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.t7 TSS g11311.t7 15528991 15528991
chr_1 g11311 g11311.t7 isoform g11311.t7 15529679 15530690
chr_1 g11311 g11311.t7 exon g11311.t7.exon1 15529679 15530550
chr_1 g11311 g11311.t7 cds g11311.t7.CDS1 15529738 15530550
chr_1 g11311 g11311.t7 exon g11311.t7.exon2 15530622 15530690
chr_1 g11311 g11311.t7 cds g11311.t7.CDS2 15530622 15530690
chr_1 g11311 g11311.t7 TTS g11311.t7 15530993 15530993

Sequences

>g11311.t7 Gene=g11311 Length=941
AACTTCGTGTACGTACAGTGTATGATAGTTTATTACTTGATTATGATGAAAATCGTAATA
TGGGTGTTTTCTGGGTGAGTTGTGAGGCTGGATCTTACATCAGAACTATGTGCGTTCATT
TAGGTTTAGTTCTTGGTGTAGGAGGTCAAATGTTAGAGTTGCGTCGCGTACGTTCAGGAA
TTCAAAGTGAAAAGCAAGGAATGGTTACAATGCACGATATTCTTGACGCTCAATACGCAT
ATGAGAATCACAAAGATGAATCTCTTCTTCGTCGTGTCATTCAACCTCTTGAAGGTTTAT
TGATCAATCACAAAAGAATTATTGTAAAGGATAGCACTGTAAATGCAATTTGTTATGGTG
CACAAGTAATGCTTCCAGGAGTTTTACGATATGAAGACGGTATTGAATTGAATGATGAAA
TTGTAATTGTTACAACTAAGGGAGAAACAATTGCTCTGGCGATTGCATTGATGACAACAG
CAACAATGGCAAGTTGTGATCATGGCGTATGTGCAAAATTGAAGCGAGTGATAATGGAAA
GAGACACTTATCCCCGCAAATGGGGTATGGGCCCAAAAGCAACAAAGAAAAAGGAAATGA
TTTCTGCTGGACTATTAGATAAACATGGAAAGCCAAACGAAAACACACCAAAAGATTGGT
TAAATACACATATTGAAAACAAGCCAGAAGCATCACAAAATGGTAATGCAGTAGCAGAGG
AGAGTAACAAAAGAAAATACAGCATAGGATCAGCAGGAGATTTATCTTTGGAACTTGCTT
CGCCAGAGAAGAAAAAGAAAAAAAAGAAACAAAAAATGGATGTTGATGAACCTGAAACAG
TTGTTGAAGAAGCTACAACTGCTGAGGTAGTTGAACCTACAAGTGAAAAAAAGAAAAAGA
AGAAGAAAGACAAGAAAAAGGACGAGGAAGCTGATGAATAA

>g11311.t7 Gene=g11311 Length=293
MGVFWVSCEAGSYIRTMCVHLGLVLGVGGQMLELRRVRSGIQSEKQGMVTMHDILDAQYA
YENHKDESLLRRVIQPLEGLLINHKRIIVKDSTVNAICYGAQVMLPGVLRYEDGIELNDE
IVIVTTKGETIALAIALMTTATMASCDHGVCAKLKRVIMERDTYPRKWGMGPKATKKKEM
ISAGLLDKHGKPNENTPKDWLNTHIENKPEASQNGNAVAEESNKRKYSIGSAGDLSLELA
SPEKKKKKKKQKMDVDEPETVVEEATTAEVVEPTSEKKKKKKKDKKKDEEADE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g11311.t7 Gene3D G3DSA:3.30.2350.10 Pseudouridine synthase 1 76 4.8E-17
8 g11311.t7 Gene3D G3DSA:2.30.130.10 - 81 196 4.3E-56
10 g11311.t7 MobiDBLite mobidb-lite consensus disorder prediction 207 221 -
12 g11311.t7 MobiDBLite mobidb-lite consensus disorder prediction 207 293 -
11 g11311.t7 MobiDBLite mobidb-lite consensus disorder prediction 239 259 -
13 g11311.t7 MobiDBLite mobidb-lite consensus disorder prediction 270 293 -
3 g11311.t7 PANTHER PTHR23127 CENTROMERE/MICROTUBULE BINDING PROTEIN CBF5 1 290 4.1E-121
4 g11311.t7 PANTHER PTHR23127:SF0 H/ACA RIBONUCLEOPROTEIN COMPLEX SUBUNIT DKC1 1 290 4.1E-121
1 g11311.t7 Pfam PF16198 tRNA pseudouridylate synthase B C-terminal domain 15 81 1.7E-19
2 g11311.t7 Pfam PF01472 PUA domain 85 158 2.1E-19
14 g11311.t7 ProSiteProfiles PS50890 PUA domain profile. 84 159 17.191
9 g11311.t7 SMART SM00359 pua_5 85 159 1.8E-20
6 g11311.t7 SUPERFAMILY SSF55120 Pseudouridine synthase 3 82 4.6E-20
5 g11311.t7 SUPERFAMILY SSF88697 PUA domain-like 84 165 2.49E-22
16 g11311.t7 TIGRFAM TIGR00425 CBF5: putative rRNA pseudouridine synthase 2 169 4.6E-76
15 g11311.t7 TIGRFAM TIGR00451 unchar_dom_2: uncharacterized domain 2 78 154 1.3E-9

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