Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Nuclear RNA export factor 2.

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 g9775 g9775.t1 TSS g9775.t1 5117866 5117866
chr_1 g9775 g9775.t1 isoform g9775.t1 5117909 5120507
chr_1 g9775 g9775.t1 exon g9775.t1.exon1 5117909 5118115
chr_1 g9775 g9775.t1 cds g9775.t1.CDS1 5117909 5118115
chr_1 g9775 g9775.t1 exon g9775.t1.exon2 5118174 5120507
chr_1 g9775 g9775.t1 cds g9775.t1.CDS2 5118174 5120507
chr_1 g9775 g9775.t1 TTS g9775.t1 5121017 5121017

Sequences

>g9775.t1 Gene=g9775 Length=2541
ATGGAAAGAAGCAATAAATATAGAAGATTTAATTATTCTCAAAGCGTTTATGATGAAGTT
GATGAAAGTAGATTTCAAAGAATTCAATTTTTAAGTGGTCACAGTGATATTGTTTTAGAT
CGACAAGATTTTCAACTTTGTGGGCCAAATAATTTAAATTATGACAAACAATTACTTTTA
TCACCTGAAAATTGGCATCAAATTATTATAAATCATCATGGAAAACTTACAAAAACACAA
ATTTTATCAGCACTTAATAAAATTACAAACGATGCAAAATTCATTCCAGTCAAATATCAA
GCTGGAAAATTTCAAGACAACTTTTTTATAATCAATCAATTTCAAGCAATGGAATTATTA
TTTGAAAATTGTTTAACGTTTAAAGTTGATAACTATAGCTATGATTTGACAGTAAAACTT
GCAGTTTCTCATGCACACAATCGTCAAATAAATCCAACTCATCAAATTAATATTGCAATT
ACTCGATATATCAATCAAATGAGAGATCAAAAACTTGATTTGAGCAACTTTAGTCAACAA
AGCAAAGAGTTGATGGAATTAGAATTTTCACTCTCAAATGAATTCAATTTTGAAATTTTT
TGTAAACAAATTGTTGAGCAATTAAAAGAAGAAGAAAAAATTATAACAATGTTGGTTTTA
TCCAATAATGGAATTCAATATCTCAGACCACTCAAACATTTTGCTAATCATCCTACATTG
ATAACTATCAGTTTGAGAAAAAATTTGATAAGTTCAATTTCTGAATTTAAATATTTACAA
CCATTACAATTGAAGCATTTGAGTATTGCTAGCAATCCTTTTGTAACTGGTGATTTTACA
ATAATAAATGAGCAAATTATGGTTATGCTGCCAACGATTGAACATACAGATCTCAAAGTA
ACGCATCAATATAACATTGAAAATCCTTCGAATGTAGTTGAAGAAATAATCAGGTCGACT
GACATTGATGATAAATTTAAGGCTGAATTTCCAAAAAGAGAATTTGTTAAAACTTATTGG
AATAAAGTTGTAATTGAGCACAATAAAAAATTTGATGGGCAAAAAGTTTTGGACGAAATG
TTTTGGAAATTTTTTGAAGATGATCTCTTTTATCCATGCTATTATGTTAGTGGTTTGACT
GAAGATTCGTTCATGCTGTACATGAATTTTGATCCACTTAATATTTTGATTCAAAATAAT
TTACAAATGATTTTTGAAGAAAATAAGCAAATTTTAAAATTCCGATTACATTTAAAATGT
GGACTATTTAAGCATGATCAAGTTAAATGGAATGAATTGATTCCCAAAGTGATTAATAAT
AGAATTACAGCATCAACATTGAATTTGAGAAATTTTAAAAATGATCCAGAGTTGAAAGAT
ATTGTTGTAAATTTATCAACAAATAAAGGAATAAACTATGTTTTAACTTGTGCATTAAAT
CAAAAACCAGACATAATAGAGATTGATTTAAGTCAAAATAATTTAGAAAAGACAAGTGAT
CTTGGAATCTTAAAGCAATTCTCAAAACTCGTATCATTGAACTTGTCAGAAAACCAAATT
GAAACACTCAAAGATTTTCCACAAAATTTACAAATTTATGAAATTAAAATGGAACAAAAT
CCGATTTGTGATAAATTCATGTCAAAGCAACATTACTCTGCAATGTTTTATGTAAAAACT
TTTAAAAATTTGTGCCCAAAATTGCAATTTATTGATGGAAAAAAGATTGATAAAACTTTA
AATATTGTTCACTTGCAAAATCATTTAGTGACACCAAAAGCTTACATGACAGTCTTAGGT
TTTATTGAATTTTTCTTCAAAAATTTTGAAAGCCGTGAGAAACGTGAACTACTTACTGCA
CTTTATTCAAAAGATTCAATTTTATCAGTTAATGATGATAGAAATAAAAAACAAATTTTT
GGTGGTCAAGTTAAAATTAGCGATCATTATGCATCATTGCCTGAATATGAACATGATTTT
GTGAATTTTACTGTCGATTCTCCTTTATTCTGTCCTAAAATTGAAAGAAATTCCATTTTA
AAATTTTGTGTTCCAAAATTTCTCGTTACTGTCACTGGAGTTTTCAGAGAAAAAGAAAAT
AAAGAAAAATTTTTCGCATTTTCTCGCACATTTTTCTTAGAAAAAGATCGAAATGGAACA
GGAAGGGCAACAGGAACATTGTCAAATACTTTTTATTTTGAAATTTCCAATGAAATTTTC
AACTATGAAATTGTAAGAGATGAAAAAATTAAAAACAAAGCATTTAAAAACCAACAAGCC
ACAGATGGTGAAATTGAGAGTAAATTTATAAACGATACTGTTGCTGAAAGATTTGAAGAG
AATCTCGAATTACTGAAACAAACAATATTAATGAAACCAGAATGGTGCAAAAGATTTTTA
GAAGAAGCAAATGGTGATTTTTGGACTGCAGTCAATTATTTTAATGAATTTTTTGAACGA
GACTTATTGAGAAATGAAGACTTTTTATTTTATGATGAAATTAAGAATAATAAAGAAGCA
ACTTCTAACAGTCGCAATTAA

>g9775.t1 Gene=g9775 Length=846
MERSNKYRRFNYSQSVYDEVDESRFQRIQFLSGHSDIVLDRQDFQLCGPNNLNYDKQLLL
SPENWHQIIINHHGKLTKTQILSALNKITNDAKFIPVKYQAGKFQDNFFIINQFQAMELL
FENCLTFKVDNYSYDLTVKLAVSHAHNRQINPTHQINIAITRYINQMRDQKLDLSNFSQQ
SKELMELEFSLSNEFNFEIFCKQIVEQLKEEEKIITMLVLSNNGIQYLRPLKHFANHPTL
ITISLRKNLISSISEFKYLQPLQLKHLSIASNPFVTGDFTIINEQIMVMLPTIEHTDLKV
THQYNIENPSNVVEEIIRSTDIDDKFKAEFPKREFVKTYWNKVVIEHNKKFDGQKVLDEM
FWKFFEDDLFYPCYYVSGLTEDSFMLYMNFDPLNILIQNNLQMIFEENKQILKFRLHLKC
GLFKHDQVKWNELIPKVINNRITASTLNLRNFKNDPELKDIVVNLSTNKGINYVLTCALN
QKPDIIEIDLSQNNLEKTSDLGILKQFSKLVSLNLSENQIETLKDFPQNLQIYEIKMEQN
PICDKFMSKQHYSAMFYVKTFKNLCPKLQFIDGKKIDKTLNIVHLQNHLVTPKAYMTVLG
FIEFFFKNFESREKRELLTALYSKDSILSVNDDRNKKQIFGGQVKISDHYASLPEYEHDF
VNFTVDSPLFCPKIERNSILKFCVPKFLVTVTGVFREKENKEKFFAFSRTFFLEKDRNGT
GRATGTLSNTFYFEISNEIFNYEIVRDEKIKNKAFKNQQATDGEIESKFINDTVAERFEE
NLELLKQTILMKPEWCKRFLEEANGDFWTAVNYFNEFFERDLLRNEDFLFYDEIKNNKEA
TSNSRN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g9775.t1 Gene3D G3DSA:3.80.10.10 Ribonuclease Inhibitor 153 303 0.0000000
9 g9775.t1 Gene3D G3DSA:3.80.10.10 Ribonuclease Inhibitor 429 581 0.0000000
10 g9775.t1 Gene3D G3DSA:3.10.450.50 - 584 761 0.0000000
4 g9775.t1 PANTHER PTHR10662 NUCLEAR RNA EXPORT FACTOR 51 301 0.0000000
3 g9775.t1 PANTHER PTHR10662 NUCLEAR RNA EXPORT FACTOR 340 820 0.0000000
2 g9775.t1 Pfam PF09162 Tap, RNA-binding 63 119 0.0000018
1 g9775.t1 Pfam PF02136 Nuclear transport factor 2 (NTF2) domain 599 719 0.0000120
13 g9775.t1 ProSiteProfiles PS51450 Leucine-rich repeat profile. 214 235 5.3480000
12 g9775.t1 ProSiteProfiles PS51450 Leucine-rich repeat profile. 239 260 6.7260000
14 g9775.t1 ProSiteProfiles PS51450 Leucine-rich repeat profile. 484 505 6.1800000
11 g9775.t1 ProSiteProfiles PS51450 Leucine-rich repeat profile. 509 530 7.5730000
15 g9775.t1 ProSiteProfiles PS50177 Nuclear transport factor 2 domain profile. 597 742 15.5010000
7 g9775.t1 SUPERFAMILY SSF52058 L domain-like 210 297 0.0000000
6 g9775.t1 SUPERFAMILY SSF52058 L domain-like 445 578 0.0000000
5 g9775.t1 SUPERFAMILY SSF54427 NTF2-like 588 740 0.0000000

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:0003723 RNA binding MF
GO:0005515 protein binding MF
GO:0005737 cytoplasm 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