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.t6 TSS g11311.t6 15528991 15528991
chr_1 g11311 g11311.t6 isoform g11311.t6 15529055 15530999
chr_1 g11311 g11311.t6 exon g11311.t6.exon1 15529055 15529067
chr_1 g11311 g11311.t6 cds g11311.t6.CDS1 15529055 15529067
chr_1 g11311 g11311.t6 exon g11311.t6.exon2 15529130 15530544
chr_1 g11311 g11311.t6 cds g11311.t6.CDS2 15529130 15530544
chr_1 g11311 g11311.t6 exon g11311.t6.exon3 15530643 15530999
chr_1 g11311 g11311.t6 cds g11311.t6.CDS3 15530643 15530690
chr_1 g11311 g11311.t6 TTS g11311.t6 15530993 15530993

Sequences

>g11311.t6 Gene=g11311 Length=1785
ATGGCTGAAATAATTGAAAAAAAGAAGAAACAAAAGAAAAAAGTCAAGGAAGAGATTGAA
AATTTAGGCGAGATTCAAAAATCTGGTGATTTTCAAATAAAACCATCTGATGCTATTACA
AAGCTTGACAGCTCTGACTGGCCATTATTACTGAAAAATTTTGATCGTCTCAATATCAGA
ACAAATCATTATACACCATTGCCATTTGGTGCATCGCCATTAAGTCGACCAATTAAAGAA
TATGTTAAATCGGGTTTTATCAATGTAGATAAACCCTCAAATCCTTCTTCTCATGAGGTT
GTAGCATGGATTAAACGAATTCTCAAGTGCGAAAAGACTGGTCATTCTGGAACTCTCGAT
CCTAAAGTTACTGGTTGCTTGATAGTTTGTATTGACAGAGCAACACGATTGGTTAAAAGC
CAACAAAGTGCCGGTAAAGAGTACGTAGCAGTATTTAAGCTACATTCAGCTGTTGAATCA
ATTCAGAGAGTTAATCAAGGGTTGGAAAAATTACGAGGTGCACTGTTTCAACGACCACCA
TTGATTTCTGCTGTAAAAAGACAACTTCGTGTACGTACAGTGTATGATAGTTTATTACTT
GATTATGATGAAAATCGTAATATGGGTGTTTTCTGGGTGAGTTGTGAGGCTGGATCTTAC
ATCAGAACTATGTGCGTTCATTTAGGTTTAGTTCTTGGTGTAGGAGGTCAAATGTTAGAG
TTGCGTCGCGTACGTTCAGGAATTCAAAGTGAAAAGCAAGGAATGGTTACAATGCACGAT
ATTCTTGACGCTCAATACGCATATGAGAATCACAAAGATGAATCTCTTCTTCGTCGTGTC
ATTCAACCTCTTGAAGGTTTATTGATCAATCACAAAAGAATTATTGTAAAGGATAGCACT
GTAAATGCAATTTGTTATGGTGCACAAGTAATGCTTCCAGGAGTTTTACGATATGAAGAC
GGTATTGAATTGAATGATGAAATTGTAATTGTTACAACTAAGGGAGAAACAATTGCTCTG
GCGATTGCATTGATGACAACAGCAACAATGGCAAGTTGTGATCATGGCGTATGTGCAAAA
TTGAAGCGAGTGATAATGGAAAGAGACACTTATCCCCGCAAATGGGGTATGGGCCCAAAA
GCAACAAAGAAAAAGGAAATGATTTCTGCTGGACTATTAGATAAACATGGAAAGCCAAAC
GAAAACACACCAAAAGATTGGTTAAATACACATATTGAAAACAAGCCAGAAGCATCACAA
AATGGTAATGCAGTAGCAGAGGAGAGTAACAAAAGAAAATACAGCATAGGATCAGCAGGA
GATTTATCTTTGGAACTTGCTTCGCCAGAGAAGAAAAAGAAAAAAAAGAAACAAAAAATG
GATGTTGATGAACCTGAAACAGTTGTTGAAGAAGCTACAACTGCTGAGAAAAAGAAGAAG
AAAGACAAGAAAAAGGACGAGGAAGCTGATGAATAATTAGGATAAATCAGACACGAGCAT
TCAATAACTTCTTTCTATCAATAATAGTTTCTAAGTTTTTCAAGAAATAATTTTTGCATT
TCCTTTTCATGAAATTTTACGAATTGATTTAATTTTGAATTCATTAATATCTTTGATTTT
AATTATAAACCTAAAGATTAGGTTTATATAAAAATATTCAAATAAAATAAATTTTTGTCT
AACTTTAGCTTTTCAATTATTTTTACGGAATATATAAGAAATTATTGAAAAAAATAAAGC
AAGTTGCAACATTGTATGCACAAGTTTATATTTTTGAAGAAAAAA

>g11311.t6 Gene=g11311 Length=491
MAEIIEKKKKQKKKVKEEIENLGEIQKSGDFQIKPSDAITKLDSSDWPLLLKNFDRLNIR
TNHYTPLPFGASPLSRPIKEYVKSGFINVDKPSNPSSHEVVAWIKRILKCEKTGHSGTLD
PKVTGCLIVCIDRATRLVKSQQSAGKEYVAVFKLHSAVESIQRVNQGLEKLRGALFQRPP
LISAVKRQLRVRTVYDSLLLDYDENRNMGVFWVSCEAGSYIRTMCVHLGLVLGVGGQMLE
LRRVRSGIQSEKQGMVTMHDILDAQYAYENHKDESLLRRVIQPLEGLLINHKRIIVKDST
VNAICYGAQVMLPGVLRYEDGIELNDEIVIVTTKGETIALAIALMTTATMASCDHGVCAK
LKRVIMERDTYPRKWGMGPKATKKKEMISAGLLDKHGKPNENTPKDWLNTHIENKPEASQ
NGNAVAEESNKRKYSIGSAGDLSLELASPEKKKKKKKQKMDVDEPETVVEEATTAEKKKK
KDKKKDEEADE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g11311.t6 CDD cd02572 PseudoU_synth_hDyskerin 83 265 1.25387E-127
11 g11311.t6 Coils Coil Coil 1 25 -
10 g11311.t6 Gene3D G3DSA:2.30.130.70 - 46 375 3.1E-162
9 g11311.t6 Gene3D G3DSA:3.30.2350.10 Pseudouridine synthase 77 283 3.1E-162
16 g11311.t6 MobiDBLite mobidb-lite consensus disorder prediction 414 491 -
17 g11311.t6 MobiDBLite mobidb-lite consensus disorder prediction 414 428 -
15 g11311.t6 MobiDBLite mobidb-lite consensus disorder prediction 446 491 -
5 g11311.t6 PANTHER PTHR23127 CENTROMERE/MICROTUBULE BINDING PROTEIN CBF5 7 488 1.6E-231
6 g11311.t6 PANTHER PTHR23127:SF0 H/ACA RIBONUCLEOPROTEIN COMPLEX SUBUNIT DKC1 7 488 1.6E-231
2 g11311.t6 Pfam PF08068 DKCLD (NUC011) domain 45 101 2.0E-30
3 g11311.t6 Pfam PF01509 TruB family pseudouridylate synthase (N terminal domain) 105 196 3.8E-19
1 g11311.t6 Pfam PF16198 tRNA pseudouridylate synthase B C-terminal domain 222 288 3.8E-19
4 g11311.t6 Pfam PF01472 PUA domain 292 365 5.0E-19
20 g11311.t6 ProSiteProfiles PS50890 PUA domain profile. 291 366 17.191
13 g11311.t6 SMART SM01136 DKCLD_2 43 101 1.2E-32
14 g11311.t6 SMART SM00359 pua_5 292 366 1.8E-20
8 g11311.t6 SUPERFAMILY SSF55120 Pseudouridine synthase 45 289 3.12E-73
7 g11311.t6 SUPERFAMILY SSF88697 PUA domain-like 291 372 6.08E-22
19 g11311.t6 TIGRFAM TIGR00425 CBF5: putative rRNA pseudouridine synthase 51 376 8.8E-154
18 g11311.t6 TIGRFAM TIGR00451 unchar_dom_2: uncharacterized domain 2 285 361 3.2E-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

Pathway

  • This transcript belongs to the following pathways

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