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.t9 TSS g11311.t9 15528991 15528991
chr_1 g11311 g11311.t9 isoform g11311.t9 15529679 15530999
chr_1 g11311 g11311.t9 exon g11311.t9.exon1 15529679 15530544
chr_1 g11311 g11311.t9 cds g11311.t9.CDS1 15529738 15530544
chr_1 g11311 g11311.t9 exon g11311.t9.exon2 15530649 15530999
chr_1 g11311 g11311.t9 cds g11311.t9.CDS2 15530649 15530690
chr_1 g11311 g11311.t9 TTS g11311.t9 15530993 15530993

Sequences

>g11311.t9 Gene=g11311 Length=1217
AACTTCGTGTACGTACAGTGTATGATAGTTTATTACTTGATTATGATGAAAATCGTAATA
TGGGTGTTTTCTGGGTGAGTTGTGAGGCTGGATCTTACATCAGAACTATGTGCGTTCATT
TAGGTTTAGTTCTTGGTGTAGGAGGTCAAATGTTAGAGTTGCGTCGCGTACGTTCAGGAA
TTCAAAGTGAAAAGCAAGGAATGGTTACAATGCACGATATTCTTGACGCTCAATACGCAT
ATGAGAATCACAAAGATGAATCTCTTCTTCGTCGTGTCATTCAACCTCTTGAAGGTTTAT
TGATCAATCACAAAAGAATTATTGTAAAGGATAGCACTGTAAATGCAATTTGTTATGGTG
CACAAGTAATGCTTCCAGGAGTTTTACGATATGAAGACGGTATTGAATTGAATGATGAAA
TTGTAATTGTTACAACTAAGGGAGAAACAATTGCTCTGGCGATTGCATTGATGACAACAG
CAACAATGGCAAGTTGTGATCATGGCGTATGTGCAAAATTGAAGCGAGTGATAATGGAAA
GAGACACTTATCCCCGCAAATGGGGTATGGGCCCAAAAGCAACAAAGAAAAAGGAAATGA
TTTCTGCTGGACTATTAGATAAACATGGAAAGCCAAACGAAAACACACCAAAAGATTGGT
TAAATACACATATTGAAAACAAGCCAGAAGCATCACAAAATGGTAATGCAGTAGCAGAGG
AGAGTAACAAAAGAAAATACAGCATAGGATCAGCAGGAGATTTATCTTTGGAACTTGCTT
CGCCAGAGAAGAAAAAGAAAAAAAAGAAACAAAAAATGGATGTTGATGAACCTGAAACAG
TTGTTGAAGAAGCTACAACTGCTGAGAAGAAGAAAGACAAGAAAAAGGACGAGGAAGCTG
ATGAATAATTAGGATAAATCAGACACGAGCATTCAATAACTTCTTTCTATCAATAATAGT
TTCTAAGTTTTTCAAGAAATAATTTTTGCATTTCCTTTTCATGAAATTTTACGAATTGAT
TTAATTTTGAATTCATTAATATCTTTGATTTTAATTATAAACCTAAAGATTAGGTTTATA
TAAAAATATTCAAATAAAATAAATTTTTGTCTAACTTTAGCTTTTCAATTATTTTTACGG
AATATATAAGAAATTATTGAAAAAAATAAAGCAAGTTGCAACATTGTATGCACAAGTTTA
TATTTTTGAAGAAAAAA

>g11311.t9 Gene=g11311 Length=282
MGVFWVSCEAGSYIRTMCVHLGLVLGVGGQMLELRRVRSGIQSEKQGMVTMHDILDAQYA
YENHKDESLLRRVIQPLEGLLINHKRIIVKDSTVNAICYGAQVMLPGVLRYEDGIELNDE
IVIVTTKGETIALAIALMTTATMASCDHGVCAKLKRVIMERDTYPRKWGMGPKATKKKEM
ISAGLLDKHGKPNENTPKDWLNTHIENKPEASQNGNAVAEESNKRKYSIGSAGDLSLELA
SPEKKKKKKKQKMDVDEPETVVEEATTAEKKKDKKKDEEADE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g11311.t9 Gene3D G3DSA:3.30.2350.10 Pseudouridine synthase 1 76 4.5E-17
8 g11311.t9 Gene3D G3DSA:2.30.130.10 - 81 196 3.9E-56
14 g11311.t9 MobiDBLite mobidb-lite consensus disorder prediction 207 221 -
15 g11311.t9 MobiDBLite mobidb-lite consensus disorder prediction 207 282 -
13 g11311.t9 MobiDBLite mobidb-lite consensus disorder prediction 239 282 -
3 g11311.t9 PANTHER PTHR23127 CENTROMERE/MICROTUBULE BINDING PROTEIN CBF5 1 278 2.4E-119
4 g11311.t9 PANTHER PTHR23127:SF0 H/ACA RIBONUCLEOPROTEIN COMPLEX SUBUNIT DKC1 1 278 2.4E-119
1 g11311.t9 Pfam PF16198 tRNA pseudouridylate synthase B C-terminal domain 15 81 1.6E-19
2 g11311.t9 Pfam PF01472 PUA domain 85 158 2.0E-19
10 g11311.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 11 -
11 g11311.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 32 -
9 g11311.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 33 282 -
18 g11311.t9 ProSiteProfiles PS50890 PUA domain profile. 84 159 17.191
12 g11311.t9 SMART SM00359 pua_5 85 159 1.8E-20
6 g11311.t9 SUPERFAMILY SSF55120 Pseudouridine synthase 3 82 4.03E-20
5 g11311.t9 SUPERFAMILY SSF88697 PUA domain-like 84 165 2.27E-22
17 g11311.t9 TIGRFAM TIGR00425 CBF5: putative rRNA pseudouridine synthase 2 169 4.1E-76
16 g11311.t9 TIGRFAM TIGR00451 unchar_dom_2: uncharacterized domain 2 78 154 1.2E-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