Gene loci information

Transcript annotation

  • This transcript has been annotated as Translation initiation factor eIF-2B subunit epsilon.

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 g10831 g10831.t1 TSS g10831.t1 12167885 12167885
chr_1 g10831 g10831.t1 isoform g10831.t1 12167976 12170080
chr_1 g10831 g10831.t1 exon g10831.t1.exon1 12167976 12168062
chr_1 g10831 g10831.t1 cds g10831.t1.CDS1 12167976 12168062
chr_1 g10831 g10831.t1 exon g10831.t1.exon2 12168126 12168250
chr_1 g10831 g10831.t1 cds g10831.t1.CDS2 12168126 12168250
chr_1 g10831 g10831.t1 exon g10831.t1.exon3 12168313 12170080
chr_1 g10831 g10831.t1 cds g10831.t1.CDS3 12168313 12170080
chr_1 g10831 g10831.t1 TTS g10831.t1 12170151 12170151

Sequences

>g10831.t1 Gene=g10831 Length=1980
ATGGAGAAAAAAGAAATTATACAAGCTGTCGTGGTAGCCGATAATTTTAGTGAATGCTTC
AAACCTTTTACTACATTTAATTCTCCGGCTTTGCTACCACTTGTAAATGTCCCAATGATT
AGTTATGTACTTGAAACTCTCAATCGAAATAGTGTCGAAGAAGTATGGATTGTGTCCTCA
ACTTTTCCTGAGAAAGTTAGAGAGTTTATAAAACGTGGTATTGAAGAGCATTTGACATGG
TCTGTTGGTATGAATGTTCAAGTAATTGCATGTGAAGTAAGATCACTTGGAGATGCTATG
CGAGAATTAGATGGGAAAGGAATGATACGTGGAGATTTCATTTTGATGAATTTTGATACG
ATAACAAATGCCAAATTAATTCCTTCAATTTTGAAGGCACACAAAGATAATTGCAAACGC
GATAAAGAAACAGCAATGACAGTTGTCTATAACAAAATCTCATCTGGTCAACGAACTGGT
AATGAAGTTGTAATTGCTACAAATAAGAGAACAAAAAGACTTTTATTTCATCAAAGAATA
CATCCGACAAATAAAGAAGAAAAGTTTAAATTTCCACTTGAAATATTTCTTGATAATAAG
GAAGTTTCACTTCATCATGATTTAATTGATCCACAAATTGCCATATGTTCAACCTCAGCA
CTTCCATTATTTTCTGATAATTTTGATTATGATACACGCGATCAATTTATTCGTGGAATT
GTTATGGATCAAGAATTACAAGCTGCTTCAATTTATGTAGAACAATTGCCAATTGATCAA
TATGCTGCGAAAGTTAGTGATTGGATTGCGTATCACACAATTTCTCAGGATATTATGAAT
AGATGGGTTTATCCGTTAGTTCCCGATATGGGAGTATGTGCATTAAAGCAACAATATCTA
TTTCTTAAAAATAACATTTATCGTAATAATTCGGTAAAAGTTGCAAGAAACTGTTCGATT
AAAAATGATGTAGTGTTACATGAAAATGTGAATATCGGTGATGAATCTTTGTTAGCTCGA
TGTGTGTTAGGTAAAAATTGCATAGTTGGTAAAAATTGTACAATTAGAAATGCTTATATA
TTTGACAACACAAAAATAAGTGACAATTGCAAACTTGAGAATTGTATAATCGGTGCATCT
GTGCTGATCAACGAAGATTGCACAATAAAGAATGGAACTGTAATAACAAATGATTGTATA
ATTATGAAAAAAGAAGAACATTCTGGTTCTCTTATTCAATCAAAAATTCCTGATGATGAT
GATTATCTGCAAGATTCATTTGAAAAACTTAACGATAAAGCATACAAATACATTGAAAAT
AGAGAATCAACCCGAAATGACTCTGAAGATGATCTTGACGATCAAGAAGATGATGATAAT
GATGCAGAAGTTTATATAAAACTTATACCAAAAGTTCCAAATTATGAATCAAGTGCTTAC
AGTTCAGAAACCGATAGCGATGATGATGAGAATGATGTAGGTGTAGCACAAGAAGATTCA
ATAATTTTCTTAACGGAAGTCATTGATTCATTAAAACGTGGATTTGATGAGAAATCAAAT
CCAGACTTTTTGATTTTGGAAATCAATTCATCTCGCTATGCTTATAATATACAACTCAAC
GAAGTTAACTTTTTCGTCATAAAAGCATGTTTTAATTTACCCGTTGTTCTCGATCATGCC
GATGCTTTGGAAGGGTTTAAACAGGTCTATAATTATCTGGGAGATAAAGTTATTAAAAAC
TATATAAAAGGTGATGGAGCAATGGTTGATTGTCTTAATGCAATCGTAGAATGTTGCGAA
GAATCTGAAAAATTAAAACCTAAACTTATGAAAACACTTCACTTTCTTTACAATGAAGAT
ATTTTAACTGAGGACATAATTATTTCGTGGTATGAAGATATCGATAAAAATTGGGTTAAA
GTAGCACTAAATAAGTTTATTACATGGCTTCAACAAGAAAGTGAATCTGATTCAGAATAA

>g10831.t1 Gene=g10831 Length=659
MEKKEIIQAVVVADNFSECFKPFTTFNSPALLPLVNVPMISYVLETLNRNSVEEVWIVSS
TFPEKVREFIKRGIEEHLTWSVGMNVQVIACEVRSLGDAMRELDGKGMIRGDFILMNFDT
ITNAKLIPSILKAHKDNCKRDKETAMTVVYNKISSGQRTGNEVVIATNKRTKRLLFHQRI
HPTNKEEKFKFPLEIFLDNKEVSLHHDLIDPQIAICSTSALPLFSDNFDYDTRDQFIRGI
VMDQELQAASIYVEQLPIDQYAAKVSDWIAYHTISQDIMNRWVYPLVPDMGVCALKQQYL
FLKNNIYRNNSVKVARNCSIKNDVVLHENVNIGDESLLARCVLGKNCIVGKNCTIRNAYI
FDNTKISDNCKLENCIIGASVLINEDCTIKNGTVITNDCIIMKKEEHSGSLIQSKIPDDD
DYLQDSFEKLNDKAYKYIENRESTRNDSEDDLDDQEDDDNDAEVYIKLIPKVPNYESSAY
SSETDSDDDENDVGVAQEDSIIFLTEVIDSLKRGFDEKSNPDFLILEINSSRYAYNIQLN
EVNFFVIKACFNLPVVLDHADALEGFKQVYNYLGDKVIKNYIKGDGAMVDCLNAIVECCE
ESEKLKPKLMKTLHFLYNEDILTEDIIISWYEDIDKNWVKVALNKFITWLQQESESDSE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g10831.t1 CDD cd04197 eIF-2B_epsilon_N 7 221 2.11376E-72
12 g10831.t1 CDD cd11558 W2_eIF2B_epsilon 498 658 2.48326E-43
11 g10831.t1 Coils Coil Coil 438 458 -
8 g10831.t1 Gene3D G3DSA:3.90.550.10 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A 1 300 1.2E-24
9 g10831.t1 Gene3D G3DSA:2.160.10.10 Hexapeptide repeat proteins 301 428 5.8E-20
10 g10831.t1 Gene3D G3DSA:1.25.40.180 - 491 659 7.4E-43
3 g10831.t1 PANTHER PTHR45887 TRANSLATION INITIATION FACTOR EIF-2B SUBUNIT EPSILON 3 659 6.9E-150
4 g10831.t1 PANTHER PTHR45887:SF1 TRANSLATION INITIATION FACTOR EIF-2B SUBUNIT EPSILON 3 659 6.9E-150
1 g10831.t1 Pfam PF00132 Bacterial transferase hexapeptide (six repeats) 363 397 1.6E-4
2 g10831.t1 Pfam PF02020 eIF4-gamma/eIF5/eIF2-epsilon 588 659 2.0E-16
15 g10831.t1 ProSiteProfiles PS51363 W2 domain profile. 497 659 22.247
14 g10831.t1 SMART SM00515 542_3 575 657 2.3E-15
7 g10831.t1 SUPERFAMILY SSF53448 Nucleotide-diphospho-sugar transferases 7 380 4.16E-25
6 g10831.t1 SUPERFAMILY SSF51161 Trimeric LpxA-like enzymes 257 398 8.46E-27
5 g10831.t1 SUPERFAMILY SSF48371 ARM repeat 503 652 1.76E-27

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:0005515 protein binding MF
GO:0005085 guanyl-nucleotide exchange factor activity MF
GO:0031369 translation initiation factor 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