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.t1 TTS g3959.t1 29276352 29276352
chr_3 g3959 g3959.t1 isoform g3959.t1 29276548 29279135
chr_3 g3959 g3959.t1 exon g3959.t1.exon1 29276548 29276658
chr_3 g3959 g3959.t1 cds g3959.t1.CDS1 29276548 29276658
chr_3 g3959 g3959.t1 exon g3959.t1.exon2 29276728 29276916
chr_3 g3959 g3959.t1 cds g3959.t1.CDS2 29276728 29276916
chr_3 g3959 g3959.t1 exon g3959.t1.exon3 29276977 29279036
chr_3 g3959 g3959.t1 cds g3959.t1.CDS3 29276977 29279036
chr_3 g3959 g3959.t1 exon g3959.t1.exon4 29279096 29279135
chr_3 g3959 g3959.t1 cds g3959.t1.CDS4 29279096 29279135
chr_3 g3959 g3959.t1 TSS g3959.t1 29279211 29279211

Sequences

>g3959.t1 Gene=g3959 Length=2400
ATGAATAGAAGACGACCTTATGAAGACGATGAAGGATATGACAGAAGACCGAAAAGACGC
CGAGTATCAGATAATCAAGAAATTGAAGATCGCTTGGAAAGTTTAATCTTGCGTGTTGGT
GAGAAAACAACTTCAAGTTTAGAATCAAATTTAGAAGGTTTAGTGGCTGTTTTGGAAGCA
GATTTGGGGACATTCAGGAATAAAATTTTGAGAATTTTAATAGACTGTGCAGTCAAACTT
CCAGAGAAATGTACCATTTATTCGACATTAGTGGGCTTGTTAAATGCCAAAAATTACAAT
TTTGGGGGCGAATTTGTTGATCACATGGTTAAGAATTTTAAGGATAGTCTTAAAAATTGT
AAATGGGATTCAGCTCGCTATTCTCTTCGTTTTCTCGCTGATTTAGTGAATTGCAATGTT
ATCTCAGCAGTTTCTTTGCTTCAACTTTTGGAATCTATGGTTGATGCGAGTACTGATGAT
ACCGTTCCACAAGTTAGACGTGATTGGTATGTTTTCTCAGTTTTATCAACTTTACCTTGG
GTAGGAAGAGATTTGTATGAGAAAAAAGAATCAGCATTAGAAAATTTACTTGTACGCATT
GAAATCTTTCTTAATAAGAGAACAAAGAAACATCATAATGCACTTCGAGTCTGGTCAGTT
GATGCACCACATCCTCAAGAGGAATATTTAGATTGTTTGTGGGCACAAATAAGAAAATTG
CGCAATGAGTCATGGGCTGAAAAGTACATTCCTCGACCATATTTGGCATTTGATTCTATT
CTTTGTGAAGCACTACAGCATTCTTTGCCGCAAATTACACCACCACCTCATCATGAGAGT
TATGTTTACCCTATGCCATGGGTTGTTTATAGAATGTTTGATTATACAGATTGTCCAGAT
GGACCGATTTTACCCGGTGCTCATTCAATCGAAAGATTTTTAATTGAAGAACATTTGCAT
TCAATCATTGAAACTCATCATTTAGAGAGAAAAGATTGCGCCAGTCAACTTTTAAGTTTC
CCGTACAAAAACAAAATTCCACTCGAATATTGTATAGTCGAGGTTATTTTCAGTGAACTT
TTTCATATGCCAACACCTCGTTATCTGGAAGTTTGCTATGGTTCTATAATGATTGAACTT
TGTAAATTACAACCATCAACTATGCCTCAAGTTTTAGCTCAGGCAACTGAAATTCTTTTT
ATGAGAATTGATTCAATGAATACATCATGTTTTGATCGCTTTGTCAATTGGTTTTCATAT
CATTTGAGTAACTTCCAATTTCGTTGGTCATGGGATGATTGGGATAGTTGCTTATTCTTG
GAACCAGAGCATCCGAGACCAAAGTTTATTCAAGAAGTCTTACAAAAATGCTTAAGATTA
TCCTATTATCAACGCATAAAGGATATGATGCCTGTAGCTTACGAAAAGTTGCTGCCACCA
ATGACTACACCAGAATATAAATATACTTCTGAAGATGCTGCTTCTTTACCAGGAACAGCA
ACTGCTCACAAACTTGTCGTAGCTATTCGTCAAAAATGTACACCAGAAGAAATCCTTAAT
GAACTCAAAGATTTGCCAAATCCACGCGATACTGAAAATGACATGGTAGAGTCAACATTT
AATCCACTGAAAATTGATGTTTTCACTCAAACACTTTTGAATTTGGGTTCAAAGAGTTTT
TCACATACATTTGCGGCAATTTCAAAGTTTCACTATGTCTTTAAACAGCTTGCTGATTCT
GAAGAAGCTCAAATATGCATATTGCATAATGTATTTGAATTGTGGCGTAATCATCAGCAA
ATGATAGTTGTTATTGTTGATAAATTACTAAAAACTCAGATTGTTGAGTGTTCTTCTGTC
GCTACTTGGGTTTTTTCAAAAGAAATGTCATCAGAATTTACTAAAATGTATTTATGGGAA
ATTTTACATTTGACTATAAAGAAAATGAACAAACACGTTATGAAATTGAGTGCAGAATTA
GCTGATGCAAAAGAAAAGTTAGCTAAAGATGCTGATTCATCATCGAGTGACGATTCAGAT
AATGAAAGCATGACACCTAAAAAGAAAAAAGATGAGACAGTGGAAAAACCAACAGAAGAA
GCTGTAGAAAAGATGGAAGAAAAACTTGAAGCAGCATATGGTGATCAAAAGAGAATCTTT
TTAATCATATTTCAACGTTTCATCATGATTCTTTCGGAACATTTAGTTAAATGTGACACT
GATGGTAGAGATTTTAGTACTGATTGGTATCGTTGGACAATTGGACGATTACAGCAAGTT
TTTCTTGTCCATCACGAGCAGGTTCAAAAGTACTCGAGTACATTGGAAAGTCTTCTTTTT
ACGCAAGTCGATTCTCATATATTGGACGTTTTTCTACAATTTGTTGCACTTACAAAATAA

>g3959.t1 Gene=g3959 Length=799
MNRRRPYEDDEGYDRRPKRRRVSDNQEIEDRLESLILRVGEKTTSSLESNLEGLVAVLEA
DLGTFRNKILRILIDCAVKLPEKCTIYSTLVGLLNAKNYNFGGEFVDHMVKNFKDSLKNC
KWDSARYSLRFLADLVNCNVISAVSLLQLLESMVDASTDDTVPQVRRDWYVFSVLSTLPW
VGRDLYEKKESALENLLVRIEIFLNKRTKKHHNALRVWSVDAPHPQEEYLDCLWAQIRKL
RNESWAEKYIPRPYLAFDSILCEALQHSLPQITPPPHHESYVYPMPWVVYRMFDYTDCPD
GPILPGAHSIERFLIEEHLHSIIETHHLERKDCASQLLSFPYKNKIPLEYCIVEVIFSEL
FHMPTPRYLEVCYGSIMIELCKLQPSTMPQVLAQATEILFMRIDSMNTSCFDRFVNWFSY
HLSNFQFRWSWDDWDSCLFLEPEHPRPKFIQEVLQKCLRLSYYQRIKDMMPVAYEKLLPP
MTTPEYKYTSEDAASLPGTATAHKLVVAIRQKCTPEEILNELKDLPNPRDTENDMVESTF
NPLKIDVFTQTLLNLGSKSFSHTFAAISKFHYVFKQLADSEEAQICILHNVFELWRNHQQ
MIVVIVDKLLKTQIVECSSVATWVFSKEMSSEFTKMYLWEILHLTIKKMNKHVMKLSAEL
ADAKEKLAKDADSSSSDDSDNESMTPKKKKDETVEKPTEEAVEKMEEKLEAAYGDQKRIF
LIIFQRFIMILSEHLVKCDTDGRDFSTDWYRWTIGRLQQVFLVHHEQVQKYSSTLESLLF
TQVDSHILDVFLQFVALTK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g3959.t1 Coils Coil Coil 646 666 -
13 g3959.t1 Gene3D G3DSA:1.25.40.180 - 1 290 1.5E-110
14 g3959.t1 Gene3D G3DSA:1.25.40.180 - 291 482 8.1E-84
12 g3959.t1 Gene3D G3DSA:1.25.40.180 - 490 682 3.1E-69
11 g3959.t1 Gene3D G3DSA:1.25.40.180 - 694 797 4.8E-31
10 g3959.t1 MobiDBLite mobidb-lite consensus disorder prediction 1 24 -
9 g3959.t1 MobiDBLite mobidb-lite consensus disorder prediction 668 701 -
4 g3959.t1 PANTHER PTHR12412 CAP BINDING PROTEIN 1 798 1.8E-283
1 g3959.t1 Pfam PF02854 MIF4G domain 44 239 3.1E-23
3 g3959.t1 Pfam PF09088 MIF4G like 345 471 3.4E-36
2 g3959.t1 Pfam PF09090 MIF4G like 486 770 2.0E-93
8 g3959.t1 SMART SM00543 if4_15 29 241 3.3E-38
7 g3959.t1 SUPERFAMILY SSF48371 ARM repeat 29 290 2.07E-86
6 g3959.t1 SUPERFAMILY SSF48371 ARM repeat 292 480 7.91E-76
5 g3959.t1 SUPERFAMILY SSF48371 ARM repeat 483 797 1.21E-100

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

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.

Raw TPM values