Gene loci information

Transcript annotation

  • This transcript has been annotated as U1 small nuclear ribonucleoprotein A.

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 g11724 g11724.t5 TTS g11724.t5 18081733 18081733
chr_1 g11724 g11724.t5 isoform g11724.t5 18081772 18082605
chr_1 g11724 g11724.t5 exon g11724.t5.exon1 18081772 18082069
chr_1 g11724 g11724.t5 cds g11724.t5.CDS1 18081772 18082069
chr_1 g11724 g11724.t5 exon g11724.t5.exon2 18082134 18082266
chr_1 g11724 g11724.t5 cds g11724.t5.CDS2 18082134 18082266
chr_1 g11724 g11724.t5 exon g11724.t5.exon3 18082335 18082413
chr_1 g11724 g11724.t5 cds g11724.t5.CDS3 18082335 18082404
chr_1 g11724 g11724.t5 exon g11724.t5.exon4 18082465 18082605
chr_1 g11724 g11724.t5 TSS g11724.t5 18082678 18082678

Sequences

>g11724.t5 Gene=g11724 Length=651
ATGGATATTCGTCCAAATCATACTATCTATGTGAATAATTTAAATGAAAAGGTGAAAAAG
GACGAGTTAAAAAAGTCTCTTTACGCCATTTTTAGTCAATTTGGACAAATTTTGGATATT
ATTGCTCTTAAAACATTAAAGTTTATTTAGATGAGAGGACAAGCATTCATAATCTTTAAG
GAAATAAACAGTGCTACGAATGCATTAAGAACAATGCAAGGATTTCCATTTTATGATAAA
CCAATGAAAATTAACTATGCGAAAACGGAAAGCGATGTAATTGCAAAGGCTAAAGGAACA
TTCAAAGAAAGAGCAAAAAAAGTTAAATTACCGAAATCGACTGAAGAGAAGAAAGCTAAA
AAGAAATCTGTTGATCCTGCACAAGCTGCAATTAATAGTTCTTCGATTGAGCAGCCACCT
AACCAGATTCTTTTCCTTACGAATTTACCAGATGAAACAAATGAAATGATGCTTAGCATG
CTCTTCAATCAATTCCCAGGATTTAAAGAGGTCCGTTTGGTACCAGGTCGTCATGATATT
GCATTTGTCGAGTTTGCATCAGAAATTCAAAGTGGTGCTGCTCGTGAAGCTCTTAATGGT
TTCAAAATAACACCAACACATGCAATGAAAATTTCATTTGCTAAGAAATAA

>g11724.t5 Gene=g11724 Length=166
MRGQAFIIFKEINSATNALRTMQGFPFYDKPMKINYAKTESDVIAKAKGTFKERAKKVKL
PKSTEEKKAKKKSVDPAQAAINSSSIEQPPNQILFLTNLPDETNEMMLSMLFNQFPGFKE
VRLVPGRHDIAFVEFASEIQSGAAREALNGFKITPTHAMKISFAKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g11724.t5 CDD cd12479 RRM2_SNF 87 166 5.6544E-51
8 g11724.t5 Gene3D G3DSA:3.30.70.330 - 1 58 1.8E-12
7 g11724.t5 Gene3D G3DSA:3.30.70.330 - 85 166 4.2E-22
11 g11724.t5 MobiDBLite mobidb-lite consensus disorder prediction 58 83 -
12 g11724.t5 MobiDBLite mobidb-lite consensus disorder prediction 58 74 -
3 g11724.t5 PANTHER PTHR10501:SF63 U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A 1 83 1.2E-74
5 g11724.t5 PANTHER PTHR10501 U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A/U2 SMALL NUCLEAR RIBONUCLEOPROTEIN B 1 83 1.2E-74
2 g11724.t5 PANTHER PTHR10501:SF63 U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A 87 166 1.2E-74
4 g11724.t5 PANTHER PTHR10501 U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A/U2 SMALL NUCLEAR RIBONUCLEOPROTEIN B 87 166 1.2E-74
1 g11724.t5 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 94 153 1.6E-13
13 g11724.t5 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 1 39 8.689
14 g11724.t5 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 92 166 12.168
10 g11724.t5 SMART SM00360 rrm1_1 93 162 8.4E-11
6 g11724.t5 SUPERFAMILY SSF54928 RNA-binding domain, RBD 2 154 4.96E-18

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:0003676 nucleic acid binding MF

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