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.t5 TSS g11061.t5 13736261 13736261
chr_1 g11061 g11061.t5 isoform g11061.t5 13736448 13739132
chr_1 g11061 g11061.t5 exon g11061.t5.exon1 13736448 13736591
chr_1 g11061 g11061.t5 cds g11061.t5.CDS1 13736448 13736591
chr_1 g11061 g11061.t5 exon g11061.t5.exon2 13736654 13736836
chr_1 g11061 g11061.t5 cds g11061.t5.CDS2 13736654 13736836
chr_1 g11061 g11061.t5 exon g11061.t5.exon3 13736900 13737044
chr_1 g11061 g11061.t5 cds g11061.t5.CDS3 13736900 13737044
chr_1 g11061 g11061.t5 exon g11061.t5.exon4 13738147 13738386
chr_1 g11061 g11061.t5 cds g11061.t5.CDS4 13738147 13738386
chr_1 g11061 g11061.t5 exon g11061.t5.exon5 13738617 13738797
chr_1 g11061 g11061.t5 cds g11061.t5.CDS5 13738617 13738627
chr_1 g11061 g11061.t5 exon g11061.t5.exon6 13739002 13739132
chr_1 g11061 g11061.t5 TTS g11061.t5 13739293 13739293

Sequences

>g11061.t5 Gene=g11061 Length=1024
ATGACTCAATATCTGCCAGCCAATTTATTGGCTTTATTCGCTGCTCGCGATCCTATTCCA
TTTTTGCCACCTCCTGATAAACTTCCACATGAGAAAAAGACGCGAGGATATTTAGGAGTT
GGTTCATTTTTAGATCAATTTGAGGATCCTAAAGATACACCACCACCCACAAGAGTCGAA
ACAAAAGAAGAACGAATGGAAAGACGTCGAAGAGAAAAAGCTGAGCAAGTAGCTTACAAG
CTTGAACGAGAAATAGCACTTTGGGATCCAACATCGATCGAAAATACAACAGAAGATCCT
TTCAAAACACTTTTTGTTGCTCGTATAAATTATGACACATCAGAATCGAAATTAAGAAGA
GAATTTGAAGTGTATGGACCAATAAGGAAAATTATAATGATCCACGATCAAGATTCAGGC
AAACCTCGTGGTTATGCGTTTATTGAGTACGAACATGAAAGAGACATGCATTCTGCATAC
AAACATGCTGATGGTAAAAAAATTGATGGTAGAAGGGTATTGGTTGACGTTGAACGTGCA
AGAACAGTTAAAGGATGGTTACCTCGAAGACTTGGAGGTGGTTTAGGTGGAACAAGACGT
GGTGGTGCTGAGGTAAATATTAAGCACAGTGGACGAGAAGATAATGTACGTGAAAAGGAG
AGATATCGTCTTGAAAGAGAAAGAGAAGATAATCGTCGTCTTGATGATAGAATTTTCTTT
TGAAACTTCAAATAAATTTATTTATTAAAGAACAAATTTCAATTGTAGAGATCGTTCTGA
ACGTAAACGCGATAAACGTGATCGTTCTAGATCACGTGAAAGACGCCGTGATAAGGACAA
GAAAGAGCGTAAACCAGAGTTCGATATTAAAATTAAGGAAGAACCCATTGATGATTATCC
GGACTACACGCAACATGATTATGGTCAATATGCCAATCAAGTTAAGTATGAATCAGGTGA
TGAAGAAAAATATAGACCAAATGAGCAAGATGGAGCCGCTTATGGTTATCGACAAGATTA
TTAA

>g11061.t5 Gene=g11061 Length=240
MTQYLPANLLALFAARDPIPFLPPPDKLPHEKKTRGYLGVGSFLDQFEDPKDTPPPTRVE
TKEERMERRRREKAEQVAYKLEREIALWDPTSIENTTEDPFKTLFVARINYDTSESKLRR
EFEVYGPIRKIIMIHDQDSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERA
RTVKGWLPRRLGGGLGGTRRGGAEVNIKHSGREDNVREKERYRLEREREDNRRLDDRIFF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g11061.t5 CDD cd12236 RRM_snRNP70 101 188 1.08797E-59
7 g11061.t5 Coils Coil Coil 217 237 -
6 g11061.t5 Gene3D G3DSA:3.30.70.330 - 89 214 1.1E-36
11 g11061.t5 MobiDBLite mobidb-lite consensus disorder prediction 47 71 -
10 g11061.t5 MobiDBLite mobidb-lite consensus disorder prediction 51 71 -
3 g11061.t5 PANTHER PTHR13952 U1 SMALL NUCLEAR RIBONUCLEOPROTEIN 70 KD 1 232 1.4E-95
4 g11061.t5 PANTHER PTHR13952:SF5 U1 SMALL NUCLEAR RIBONUCLEOPROTEIN 70 KDA 1 232 1.4E-95
1 g11061.t5 Pfam PF12220 U1 small nuclear ribonucleoprotein of 70kDa MW N terminal 4 91 7.4E-25
2 g11061.t5 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 104 173 1.5E-17
12 g11061.t5 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 102 180 17.933
9 g11061.t5 SMART SM00360 rrm1_1 103 176 3.5E-23
5 g11061.t5 SUPERFAMILY SSF54928 RNA-binding domain, RBD 85 202 3.76E-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

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