Gene loci information

Transcript annotation

  • This transcript has been annotated as Eukaryotic translation initiation factor 4 gamma 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_3 g2255 g2255.t1 TTS g2255.t1 16312156 16312156
chr_3 g2255 g2255.t1 isoform g2255.t1 16312418 16317597
chr_3 g2255 g2255.t1 exon g2255.t1.exon1 16312418 16312599
chr_3 g2255 g2255.t1 cds g2255.t1.CDS1 16312418 16312599
chr_3 g2255 g2255.t1 exon g2255.t1.exon2 16312665 16312851
chr_3 g2255 g2255.t1 cds g2255.t1.CDS2 16312665 16312851
chr_3 g2255 g2255.t1 exon g2255.t1.exon3 16312911 16314723
chr_3 g2255 g2255.t1 cds g2255.t1.CDS3 16312911 16314723
chr_3 g2255 g2255.t1 exon g2255.t1.exon4 16314786 16315678
chr_3 g2255 g2255.t1 cds g2255.t1.CDS4 16314786 16315678
chr_3 g2255 g2255.t1 exon g2255.t1.exon5 16315762 16315934
chr_3 g2255 g2255.t1 cds g2255.t1.CDS5 16315762 16315934
chr_3 g2255 g2255.t1 exon g2255.t1.exon6 16317555 16317597
chr_3 g2255 g2255.t1 cds g2255.t1.CDS6 16317555 16317597
chr_3 g2255 g2255.t1 TSS g2255.t1 NA NA

Sequences

>g2255.t1 Gene=g2255 Length=3291
ATGAATGATAGGAAGCATTATAAAATTATTTTCAAACATGAAACGTCCCAAAAGATTTTG
TCAAAAACCATCAAAACGGAAGTTTCTAAGCAAGCAGGAACCGAGCCGCGATTGGGGAGA
GAACAACTCCCCGAAGTTCGAGCTTGGATTCCACCATCATTGCGACCACAGCATGGACTA
TCTGAAGAGGCCCAACGTGATGAAATATTTAGAAAAGTTCGTGGTATTTTGAATAAACTC
ACACCAGAAAAATTCCAACCTCTCAGCGATGATTTGTTAAGGCTTAACTTGAATTCAAAG
AAAATTCTTCTTGGCGTTATTCACTTGATTTTCGAGAAAGCATTAGATGAACCCAAGTAT
TCGTCTATGTACGCGCAGTTATGCCGTCGTATATCGAAAGAAGGATCAACTCTTGAAACA
GACGGCGATAATCGCTTTACATTTGAACTACTTTTAATTCGTGTGTGCCAGGACAAATTC
GTTAATCGTTCACAGTACACTGAAAAGATAATTAATGCACCAACTTCTGAGGACATTGAT
GAGGAGGAACGACGTTATATTGCAAAACAAAAAATTCTCGGCAATGTCAAATTTATTGGA
GAACTCTTTAAGCTTGAGATCCTCAATGAGGGAACTCTGCACAAAATGCTCGAACAGTTG
CTGGATAAGAAAAGTAGACCCAACTCAAATTTGGAAGACAGATGCGAGGATATGGAATGC
TTGTCACAGATTTTTAGAACATGTGGCAAGCAATTGGACACAGAAAAATCCAAATTCTTA
ATTGACCAATATTTCGCAAACATGGAACATAAATCAAATTCATTCAAATATCCGCCACGC
ATACGATTTATGCTACGCGATATAATCGAATTGCGAAAGGGTGGATGGAAGCCGCGTAAA
GTGGCTCGCATAGAAGGACCTGTGCCAATTCAAGATTTGAGCACAGATGAAGAGTACATA
CGGCAACAGCGTGATTTGCGAACACGTACGATGGAGAGTCGAAATGCTGATCGCAATTGG
ATGGATAAATTGCCGTTGAGCTTGCAATCGATGAACAATTATAACGGAACTTTATCTATG
ACCAGCTCAAGTTCTTTAATTAGCGGACCATATAATCCGCAAATGAATTACAATTCCGGC
CGTGATTCTTTGATGAGTGGCAATAGTTATCGAAATAACAATGGCAACAGTAACAGTCAT
CATCATCATCATAGAAATCATCATGATAATCGTCCGATGAATAAATATAATAATAATAAC
GATGGAGGAGGAGGTAATATTAGTGGTGGAAAGATGAGCCACAATAAGATGAAACATAAT
AACAACATGCACCACCATCGTCAAAATGATGGTTCAAATCATCATCATCATAATATGAAC
AATCAAAATTCGTATAATAATAACAATAGCAACAGCAACAACATATTAAATAACAAAGAG
CTTGCACCTCGCTTTAAACGCAATCTTGTTACAACCACTACAACTAATTCAGTAGATGAT
TTGCAGATGCGTCCAGCACCAAATAGCTTGCTATTCAAAGCTTCAAATATTAAGCCGAAT
CCTCAGCAGTTGCCTTTGAATCCACAAAGTCGTAGTGGAACTTCATCACCAGGCTTTTCT
ACATCAAATGTTGATAATTTGATTCCAACATTTAATAATACATTGCAAATGAACACTATG
AATGGTAAACAACAGCAACAACAAACACAACAAAATGCTAATCAACATTTTTCACATCAA
ACTGGTACATCTCATCATCAAGGCGGTGGTAATAATAACTTTTCTTCATCTTCTGCATCA
AACGTTCAAGGATCAAAGTCAAATCACTCGAATTCGTCTCAACATTTGAATTCGGCGTCA
AATTCTCAACCACAATCGCCACAAAATAATCAAAATGCAGCTGCAGCAGCCGTTAAAGAT
CAGCAGGCTGTCACCAAACAAGGTTCAGTTGAGAAACAAAAGACAAAGAAAGACAAAGGA
CCGAGTCGTGACGATGTTTTGAAGAAAGTTGCGCAGTTCATAAATGAATCTTTATTGGAT
AAGAAGTTTATTGAAAAATTGCATGCAACGCGCAACATTGATGACAAAATAGGAGATGCA
AAGAAAGAGGATTTATTAACCGATTCTCATAATAATAATAGTAATGGTCATACAAATGGT
GATGTTGAAATAATTGAAGAATGTGCTGTTGAGAATGGTGAAGAAAGCAAGCCTGATATC
ACATTAATTGGTGAAGAGGAAATTTCAGTTCCAACTATGGAAGATGTAGTCAAATTATAC
TATGAACTAAAAGTGCCTGATAAATTCCTCAAAGACTCGAATGTTAAAATTCTTAACGAG
TCACTTGACAAGGGTGAAAATGCACAAGATACGGCAATTGAGTTCCTGATGGCTTTACAG
AAAGACAAAAAATTAACAGCCAATCAGACACTCGATGCATTCCGTGGCGTAATTAATGGC
ATGAGTGAGCGTGAAAAAACAATTCCAAAAGTTACTACACATGTCGCATCGTTGCTGGCA
CGATCGATGACAAAGAAAATTTGTAAACTTACCGACGTTGCCAATTTTACTGATAATGGT
CAACACTATCCATTGCTATTGCTTGTATTGCAACAATTGAACAAACTTCTTGGAGAAGAT
CAGTTGGTTGAAATGTTTAATAGCAGCAAAATTAATCTCATGAACAATTTACCAGAGTGT
GACCGTTCGAAAGATCGTTTAGCAGAAATTCTTGATGACAGAAAGTTGAGCTTTTTGCAA
CCATTATTGCGCATTGAATCTGAATTGTGGCGTCAAATCAAAGAAGATCCACAACCACAG
ACATTCTATAAATGGATAAAAGATAATGTCGATTCTGCTAGATACAATGATCCTGGATTT
ATTACAGCTCTAATGACTGTTCTTTTAAAATACATCACTCAGGAAACAACTTTCCCAGAA
AACAGTGATCCGACCAAACTTCCTGAAAAACAAACCGTTGAGGCCGAGAAAAAATTACTC
ATTTCATTCAGTCGAATTTTGAATGCATTTTTAAATGGAAACTTGGATTTACAGCTCATT
GCAATATATGCATTGCAAGTTTATTGCTTCAATCAAAAATTCCCTAAAGGAATGTTATTG
AGATGGTTTACAGCATTATATGAGTTGGAAATTATTGAAGAAGAAGCATTCTTGAGATGG
AAAGAGGATATTACTGATGCTTTTCCAGGCAAAGGAAAAGCTTTGTTCCAAGTGAATTCA
TGGCTAACATGGCTTCAAGAAGCAGAATCAGAGGAAGAAGACGATGAATAA

>g2255.t1 Gene=g2255 Length=1096
MNDRKHYKIIFKHETSQKILSKTIKTEVSKQAGTEPRLGREQLPEVRAWIPPSLRPQHGL
SEEAQRDEIFRKVRGILNKLTPEKFQPLSDDLLRLNLNSKKILLGVIHLIFEKALDEPKY
SSMYAQLCRRISKEGSTLETDGDNRFTFELLLIRVCQDKFVNRSQYTEKIINAPTSEDID
EEERRYIAKQKILGNVKFIGELFKLEILNEGTLHKMLEQLLDKKSRPNSNLEDRCEDMEC
LSQIFRTCGKQLDTEKSKFLIDQYFANMEHKSNSFKYPPRIRFMLRDIIELRKGGWKPRK
VARIEGPVPIQDLSTDEEYIRQQRDLRTRTMESRNADRNWMDKLPLSLQSMNNYNGTLSM
TSSSSLISGPYNPQMNYNSGRDSLMSGNSYRNNNGNSNSHHHHHRNHHDNRPMNKYNNNN
DGGGGNISGGKMSHNKMKHNNNMHHHRQNDGSNHHHHNMNNQNSYNNNNSNSNNILNNKE
LAPRFKRNLVTTTTTNSVDDLQMRPAPNSLLFKASNIKPNPQQLPLNPQSRSGTSSPGFS
TSNVDNLIPTFNNTLQMNTMNGKQQQQQTQQNANQHFSHQTGTSHHQGGGNNNFSSSSAS
NVQGSKSNHSNSSQHLNSASNSQPQSPQNNQNAAAAAVKDQQAVTKQGSVEKQKTKKDKG
PSRDDVLKKVAQFINESLLDKKFIEKLHATRNIDDKIGDAKKEDLLTDSHNNNSNGHTNG
DVEIIEECAVENGEESKPDITLIGEEEISVPTMEDVVKLYYELKVPDKFLKDSNVKILNE
SLDKGENAQDTAIEFLMALQKDKKLTANQTLDAFRGVINGMSEREKTIPKVTTHVASLLA
RSMTKKICKLTDVANFTDNGQHYPLLLLVLQQLNKLLGEDQLVEMFNSSKINLMNNLPEC
DRSKDRLAEILDDRKLSFLQPLLRIESELWRQIKEDPQPQTFYKWIKDNVDSARYNDPGF
ITALMTVLLKYITQETTFPENSDPTKLPEKQTVEAEKKLLISFSRILNAFLNGNLDLQLI
AIYALQVYCFNQKFPKGMLLRWFTALYELEIIEEEAFLRWKEDITDAFPGKGKALFQVNS
WLTWLQEAESEEEDDE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g2255.t1 CDD cd11559 W2_eIF4G1_like 921 1067 2.6166E-40
12 g2255.t1 Gene3D G3DSA:1.25.40.180 - 70 310 2.7E-71
11 g2255.t1 Gene3D G3DSA:1.25.40.180 - 730 919 4.0E-48
10 g2255.t1 Gene3D G3DSA:1.25.40.180 - 922 1088 1.2E-58
16 g2255.t1 MobiDBLite mobidb-lite consensus disorder prediction 561 649 -
17 g2255.t1 MobiDBLite mobidb-lite consensus disorder prediction 561 664 -
18 g2255.t1 MobiDBLite mobidb-lite consensus disorder prediction 650 664 -
3 g2255.t1 PANTHER PTHR23253:SF63 EUKARYOTIC TRANSLATION INITIATION FACTOR 4G1, ISOFORM B-RELATED 47 487 5.6E-118
5 g2255.t1 PANTHER PTHR23253 EUKARYOTIC TRANSLATION INITIATION FACTOR 4 GAMMA 47 487 5.6E-118
4 g2255.t1 PANTHER PTHR23253:SF63 EUKARYOTIC TRANSLATION INITIATION FACTOR 4G1, ISOFORM B-RELATED 560 1094 5.6E-118
6 g2255.t1 PANTHER PTHR23253 EUKARYOTIC TRANSLATION INITIATION FACTOR 4 GAMMA 560 1094 5.6E-118
1 g2255.t1 Pfam PF02854 MIF4G domain 70 293 4.5E-46
2 g2255.t1 Pfam PF02020 eIF4-gamma/eIF5/eIF2-epsilon 1018 1095 8.5E-19
19 g2255.t1 ProSiteProfiles PS51366 MI domain profile. 735 858 13.695
20 g2255.t1 ProSiteProfiles PS51363 W2 domain profile. 912 1095 25.147
14 g2255.t1 SMART SM00543 if4_15 70 295 5.0E-43
15 g2255.t1 SMART SM00515 542_3 1004 1091 7.7E-21
8 g2255.t1 SUPERFAMILY SSF48371 ARM repeat 64 298 4.99E-60
7 g2255.t1 SUPERFAMILY SSF48371 ARM repeat 748 919 3.57E-18
9 g2255.t1 SUPERFAMILY SSF48371 ARM repeat 921 1060 1.84E-31

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:0003723 RNA binding MF
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