Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative U5 small nuclear ribonucleoprotein 200 kDa helicase.

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 g3816 g3816.t3 isoform g3816.t3 28172986 28174346
chr_3 g3816 g3816.t3 exon g3816.t3.exon1 28172986 28173978
chr_3 g3816 g3816.t3 cds g3816.t3.CDS1 28172988 28173978
chr_3 g3816 g3816.t3 exon g3816.t3.exon2 28174040 28174203
chr_3 g3816 g3816.t3 cds g3816.t3.CDS2 28174040 28174203
chr_3 g3816 g3816.t3 exon g3816.t3.exon3 28174302 28174346
chr_3 g3816 g3816.t3 cds g3816.t3.CDS3 28174302 28174346
chr_3 g3816 g3816.t3 TSS g3816.t3 28175133 28175133
chr_3 g3816 g3816.t3 TTS g3816.t3 NA NA

Sequences

>g3816.t3 Gene=g3816 Length=1202
ATGGCTGACGCTGCTGCACGTCAACTACAATACGAGTACAAGGCTAACTCAAATTTAGTT
TTACAAGCTGATGTTAGATTAATTGAACGACCTAGAAGAGATGAAGCGACTGGTGAAGTA
CTTTCTTTGGTTGGAAAACTCGAAGGCACAAAAATGGGAGATCGAGCTCAACGCTCAAAA
CCGGAAAAAGCTGAAGAGAAAAAAGCAATGCGTCGTAAACGTGATGAACAACAATATGAT
TTTAATAGTATGAGAGGTGCTACATTATTATCTGAAGGAATCGATGATATGGTTGGAATT
ATTTATCGACCAAAAACTCAAGAAACCCGTCAAACATACGAAGTTCTTCTCAGTTTCATC
CAAGAGGCGCTTGGTGATCAACCTAGAGATATTTTGTGTGGTGCTGCAGATGAAATTCTT
GCTGTTCTCAAAAACGACAAATTGAAAGACCGTGAACGGAAAAAGGAAATTGATGGTCTG
CTAGGCACAGTTGCGGAAGAAAGATTTGCATTACTTGTTAATCTTGGCAAGAAAATCACA
GATTTTGGTAGTGATTCACTTAATATTGCAGCACTCGGCATTAATGAAGATCAACAAATT
GATGAGACATATGGTATAAATGTTCAATTTGAAGAATCGTCAGATGAAAGTGTTGACGAT
GATTTCGGAGAAATTCGAGATGATGGTGATCAAGATGAAGGCGAAGAAGCAGTTGGTGAT
GGCGTTATTCATTCAGAAAACTTGGGAGCTTCAGAAGGCGATAAAAAAGAGAAAGCTCTT
CATCCATTAGATATTGATGCTTATTGGTTGCAACGTCGTTTAAGAGACTATTTTCAAGAT
CCTTTAGTATCTCAATCAAAGGCTGATGAAGTTTTAAGTATTTTAAAAAATTCCAATGAT
GATCGAGATTGTGAAAATCAAATGGTATTGCTTTTGGGATATGATTGTTTTGATTTCATC
AAAATTTTAAAAAAGAATCGTCAAATGATTCTTTATTGTACGCTTTTAGCAAAAGCACAA
ACCGAAAATGAACGACAAAGGATTAGAGAGGACATGAAAAATGATGCATTTCTTTTAAAA
GTTTTAAGACAATTGGATACTGGAAAAGGTGAAGATAATGTTGAATATGAAGAGAAAAAC
AAAGCAAAAAAACGTCGCATGAATGATGATGAGGAAGATATGATGATCGAAGATGGAGCT
GG

>g3816.t3 Gene=g3816 Length=400
MADAAARQLQYEYKANSNLVLQADVRLIERPRRDEATGEVLSLVGKLEGTKMGDRAQRSK
PEKAEEKKAMRRKRDEQQYDFNSMRGATLLSEGIDDMVGIIYRPKTQETRQTYEVLLSFI
QEALGDQPRDILCGAADEILAVLKNDKLKDRERKKEIDGLLGTVAEERFALLVNLGKKIT
DFGSDSLNIAALGINEDQQIDETYGINVQFEESSDESVDDDFGEIRDDGDQDEGEEAVGD
GVIHSENLGASEGDKKEKALHPLDIDAYWLQRRLRDYFQDPLVSQSKADEVLSILKNSND
DRDCENQMVLLLGYDCFDFIKILKKNRQMILYCTLLAKAQTENERQRIREDMKNDAFLLK
VLRQLDTGKGEDNVEYEEKNKAKKRRMNDDEEDMMIEDGA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g3816.t3 Coils Coil Coil 373 393 -
5 g3816.t3 MobiDBLite mobidb-lite consensus disorder prediction 51 77 -
4 g3816.t3 MobiDBLite mobidb-lite consensus disorder prediction 371 392 -
6 g3816.t3 MobiDBLite mobidb-lite consensus disorder prediction 371 400 -
2 g3816.t3 PANTHER PTHR24075 SEC63 DOMAIN-CONTAINING 8 399 2.9E-107
3 g3816.t3 PANTHER PTHR24075:SF13 U5 SMALL NUCLEAR RIBONUCLEOPROTEIN 200 KDA HELICASE 8 399 2.9E-107
1 g3816.t3 Pfam PF18149 N-terminal helicase PWI domain 257 365 4.9E-38

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

There are no GO annotations for this transcript.

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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. There were no conditions that were differentially expressed