General information for g11311.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as H/ACA ribonucleoprotein complex subunit 4.
Parent gene
- The parent gene g11311 is located on chr_1: 15529679..15530999 (+ strand)
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.t3 | TSS | g11311.t3 | 15528991 | 15528991 |
| chr_1 | g11311 | g11311.t3 | isoform | g11311.t3 | 15529055 | 15530550 |
| chr_1 | g11311 | g11311.t3 | exon | g11311.t3.exon1 | 15529055 | 15530550 |
| chr_1 | g11311 | g11311.t3 | cds | g11311.t3.CDS1 | 15529738 | 15530550 |
| chr_1 | g11311 | g11311.t3 | TTS | g11311.t3 | 15530993 | 15530993 |
Sequences
>g11311.t3 Gene=g11311 Length=1496
ATGGCTGAAATAAGTAATAAAATTATAGAAAATAAACACTATTTACTTAATTAATATTTG
TTTTATCAATTTTAGTTGAAAAAAAGAAGAAACAAAAGAAAAAAGTCAAGGAAGAGATTG
AAAATTTAGGCGAGATTCAAAAATCTGGTGATTTTCAAATAAAACCATCTGATGCTATTA
CAAAGCTTGACAGCTCTGACTGGCCATTATTACTGAAAAATTTTGATCGTCTCAATATCA
GAACAAATCATTATACACCATTGCCATTTGGTGCATCGCCATTAAGTCGACCAATTAAAG
AATATGTTAAATCGGGTTTTATCAATGTAGATAAACCCTCAAATCCTTCTTCTCATGAGG
TTGTAGCATGGATTAAACGAATTCTCAAGTGCGAAAAGACTGGTCATTCTGGAACTCTCG
ATCCTAAAGTTACTGGTTGCTTGATAGTTTGTATTGACAGAGCAACACGATTGGTTAAAA
GCCAACAAAGTGCCGGTAAAGAGTACGTAGCAGTATTTAAGCTACATTCAGCTGTTGAAT
CAATTCAGAGAGTTAATCAAGGGTTGGAAAAATTACGAGGTGCACTGTTTCAACGACCAC
CATTGATTTCTGCTGTAAAAAGACAACTTCGTGTACGTACAGTGTATGATAGTTTATTAC
TTGATTATGATGAAAATCGTAATATGGGTGTTTTCTGGGTGAGTTGTGAGGCTGGATCTT
ACATCAGAACTATGTGCGTTCATTTAGGTTTAGTTCTTGGTGTAGGAGGTCAAATGTTAG
AGTTGCGTCGCGTACGTTCAGGAATTCAAAGTGAAAAGCAAGGAATGGTTACAATGCACG
ATATTCTTGACGCTCAATACGCATATGAGAATCACAAAGATGAATCTCTTCTTCGTCGTG
TCATTCAACCTCTTGAAGGTTTATTGATCAATCACAAAAGAATTATTGTAAAGGATAGCA
CTGTAAATGCAATTTGTTATGGTGCACAAGTAATGCTTCCAGGAGTTTTACGATATGAAG
ACGGTATTGAATTGAATGATGAAATTGTAATTGTTACAACTAAGGGAGAAACAATTGCTC
TGGCGATTGCATTGATGACAACAGCAACAATGGCAAGTTGTGATCATGGCGTATGTGCAA
AATTGAAGCGAGTGATAATGGAAAGAGACACTTATCCCCGCAAATGGGGTATGGGCCCAA
AAGCAACAAAGAAAAAGGAAATGATTTCTGCTGGACTATTAGATAAACATGGAAAGCCAA
ACGAAAACACACCAAAAGATTGGTTAAATACACATATTGAAAACAAGCCAGAAGCATCAC
AAAATGGTAATGCAGTAGCAGAGGAGAGTAACAAAAGAAAATACAGCATAGGATCAGCAG
GAGATTTATCTTTGGAACTTGCTTCGCCAGAGAAGAAAAAGAAAAAAAAGAAACAAAAAA
TGGATGTTGATGAACCTGAAACAGTTGTTGAAGAAGCTACAACTGCTGAGGTAGTT
>g11311.t3 Gene=g11311 Length=271
MGVFWVSCEAGSYIRTMCVHLGLVLGVGGQMLELRRVRSGIQSEKQGMVTMHDILDAQYA
YENHKDESLLRRVIQPLEGLLINHKRIIVKDSTVNAICYGAQVMLPGVLRYEDGIELNDE
IVIVTTKGETIALAIALMTTATMASCDHGVCAKLKRVIMERDTYPRKWGMGPKATKKKEM
ISAGLLDKHGKPNENTPKDWLNTHIENKPEASQNGNAVAEESNKRKYSIGSAGDLSLELA
SPEKKKKKKKQKMDVDEPETVVEEATTAEVV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g11311.t3 | Gene3D | G3DSA:3.30.2350.10 | Pseudouridine synthase | 1 | 76 | 4.2E-17 |
| 8 | g11311.t3 | Gene3D | G3DSA:2.30.130.10 | - | 81 | 196 | 3.6E-56 |
| 13 | g11311.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 207 | 221 | - |
| 15 | g11311.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 207 | 271 | - |
| 14 | g11311.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 239 | 259 | - |
| 3 | g11311.t3 | PANTHER | PTHR23127 | CENTROMERE/MICROTUBULE BINDING PROTEIN CBF5 | 1 | 259 | 1.5E-117 |
| 4 | g11311.t3 | PANTHER | PTHR23127:SF0 | H/ACA RIBONUCLEOPROTEIN COMPLEX SUBUNIT DKC1 | 1 | 259 | 1.5E-117 |
| 1 | g11311.t3 | Pfam | PF16198 | tRNA pseudouridylate synthase B C-terminal domain | 15 | 81 | 1.5E-19 |
| 2 | g11311.t3 | Pfam | PF01472 | PUA domain | 85 | 158 | 1.8E-19 |
| 10 | g11311.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 11 | - |
| 11 | g11311.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 12 | 32 | - |
| 9 | g11311.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 33 | 271 | - |
| 18 | g11311.t3 | ProSiteProfiles | PS50890 | PUA domain profile. | 84 | 159 | 17.191 |
| 12 | g11311.t3 | SMART | SM00359 | pua_5 | 85 | 159 | 1.8E-20 |
| 6 | g11311.t3 | SUPERFAMILY | SSF55120 | Pseudouridine synthase | 3 | 82 | 3.74E-20 |
| 5 | g11311.t3 | SUPERFAMILY | SSF88697 | PUA domain-like | 84 | 165 | 2.1E-22 |
| 17 | g11311.t3 | TIGRFAM | TIGR00425 | CBF5: putative rRNA pseudouridine synthase | 2 | 169 | 3.7E-76 |
| 16 | g11311.t3 | TIGRFAM | TIGR00451 | unchar_dom_2: uncharacterized domain 2 | 78 | 154 | 1.1E-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.
