Gene loci information

Transcript annotation

  • This transcript has been annotated as Eukaryotic translation initiation factor 5.

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 g2176 g2176.t5 isoform g2176.t5 15790409 15792941
chr_3 g2176 g2176.t5 exon g2176.t5.exon1 15790409 15792313
chr_3 g2176 g2176.t5 cds g2176.t5.CDS1 15790775 15792070
chr_3 g2176 g2176.t5 exon g2176.t5.exon2 15792418 15792514
chr_3 g2176 g2176.t5 exon g2176.t5.exon3 15792704 15792941
chr_3 g2176 g2176.t5 TSS g2176.t5 15793180 15793180
chr_3 g2176 g2176.t5 TTS g2176.t5 NA NA

Sequences

>g2176.t5 Gene=g2176 Length=2240
GCGAATTAATGGCAAAGTTGATTTAAATTTCAACATCCAGACAATTATTTTACACTAAAA
AGATTCTTCTCGAAAAAGTCGAATTCAATTTCAATATAATGCGCAATCGCTCAATTAGAC
ATAATAAATTCTTTTTACTATTCTCTTTATTGTAATTTGAGTAAATAATTCTGAAATATT
GCATACAATTGAAAGTTTCACTGCCAACTCATTAACTTATCGCTAGGTGTAAATCAGGAA
AACTTTGATCAGATCGAACAGCCGATATTTTTAAATTTATCACATCAGAATCCTTTAAAG
TGCATGTCAGCGAATTTAAATCAGTTGAGTCATAGGACTTCAAAATTTTCAAGCAATCGA
CATCGGAAATTGCAACCATTTAGAAAAACATCGTGAATTAGTCATAAACATTGAGTAAAG
TGAACAAGAGTTCTATTATTATCATCATCATCACCATCATCAAAGAATATAATACATAAT
CAAAAAAATAAGGGAACGTAATTCAAATTTAATTTGATAGAAGGATGGGGACTTTGAATG
TCAATCGTAATGTTACGGACTTGTATTATCGCTACAAGATGCCACGTATTTGTGCCAAAG
TAGAAGGCAAGGGCAATGGCATTAAGACCGTTATTGTCAATATGGCTGAAGTAGCTAAAG
CACTCAATCGTCCTGCTACTTATCCAACTAAATACTTTGGTTGCGAGCTTGGCGCTCAGA
CTCAATTCGATCATAAGAATGAACGTTTTATTGTCAATGGCTCGCATGATGCATCAAAAT
TGCAAGATCTTCTTGATGGATTTATTCGCAAATATGTCTTGTGTCCAGAATGCGACAATC
CTGAGACCGATTTAATCATTGTTGCAAAGAAAGAGCAAATTTCGCAAACTTGTAAAGCAT
GCGGTTTTCATGGATTGCTAAAAGTTCAGCATAAGGTGAATACTTTTATCTTGAAAAATC
CACCAACAATGAATCCAGCTGCACCAGGTGCATCTTTGACTGAGGGAAAACGTTCTAAGC
GCTCCAAGAAAGCTGAAGGTGATTCAAATCATGCTACAAATGGCGATAGCTCAAAAGATT
CCGATGATTTTCATACTAATAGCAAAATCACCAATAATGATAATGATGATGATGACGATG
GTCAATGGACAACTGAGGTTAGTGAGGAAGCAGTTCGTGCTCGTATGTTGGATTTATCAG
AGGGTGCAAAGAACATTACCATCTCTGAAGATACTGAAAAGACCGAGAAGCAACGTATGG
ATATTTTCTACGAGTACGTAAAGAAACGTCGTGATACTGGTGAACTTGATAATATTCAAG
CTCATAAGGAAATTCATAATGAAGCAACTCGTTTGGAAATCAATCAGAAGGCACCATTGA
TTCTCGCAGAATTGCTTTTCACTGAAAATATTACTGCTGAGATAAAGAAACATCGAAATT
TGTTGTTGCGCTTCACCCATGAAGATGAGAAAGCCCAAAAATATTTATTGGGTGGAGTTG
AGCAGGTCATCGCTTTGCATGCTGCAAAATTGATTGATAAATCTGCTGTCATTTTGAAAT
TGTTTTATGACACTGATTTGATAGATGAAAAGGTTATTTTAGAATGGGGTTCTAAAATCA
GCAAAAAATATGTGTCAAAGGAAGTTGCTCAACAAATTCATGATAAGGCCGCACCATTTG
TCAAATGGTTGAAGGAAGCAGAAGAAGAATCTGAGGACTCTGAAGAGGAAGATGATGATG
TTGAAATTGGCTTCGATGATCGTGCAAAGGTTGATTCGTTGTCAAGCAATGCTGTTAAAC
CAGTAGCTCCTGTGAAGAAACCTATTGTCGATGATGACGAAGATGGAGAAGAGCTAGACA
TTGATAATATATAAAGACATTGTCTTATATTCATTATGTTTTCTTTGAATATTAATCTAC
ACATATAAAAATAATATAGCAACCACAATAATGTCAAAGTTTTCTTTTTTTTTGCAAATT
GGTTTTTGTAGCTTCACTATATTATCAAATTATAATTTTTTCTCAATGCACACAAGTTTT
ATGATTTTTTGCCAACTTTTTTTATAGTGTTTTCTTACTTTTATTCCATTTTTAAAAAGT
CATATTTGATGAAACATAAAGATTGATGGAAAAAAGATTTATTGGATATTATCTGGAATT
TCAAAAAATGATATGAAAACAGAAATCAATTGAAATAAACCTATATTTGGAAGAATACAA
AATTTTTTTTCTTATTCTAT

>g2176.t5 Gene=g2176 Length=431
MPRICAKVEGKGNGIKTVIVNMAEVAKALNRPATYPTKYFGCELGAQTQFDHKNERFIVN
GSHDASKLQDLLDGFIRKYVLCPECDNPETDLIIVAKKEQISQTCKACGFHGLLKVQHKV
NTFILKNPPTMNPAAPGASLTEGKRSKRSKKAEGDSNHATNGDSSKDSDDFHTNSKITNN
DNDDDDDGQWTTEVSEEAVRARMLDLSEGAKNITISEDTEKTEKQRMDIFYEYVKKRRDT
GELDNIQAHKEIHNEATRLEINQKAPLILAELLFTENITAEIKKHRNLLLRFTHEDEKAQ
KYLLGGVEQVIALHAAKLIDKSAVILKLFYDTDLIDEKVILEWGSKISKKYVSKEVAQQI
HDKAAPFVKWLKEAEEESEDSEEEDDDVEIGFDDRAKVDSLSSNAVKPVAPVKKPIVDDD
EDGEELDIDNI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g2176.t5 CDD cd11561 W2_eIF5 220 372 2.36705E-57
11 g2176.t5 Coils Coil Coil 371 391 -
9 g2176.t5 Gene3D G3DSA:3.30.30.50 Translation initiation factor 2 beta 5 81 3.3E-36
8 g2176.t5 Gene3D G3DSA:2.20.25.350 - 82 127 1.2E-20
10 g2176.t5 Gene3D G3DSA:1.25.40.180 - 219 396 1.8E-56
17 g2176.t5 MobiDBLite mobidb-lite consensus disorder prediction 127 170 -
15 g2176.t5 MobiDBLite mobidb-lite consensus disorder prediction 143 170 -
16 g2176.t5 MobiDBLite mobidb-lite consensus disorder prediction 412 431 -
3 g2176.t5 PANTHER PTHR23001:SF22 EUKARYOTIC TRANSLATION INITIATION FACTOR 5 1 402 3.9E-138
4 g2176.t5 PANTHER PTHR23001 EUKARYOTIC TRANSLATION INITIATION FACTOR 1 402 3.9E-138
1 g2176.t5 Pfam PF01873 Domain found in IF2B/IF5 1 110 1.5E-36
2 g2176.t5 Pfam PF02020 eIF4-gamma/eIF5/eIF2-epsilon 299 381 2.6E-20
18 g2176.t5 ProSiteProfiles PS51363 W2 domain profile. 220 381 29.334
14 g2176.t5 SMART SM00653 eIF2Bneu4 1 111 2.8E-55
13 g2176.t5 SMART SM00515 542_3 287 377 2.3E-30
5 g2176.t5 SUPERFAMILY SSF100966 Translation initiation factor 2 beta, aIF2beta, N-terminal domain 1 82 5.23E-21
7 g2176.t5 SUPERFAMILY SSF75689 Zinc-binding domain of translation initiation factor 2 beta 79 112 5.49E-6
6 g2176.t5 SUPERFAMILY SSF48371 ARM repeat 222 375 2.88E-28

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:0006413 translational initiation BP
GO:0003743 translation initiation factor activity MF
GO:0005515 protein binding MF

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