHFLYTGNGGKSRDDIFLLVDENGKFLTEGYEKAKNCKAARQK
EFQKNFGSKQSNFLNPKQEKTMWEGLIGHLKKNDRLPVVAFTLSRNRCDTNAEALKSCDL
TTAREKFKISSFFKACIQKLKTEDRELPQVLTIQDCLERGIGIHHSGILPILKEIVEMCF
QSGLVKLLFATETFAMGVNMPARTVIFDSITKFDGKNSRNLESAEYTQMAGRAGRRGLDS
TGTVIILCKTSEIPHPDVLKRMILGRPIQLESKFKLTYAMILSLLRVERVSVEDMMQHSF
REFGKQLKVPENKKQLELAEKKLAELTEISEHLTPLCNFYTACKAFLDFHEEIMPKFIAQ
QKVSNELKAGRVLIVTSENHYNKYGILLKADLQSMTFKVLIMNSHNHFEEIYQKKSVLWH
KIIALSQNYNNLSNDNGDHTILTLKASDIMEITRTIFKCDAEKIILNWEQRQIPRFKDSP
AGPSVVQAINDLNALIKSNTKLECLSLTSQNIELFEQLKQLVELKENIAIYQPYTNVPNF
LEKFSQVFDRKILEDRKETLMFQLSNKNLSLYPDYCNKLLVLQELKYIDELNQVALKGRV
ACEMGQNELIITELVLRNVLTNLEPAEIAALLSSLVFQAKTDVEPSVSEKMKSLIQKVTE
VEESIREVEMKYNVGKSDETVERDRLNFGLIEVVYEWARNKPFSEIIQLTDIKEGVIVRC
IQQLHETLSDVKDAARIIGDPVLHSKMEEASNAIKRDIVFAASLYTSNDTITITA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g8095.t1 CDD cd18795 SF2_C_Ski2 433 669 9.0166E-47
14 g8095.t1 Coils Coil Coil 729 749 -
15 g8095.t1 Coils Coil Coil 1071 1091 -
10 g8095.t1 Gene3D G3DSA:3.40.50.300 - 235 433 1.2E-72
9 g8095.t1 Gene3D G3DSA:3.40.50.300 - 434 691 4.5E-88
13 g8095.t1 Gene3D G3DSA:1.10.3380.30 - 698 1177 1.0E-108
11 g8095.t1 Gene3D G3DSA:1.20.1500.20 - 720 986 1.0E-108
12 g8095.t1 Gene3D G3DSA:2.40.30.300 - 788 919 1.0E-108
6 g8095.t1 PANTHER PTHR12131 ATP-DEPENDENT RNA AND DNA HELICASE 74 1186 0.0
7 g8095.t1 PANTHER PTHR12131:SF8 HELICASE SKI2W 74 1186 0.0
16 g8095.t1 PIRSF PIRSF005198 SKI2 2 1186 0.0
1 g8095.t1 Pfam PF17911 Ski2 N-terminal region 37 154 1.4E-22
2 g8095.t1 Pfam PF00270 DEAD/DEAH box helicase 264 409 6.0E-17
4 g8095.t1 Pfam PF00271 Helicase conserved C-terminal domain 578 657 1.7E-5
5 g8095.t1 Pfam PF13234 rRNA-processing arch domain 713 985 1.2E-15
3 g8095.t1 Pfam PF08148 DSHCT (NUC185) domain 1012 1181 4.0E-46
22 g8095.t1 ProSiteProfiles PS51192 Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. 269 425 21.94
21 g8095.t1 ProSiteProfiles PS51194 Superfamilies 1 and 2 helicase C-terminal domain profile. 539 705 11.475
20 g8095.t1 SMART SM00487 ultradead3 257 440 5.4E-29
19 g8095.t1 SMART SM00490 helicmild6 571 657 5.4E-15
18 g8095.t1 SMART SM01142 DSHCT_2 1009 1186 1.4E-72
8 g8095.t1 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 272 670 3.29E-44

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:0006401 RNA catabolic process BP
GO:0003723 RNA binding MF
GO:0005524 ATP binding MF
GO:0003724 RNA helicase activity MF
GO:0003676 nucleic acid binding MF

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