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.t2 isoform g3816.t2 28172986 28174346
chr_3 g3816 g3816.t2 exon g3816.t2.exon1 28172986 28173978
chr_3 g3816 g3816.t2 cds g3816.t2.CDS1 28172988 28173978
chr_3 g3816 g3816.t2 exon g3816.t2.exon2 28174040 28174203
chr_3 g3816 g3816.t2 cds g3816.t2.CDS2 28174040 28174095
chr_3 g3816 g3816.t2 exon g3816.t2.exon3 28174298 28174346
chr_3 g3816 g3816.t2 TSS g3816.t2 28175133 28175133
chr_3 g3816 g3816.t2 TTS g3816.t2 NA NA

Sequences

>g3816.t2 Gene=g3816 Length=1206
ATGGCTGACGCTGCTGCACGTCAACTACAATACGAGTACAAGGCTGTAAAACTCAAATTT
AGTTTTACAAGCTGATGTTAGATTAATTGAACGACCTAGAAGAGATGAAGCGACTGGTGA
AGTACTTTCTTTGGTTGGAAAACTCGAAGGCACAAAAATGGGAGATCGAGCTCAACGCTC
AAAACCGGAAAAAGCTGAAGAGAAAAAAGCAATGCGTCGTAAACGTGATGAACAACAATA
TGATTTTAATAGTATGAGAGGTGCTACATTATTATCTGAAGGAATCGATGATATGGTTGG
AATTATTTATCGACCAAAAACTCAAGAAACCCGTCAAACATACGAAGTTCTTCTCAGTTT
CATCCAAGAGGCGCTTGGTGATCAACCTAGAGATATTTTGTGTGGTGCTGCAGATGAAAT
TCTTGCTGTTCTCAAAAACGACAAATTGAAAGACCGTGAACGGAAAAAGGAAATTGATGG
TCTGCTAGGCACAGTTGCGGAAGAAAGATTTGCATTACTTGTTAATCTTGGCAAGAAAAT
CACAGATTTTGGTAGTGATTCACTTAATATTGCAGCACTCGGCATTAATGAAGATCAACA
AATTGATGAGACATATGGTATAAATGTTCAATTTGAAGAATCGTCAGATGAAAGTGTTGA
CGATGATTTCGGAGAAATTCGAGATGATGGTGATCAAGATGAAGGCGAAGAAGCAGTTGG
TGATGGCGTTATTCATTCAGAAAACTTGGGAGCTTCAGAAGGCGATAAAAAAGAGAAAGC
TCTTCATCCATTAGATATTGATGCTTATTGGTTGCAACGTCGTTTAAGAGACTATTTTCA
AGATCCTTTAGTATCTCAATCAAAGGCTGATGAAGTTTTAAGTATTTTAAAAAATTCCAA
TGATGATCGAGATTGTGAAAATCAAATGGTATTGCTTTTGGGATATGATTGTTTTGATTT
CATCAAAATTTTAAAAAAGAATCGTCAAATGATTCTTTATTGTACGCTTTTAGCAAAAGC
ACAAACCGAAAATGAACGACAAAGGATTAGAGAGGACATGAAAAATGATGCATTTCTTTT
AAAAGTTTTAAGACAATTGGATACTGGAAAAGGTGAAGATAATGTTGAATATGAAGAGAA
AAACAAAGCAAAAAAACGTCGCATGAATGATGATGAGGAAGATATGATGATCGAAGATGG
AGCTGG

>g3816.t2 Gene=g3816 Length=349
MGDRAQRSKPEKAEEKKAMRRKRDEQQYDFNSMRGATLLSEGIDDMVGIIYRPKTQETRQ
TYEVLLSFIQEALGDQPRDILCGAADEILAVLKNDKLKDRERKKEIDGLLGTVAEERFAL
LVNLGKKITDFGSDSLNIAALGINEDQQIDETYGINVQFEESSDESVDDDFGEIRDDGDQ
DEGEEAVGDGVIHSENLGASEGDKKEKALHPLDIDAYWLQRRLRDYFQDPLVSQSKADEV
LSILKNSNDDRDCENQMVLLLGYDCFDFIKILKKNRQMILYCTLLAKAQTENERQRIRED
MKNDAFLLKVLRQLDTGKGEDNVEYEEKNKAKKRRMNDDEEDMMIEDGA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g3816.t2 Coils Coil Coil 322 342 -
5 g3816.t2 MobiDBLite mobidb-lite consensus disorder prediction 1 26 -
4 g3816.t2 MobiDBLite mobidb-lite consensus disorder prediction 320 341 -
6 g3816.t2 MobiDBLite mobidb-lite consensus disorder prediction 320 349 -
2 g3816.t2 PANTHER PTHR24075 SEC63 DOMAIN-CONTAINING 1 348 8.3E-84
3 g3816.t2 PANTHER PTHR24075:SF13 U5 SMALL NUCLEAR RIBONUCLEOPROTEIN 200 KDA HELICASE 1 348 8.3E-84
1 g3816.t2 Pfam PF18149 N-terminal helicase PWI domain 206 314 3.8E-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