Gene loci information

Transcript annotation

  • This transcript has been annotated as mRNA export factor.

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_2 g7270 g7270.t1 TTS g7270.t1 22563692 22563692
chr_2 g7270 g7270.t1 isoform g7270.t1 22563757 22564961
chr_2 g7270 g7270.t1 exon g7270.t1.exon1 22563757 22563846
chr_2 g7270 g7270.t1 cds g7270.t1.CDS1 22563757 22563846
chr_2 g7270 g7270.t1 exon g7270.t1.exon2 22563927 22564717
chr_2 g7270 g7270.t1 cds g7270.t1.CDS2 22563927 22564717
chr_2 g7270 g7270.t1 exon g7270.t1.exon3 22564781 22564961
chr_2 g7270 g7270.t1 cds g7270.t1.CDS3 22564781 22564961
chr_2 g7270 g7270.t1 TSS g7270.t1 22565173 22565173

Sequences

>g7270.t1 Gene=g7270 Length=1062
ATGTTTTCGCAGAGTAATGTAATAAATCAATCGAATCCTATGAAGGATATCGAAGTAACA
TCTCCTCCAGATGATACAATATCTGCATTGAAATTCTCACCACAAACAATTTTACCTAAA
AATTTTCTTCTTGCTGGAAGTTGGGATTGTTCTGTAAGATGTTGGGAAGTTGCTGATACA
GGATTAACAACTCCCAAAGCAATGAAAACAATGACTGCACCAGTACTTGATGTTTGTTGG
CATGATGATGGTACAAAAGCATTTTTTGCAGGCGCTGATAAAACTGCAAGAGCGTGGGAT
TTAGCAGCTGATCAAGTCATGCAAGTTGCAGCACATGATAACACAGTCAAGACATGCCAT
TGGATTAAAGCTCCAAATTACACTTGCTTAATGACAGGTAGTTGGGATAAAACACTTAAA
TTCTGGGATTTGAGACAACAAAATCCTATTTTACAACTACAATTACCTGAAAGATGTTAT
ACAGCAGATGTAGAATACCCAATGGCAGTAGTTGGCACAGCAAATCGCCATATAATTATT
TACTCACTAGATAATCAACCTACTGAATTCAAACGATATGAAAGTCCATTAAAATATCAA
CATCGCTGTGTGTCAGTGTTTAGTGATATGAAAAAGAAACAGCCAGTTGGTTATGCTCTC
GGTTCTATTGAAGGTCGAGTTGCTATTCAATATTTGAATCCTCAGAATCCCAAAGATAAT
TTCACATTTAAATGTCATCGTGTAAATGGAGCATCAAATTTTCAAGATATTTATGCAGTT
AATGATATTGCTTTCCATCCAATTCATGGAACATTAGCAACAGTAGGATCAGATGGAACT
TTCAGTTTTTGGGATAAAGACGCAAGAACGAAACTAAAGAGTTCTGAGACAATCGATCAG
TCAATAACAAAATGCGCTTTCTCAGCTGGCGGACAGATTTTCGCATATGCAGTCGGTTAC
GATTGGTCAAAGGGTCACGAGTTTTACAATCCTCAAAAGAAAAGTTATATTTTATTAAGA
TCATGCTTTGAAGAACTCAAACCTCGTGTACACAATTCTTAA

>g7270.t1 Gene=g7270 Length=353
MFSQSNVINQSNPMKDIEVTSPPDDTISALKFSPQTILPKNFLLAGSWDCSVRCWEVADT
GLTTPKAMKTMTAPVLDVCWHDDGTKAFFAGADKTARAWDLAADQVMQVAAHDNTVKTCH
WIKAPNYTCLMTGSWDKTLKFWDLRQQNPILQLQLPERCYTADVEYPMAVVGTANRHIII
YSLDNQPTEFKRYESPLKYQHRCVSVFSDMKKKQPVGYALGSIEGRVAIQYLNPQNPKDN
FTFKCHRVNGASNFQDIYAVNDIAFHPIHGTLATVGSDGTFSFWDKDARTKLKSSETIDQ
SITKCAFSAGGQIFAYAVGYDWSKGHEFYNPQKKSYILLRSCFEELKPRVHNS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g7270.t1 Gene3D G3DSA:2.130.10.10 - 1 352 2.1E-115
4 g7270.t1 PANTHER PTHR10971 MRNA EXPORT FACTOR AND BUB3 8 348 4.3E-139
5 g7270.t1 PANTHER PTHR10971:SF11 MRNA EXPORT FACTOR 8 348 4.3E-139
8 g7270.t1 PRINTS PR00320 G protein beta WD-40 repeat signature 43 57 7.8E-6
7 g7270.t1 PRINTS PR00320 G protein beta WD-40 repeat signature 130 144 7.8E-6
6 g7270.t1 PRINTS PR00320 G protein beta WD-40 repeat signature 272 286 7.8E-6
2 g7270.t1 Pfam PF00400 WD domain, G-beta repeat 27 55 0.027
3 g7270.t1 Pfam PF00400 WD domain, G-beta repeat 111 143 0.0046
1 g7270.t1 Pfam PF00400 WD domain, G-beta repeat 242 285 0.035
11 g7270.t1 ProSitePatterns PS00678 Trp-Asp (WD) repeats signature. 130 144 -
16 g7270.t1 ProSiteProfiles PS50294 Trp-Asp (WD) repeats circular profile. 20 152 16.269
17 g7270.t1 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 68 109 9.205
19 g7270.t1 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 109 152 9.673
18 g7270.t1 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 260 294 8.938
13 g7270.t1 SMART SM00320 WD40_4 13 56 0.71
12 g7270.t1 SMART SM00320 WD40_4 64 100 0.015
15 g7270.t1 SMART SM00320 WD40_4 102 143 0.013
14 g7270.t1 SMART SM00320 WD40_4 236 285 9.3E-4
9 g7270.t1 SUPERFAMILY SSF50978 WD40 repeat-like 18 320 2.01E-46

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:0006406 mRNA export from nucleus BP
GO:0005515 protein 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.

Raw TPM values