Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Probable H/ACA ribonucleoprotein complex subunit 1.

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_2 g5341 g5341.t8 TTS g5341.t8 9017475 9017475
chr_2 g5341 g5341.t8 isoform g5341.t8 9017585 9018740
chr_2 g5341 g5341.t8 exon g5341.t8.exon1 9017585 9017616
chr_2 g5341 g5341.t8 cds g5341.t8.CDS1 9017585 9017616
chr_2 g5341 g5341.t8 exon g5341.t8.exon2 9017678 9017707
chr_2 g5341 g5341.t8 cds g5341.t8.CDS2 9017678 9017707
chr_2 g5341 g5341.t8 exon g5341.t8.exon3 9017781 9017819
chr_2 g5341 g5341.t8 cds g5341.t8.CDS3 9017781 9017819
chr_2 g5341 g5341.t8 exon g5341.t8.exon4 9018023 9018409
chr_2 g5341 g5341.t8 cds g5341.t8.CDS4 9018023 9018409
chr_2 g5341 g5341.t8 exon g5341.t8.exon5 9018473 9018562
chr_2 g5341 g5341.t8 cds g5341.t8.CDS5 9018473 9018562
chr_2 g5341 g5341.t8 exon g5341.t8.exon6 9018695 9018740
chr_2 g5341 g5341.t8 cds g5341.t8.CDS6 9018695 9018740
chr_2 g5341 g5341.t8 TSS g5341.t8 9018838 9018838

Sequences

>g5341.t8 Gene=g5341 Length=624
ATGGGATTTGGAGGTCGAGGAGGTGGTAATCGTGGAGGTGAGCTTTGCGGCAATCGAGGT
GGAGGAGGAGGACGAGGCGGCTTTGGAAATAAAGGAAAATTTGACCAAGGGCCGCCGGCA
AGAGTTGTTCCATTTGGATATTTTGATTACACATGTCAAGATGATCTTGTTCTTAAAGCA
GAAATTGAAGACGTTCCCTATTTCAATGCACCAATTTTTCTTGAAAACAAATCACAAATC
GGAAAAATTGATGAGATTTTTGGAACATTACGTGATTATTCAGTGTCAGTGAAATTGGGT
GAAAATATGAAAGCATCAAGTTTTGTGCCGAAACAGAAACTTTTTATTGATCCAGCCAAG
TTACTTCCATTACAAAGATTTTTACCGCAACCACCAAAGCCGAAAGGAATTGGAAAGAAA
AAGAAAGGAGACAAGTCACAAGCTGGTGCAGCTGGTGGAAACAATTCATTTGGAGCAAAA
CGTGGAGGATTTGGCGGAAGAGGTAGTGGTGGTGGTCGAGGAAGAGGAGCTGGTGGAAAT
AGAGGTGGTGGTGGCGGTTTTAATCGTGGACGTGGTGGTGGCGGTGGATTTAATCGTGGA
GGAGGTGGTGGTAAAAGATGGTAG

>g5341.t8 Gene=g5341 Length=207
MGFGGRGGGNRGGELCGNRGGGGGRGGFGNKGKFDQGPPARVVPFGYFDYTCQDDLVLKA
EIEDVPYFNAPIFLENKSQIGKIDEIFGTLRDYSVSVKLGENMKASSFVPKQKLFIDPAK
LLPLQRFLPQPPKPKGIGKKKKGDKSQAGAAGGNNSFGAKRGGFGGRGSGGGRGRGAGGN
RGGGGGFNRGRGGGGGFNRGGGGGKRW

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g5341.t8 Gene3D G3DSA:2.40.10.230 Probable tRNA pseudouridine synthase domain 38 129 7.8E-36
5 g5341.t8 MobiDBLite mobidb-lite consensus disorder prediction 125 207 -
2 g5341.t8 PANTHER PTHR23237 NUCLEOLAR PROTEIN FAMILY A MEMBER 1 SNORNP PROTEIN GAR1 4 179 8.6E-45
3 g5341.t8 PANTHER PTHR23237:SF6 H/ACA RIBONUCLEOPROTEIN COMPLEX SUBUNIT 1 4 179 8.6E-45
1 g5341.t8 Pfam PF04410 Gar1/Naf1 RNA binding region 30 130 2.3E-31
4 g5341.t8 SUPERFAMILY SSF50447 Translation proteins 43 117 8.12E-13

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5341/g5341.t8; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5341.t8.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0042254 ribosome biogenesis BP
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. There were no conditions that were differentially expressed