Gene loci information

Transcript annotation

  • This transcript has been annotated as H/ACA ribonucleoprotein complex subunit 4.

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_1 g11311 g11311.t2 TSS g11311.t2 15528991 15528991
chr_1 g11311 g11311.t2 isoform g11311.t2 15529055 15529679
chr_1 g11311 g11311.t2 exon g11311.t2.exon1 15529055 15529067
chr_1 g11311 g11311.t2 cds g11311.t2.CDS1 15529055 15529067
chr_1 g11311 g11311.t2 exon g11311.t2.exon2 15529130 15529679
chr_1 g11311 g11311.t2 cds g11311.t2.CDS2 15529130 15529677
chr_1 g11311 g11311.t2 TTS g11311.t2 15530469 15530469

Sequences

>g11311.t2 Gene=g11311 Length=563
ATGGCTGAAATAATTGAAAAAAAGAAGAAACAAAAGAAAAAAGTCAAGGAAGAGATTGAA
AATTTAGGCGAGATTCAAAAATCTGGTGATTTTCAAATAAAACCATCTGATGCTATTACA
AAGCTTGACAGCTCTGACTGGCCATTATTACTGAAAAATTTTGATCGTCTCAATATCAGA
ACAAATCATTATACACCATTGCCATTTGGTGCATCGCCATTAAGTCGACCAATTAAAGAA
TATGTTAAATCGGGTTTTATCAATGTAGATAAACCCTCAAATCCTTCTTCTCATGAGGTT
GTAGCATGGATTAAACGAATTCTCAAGTGCGAAAAGACTGGTCATTCTGGAACTCTCGAT
CCTAAAGTTACTGGTTGCTTGATAGTTTGTATTGACAGAGCAACACGATTGGTTAAAAGC
CAACAAAGTGCCGGTAAAGAGTACGTAGCAGTATTTAAGCTACATTCAGCTGTTGAATCA
ATTCAGAGAGTTAATCAAGGGTTGGAAAAATTACGAGGTGCACTGTTTCAACGACCACCA
TTGATTTCTGCTGTAAAAAGACA

>g11311.t2 Gene=g11311 Length=187
MAEIIEKKKKQKKKVKEEIENLGEIQKSGDFQIKPSDAITKLDSSDWPLLLKNFDRLNIR
TNHYTPLPFGASPLSRPIKEYVKSGFINVDKPSNPSSHEVVAWIKRILKCEKTGHSGTLD
PKVTGCLIVCIDRATRLVKSQQSAGKEYVAVFKLHSAVESIQRVNQGLEKLRGALFQRPP
LISAVKR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g11311.t2 Coils Coil Coil 1 25 -
8 g11311.t2 Gene3D G3DSA:2.30.130.70 - 45 89 2.6E-19
7 g11311.t2 Gene3D G3DSA:3.30.2350.10 Pseudouridine synthase 90 187 2.5E-25
3 g11311.t2 PANTHER PTHR23127 CENTROMERE/MICROTUBULE BINDING PROTEIN CBF5 6 187 2.0E-89
4 g11311.t2 PANTHER PTHR23127:SF0 H/ACA RIBONUCLEOPROTEIN COMPLEX SUBUNIT DKC1 6 187 2.0E-89
1 g11311.t2 Pfam PF08068 DKCLD (NUC011) domain 45 101 4.0E-31
2 g11311.t2 Pfam PF01509 TruB family pseudouridylate synthase (N terminal domain) 105 186 3.6E-19
6 g11311.t2 SMART SM01136 DKCLD_2 43 101 1.2E-32
5 g11311.t2 SUPERFAMILY SSF55120 Pseudouridine synthase 45 187 1.5E-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:0006396 RNA processing BP
GO:0003723 RNA binding MF
GO:0009451 RNA modification BP
GO:0009982 pseudouridine synthase activity MF
GO:0001522 pseudouridine synthesis BP

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.

Raw TPM values