Gene loci information

Transcript annotation

  • This transcript has been annotated as Nuclear cap-binding protein 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_3 g3959 g3959.t5 TTS g3959.t5 29277019 29277019
chr_3 g3959 g3959.t5 isoform g3959.t5 29277905 29279135
chr_3 g3959 g3959.t5 exon g3959.t5.exon1 29277905 29279036
chr_3 g3959 g3959.t5 cds g3959.t5.CDS1 29277907 29279036
chr_3 g3959 g3959.t5 exon g3959.t5.exon2 29279096 29279135
chr_3 g3959 g3959.t5 cds g3959.t5.CDS2 29279096 29279135
chr_3 g3959 g3959.t5 TSS g3959.t5 29279211 29279211

Sequences

>g3959.t5 Gene=g3959 Length=1172
ATGAATAGAAGACGACCTTATGAAGACGATGAAGGATATGACAGAAGACCGAAAAGACGC
CGAGTATCAGATAATCAAGAAATTGAAGATCGCTTGGAAAGTTTAATCTTGCGTGTTGGT
GAGAAAACAACTTCAAGTTTAGAATCAAATTTAGAAGGTTTAGTGGCTGTTTTGGAAGCA
GATTTGGGGACATTCAGGAATAAAATTTTGAGAATTTTAATAGACTGTGCAGTCAAACTT
CCAGAGAAATGTACCATTTATTCGACATTAGTGGGCTTGTTAAATGCCAAAAATTACAAT
TTTGGGGGCGAATTTGTTGATCACATGGTTAAGAATTTTAAGGATAGTCTTAAAAATTGT
AAATGGGATTCAGCTCGCTATTCTCTTCGTTTTCTCGCTGATTTAGTGAATTGCAATGTT
ATCTCAGCAGTTTCTTTGCTTCAACTTTTGGAATCTATGGTTGATGCGAGTACTGATGAT
ACCGTTCCACAAGTTAGACGTGATTGGTATGTTTTCTCAGTTTTATCAACTTTACCTTGG
GTAGGAAGAGATTTGTATGAGAAAAAAGAATCAGCATTAGAAAATTTACTTGTACGCATT
GAAATCTTTCTTAATAAGAGAACAAAGAAACATCATAATGCACTTCGAGTCTGGTCAGTT
GATGCACCACATCCTCAAGAGGAATATTTAGATTGTTTGTGGGCACAAATAAGAAAATTG
CGCAATGAGTCATGGGCTGAAAAGTACATTCCTCGACCATATTTGGCATTTGATTCTATT
CTTTGTGAAGCACTACAGCATTCTTTGCCGCAAATTACACCACCACCTCATCATGAGAGT
TATGTTTACCCTATGCCATGGGTTGTTTATAGAATGTTTGATTATACAGATTGTCCAGAT
GGACCGATTTTACCCGGTGCTCATTCAATCGAAAGATTTTTAATTGAAGAACATTTGCAT
TCAATCATTGAAACTCATCATTTAGAGAGAAAAGATTGCGCCAGTCAACTTTTAAGTTTC
CCGTACAAAAACAAAATTCCACTCGAATATTGTATAGTCGAGGTTATTTTCAGTGAACTT
TTTCATATGCCAACACCTCGTTATCTGGAAGTTTGCTATGGTTCTATAATGATTGAACTT
TGTAAATTACAACCATCAACTATGCCTCAAGT

>g3959.t5 Gene=g3959 Length=390
MNRRRPYEDDEGYDRRPKRRRVSDNQEIEDRLESLILRVGEKTTSSLESNLEGLVAVLEA
DLGTFRNKILRILIDCAVKLPEKCTIYSTLVGLLNAKNYNFGGEFVDHMVKNFKDSLKNC
KWDSARYSLRFLADLVNCNVISAVSLLQLLESMVDASTDDTVPQVRRDWYVFSVLSTLPW
VGRDLYEKKESALENLLVRIEIFLNKRTKKHHNALRVWSVDAPHPQEEYLDCLWAQIRKL
RNESWAEKYIPRPYLAFDSILCEALQHSLPQITPPPHHESYVYPMPWVVYRMFDYTDCPD
GPILPGAHSIERFLIEEHLHSIIETHHLERKDCASQLLSFPYKNKIPLEYCIVEVIFSEL
FHMPTPRYLEVCYGSIMIELCKLQPSTMPQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g3959.t5 Gene3D G3DSA:1.25.40.180 - 1 290 2.3E-111
8 g3959.t5 Gene3D G3DSA:1.25.40.180 - 291 390 2.4E-37
7 g3959.t5 MobiDBLite mobidb-lite consensus disorder prediction 1 24 -
3 g3959.t5 PANTHER PTHR12412 CAP BINDING PROTEIN 1 390 2.2E-133
1 g3959.t5 Pfam PF02854 MIF4G domain 44 239 6.8E-24
2 g3959.t5 Pfam PF09088 MIF4G like 345 388 8.1E-6
6 g3959.t5 SMART SM00543 if4_15 29 241 3.3E-38
5 g3959.t5 SUPERFAMILY SSF48371 ARM repeat 29 290 3.51E-87
4 g3959.t5 SUPERFAMILY SSF48371 ARM repeat 292 390 6.33E-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:0016070 RNA metabolic process BP
GO:0003723 RNA binding MF
GO:0005515 protein binding MF
GO:0000339 RNA cap binding MF
GO:0045292 mRNA cis splicing, via spliceosome BP
GO:0051028 mRNA transport BP
GO:0005846 nuclear cap binding complex CC

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