Gene loci information

Transcript annotation

  • This transcript has been annotated as U1 small nuclear ribonucleoprotein 70 kDa.

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 g11061 g11061.t7 TSS g11061.t7 13736261 13736261
chr_1 g11061 g11061.t7 isoform g11061.t7 13736448 13739132
chr_1 g11061 g11061.t7 exon g11061.t7.exon1 13736448 13736836
chr_1 g11061 g11061.t7 cds g11061.t7.CDS1 13736705 13736836
chr_1 g11061 g11061.t7 exon g11061.t7.exon2 13736900 13737044
chr_1 g11061 g11061.t7 cds g11061.t7.CDS2 13736900 13737044
chr_1 g11061 g11061.t7 exon g11061.t7.exon3 13738147 13738386
chr_1 g11061 g11061.t7 cds g11061.t7.CDS3 13738147 13738386
chr_1 g11061 g11061.t7 exon g11061.t7.exon4 13738446 13738611
chr_1 g11061 g11061.t7 cds g11061.t7.CDS4 13738446 13738611
chr_1 g11061 g11061.t7 exon g11061.t7.exon5 13738673 13738797
chr_1 g11061 g11061.t7 cds g11061.t7.CDS5 13738673 13738797
chr_1 g11061 g11061.t7 exon g11061.t7.exon6 13739002 13739132
chr_1 g11061 g11061.t7 cds g11061.t7.CDS6 13739002 13739132
chr_1 g11061 g11061.t7 TTS g11061.t7 13739293 13739293

Sequences

>g11061.t7 Gene=g11061 Length=1196
ATGACTCAATATCTGCCAGCCAATTTATTGGCTTTATTCGCTGCTCGCGATCCTATTCCA
TTTTTGCCACCTCCTGATAAACTTCCACATGAGAAAAAGACGCGAGGATATTTAGGAGTT
GGTTCATTTTTAGATCAATTTGAGGTAAGTCTAAAATTTCAACTTTTCTCAACTGGATCA
TAACTAGATGTCTCATTTTTGTTAAGGATCCTAAAGATACACCACCACCCACAAGAGTCG
AAACAAAAGAAGAACGAATGGAAAGACGTCGAAGAGAAAAAGCTGAGCAAGTAGCTTACA
AGCTTGAACGAGAAATAGCACTTTGGGATCCAACATCGATCGAAAATACAACAGAAGATC
CTTTCAAAACACTTTTTGTTGCTCGTATAAATTATGACACATCAGAATCGAAATTAAGAA
GAGAATTTGAAGTGTATGGACCAATAAGGAAAATTATAATGATCCACGATCAAGATTCAG
GCAAACCTCGTGGTTATGCGTTTATTGAGTACGAACATGAAAGAGACATGCATTCTGCAT
ACAAACATGCTGATGGTAAAAAAATTGATGGTAGAAGGGTATTGGTTGACGTTGAACGTG
CAAGAACAGTTAAAGGATGGTTACCTCGAAGACTTGGAGGTGGTTTAGGTGGAACAAGAC
GTGGTGGTGCTGAGGTAAATATTAAGCACAGTGGACGAGAAGATAATGTACGTGAAAAGG
AGAGATATCGTCTTGAAAGAGAAAGAGAAGATAATCGTCGTCTTGATGATAGAAGATTTG
ATAGAAGACGATCTCGATCACATGAAAAAAGTCGTGAAAGAAGACGATCTCGATCGAAAG
AACGTAGAAGACATAGGTCGCGTGAAGAAGATTATGAAAGACATGATAGAAGAGAAAAAT
CGCGTGAGAAGAAACGCCGAAGAACACGTTCTAGAGATCGAGATCGTTCTGAACGTAAAC
GCGATAAACGTGATCGTTCTAGATCACGTGAAAGACGCCGTGATAAGGACAAGAAAGAGC
GTAAACCAGAGTTCGATATTAAAATTAAGGAAGAACCCATTGATGATTATCCGGACTACA
CGCAACATGATTATGGTCAATATGCCAATCAAGTTAAGTATGAATCAGGTGATGAAGAAA
AATATAGACCAAATGAGCAAGATGGAGCCGCTTATGGTTATCGACAAGATTATTAA

>g11061.t7 Gene=g11061 Length=312
MERRRREKAEQVAYKLEREIALWDPTSIENTTEDPFKTLFVARINYDTSESKLRREFEVY
GPIRKIIMIHDQDSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERARTVKG
WLPRRLGGGLGGTRRGGAEVNIKHSGREDNVREKERYRLEREREDNRRLDDRRFDRRRSR
SHEKSRERRRSRSKERRRHRSREEDYERHDRREKSREKKRRRTRSRDRDRSERKRDKRDR
SRSRERRRDKDKKERKPEFDIKIKEEPIDDYPDYTQHDYGQYANQVKYESGDEEKYRPNE
QDGAAYGYRQDY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g11061.t7 CDD cd12236 RRM_snRNP70 36 123 1.81734E-54
6 g11061.t7 Coils Coil Coil 152 172 -
5 g11061.t7 Gene3D G3DSA:3.30.70.330 - 24 149 2.0E-36
14 g11061.t7 MobiDBLite mobidb-lite consensus disorder prediction 132 153 -
13 g11061.t7 MobiDBLite mobidb-lite consensus disorder prediction 175 274 -
11 g11061.t7 MobiDBLite mobidb-lite consensus disorder prediction 182 197 -
9 g11061.t7 MobiDBLite mobidb-lite consensus disorder prediction 198 213 -
12 g11061.t7 MobiDBLite mobidb-lite consensus disorder prediction 214 228 -
15 g11061.t7 MobiDBLite mobidb-lite consensus disorder prediction 229 273 -
10 g11061.t7 MobiDBLite mobidb-lite consensus disorder prediction 288 312 -
2 g11061.t7 PANTHER PTHR13952 U1 SMALL NUCLEAR RIBONUCLEOPROTEIN 70 KD 7 249 1.1E-72
3 g11061.t7 PANTHER PTHR13952:SF5 U1 SMALL NUCLEAR RIBONUCLEOPROTEIN 70 KDA 7 249 1.1E-72
1 g11061.t7 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 39 108 2.4E-17
16 g11061.t7 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 37 115 17.933
8 g11061.t7 SMART SM00360 rrm1_1 38 111 3.5E-23
4 g11061.t7 SUPERFAMILY SSF54928 RNA-binding domain, RBD 20 137 7.47E-29

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:0030619 U1 snRNA binding MF
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