Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Eukaryotic translation initiation factor 4 gamma 3.

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 g11510 g11510.t1 TTS g11510.t1 16711123 16711123
chr_1 g11510 g11510.t1 isoform g11510.t1 16711765 16715131
chr_1 g11510 g11510.t1 exon g11510.t1.exon1 16711765 16711856
chr_1 g11510 g11510.t1 cds g11510.t1.CDS1 16711765 16711856
chr_1 g11510 g11510.t1 exon g11510.t1.exon2 16711945 16712275
chr_1 g11510 g11510.t1 cds g11510.t1.CDS2 16711945 16712275
chr_1 g11510 g11510.t1 exon g11510.t1.exon3 16712357 16712485
chr_1 g11510 g11510.t1 cds g11510.t1.CDS3 16712357 16712485
chr_1 g11510 g11510.t1 exon g11510.t1.exon4 16712576 16715131
chr_1 g11510 g11510.t1 cds g11510.t1.CDS4 16712576 16715131
chr_1 g11510 g11510.t1 TSS g11510.t1 NA NA

Sequences

>g11510.t1 Gene=g11510 Length=3108
ATGGATCAAAGTTCTTCTGAGGAGCTTAGTCACACTTTTGAAATAATCGACAAGAAAGAG
CTCTTGATGACATCTACTGAAAACGATAGTGATAGCCTGAACAACAATAACAACATAAAC
ACCGACTGTGACACAAACATAAACGATCAAATGACTACGACGATAATTGCAGCTGATAAA
ATATCCGAAAAGAATACAGACGATGATAATGGCAACAATAATACTGATAATTCAAACAGT
AAAAAGTATACTAGAGATCAATTGATTCAAATGAAGCAGATAGCTTCAACAATGCTACCG
GATTTAAAGCGTGAAGTGAAAAATCTTATTTTTACTGAAACTTCTGCACTTGACAATACA
CTCAATCGAAAAATTAGAGCTGATGCTGTAATACCAAACTTTATGCCTCTTCCTGGTCGT
AACTCAGCACAGCGACCAAAATCTGAATATGCCGGTAATAGAAAATCACAGCAGGGTAAT
AAAGGCCAAATAATCACTATGAGATTGACATCAAATGAAGAAGTTAAATTAAATGAAGCT
AAAAATGCATGGAAACCATCAACTTTAGCACAAGAAGAAGTTGTGTTATCAGAGGAAGAA
AAGAAAACTGAAGAATTGAAAAAACAATTCCGTGGAATATTAAACAAACTTTCGCCTGAT
AATTTCCTTACACTTGTAGGAAAGCTTAAAACATTGCAAATAGATACAGTAGATCGATTA
GACGAATGTATATCATTAGTGTTTGAAAAAGCTATCACAGAACCGAATTATGCACCAAGT
TATGCTCTTCTTTGTAAAGAAGTTTCTGATGTTTTTATTGTGCCATTAGACCCGACTAAT
GCTCAACAACAAAATGCCGTGTTTAAAAAGCGACTCATCACACAATGTCAACGAGAATTT
GAAAAGCATCGCGACAATGAGCTAATCAAAAATACAGCTGAACGACTGAAAAAAATTGAA
GCAGAAGAAGATCCAGTAAAAAGAGAAGAACTAAAAAATGATTTCGAGTATGAGAGCATG
AAAGTCAGAAAACGTGCTGTAGGAACTGTACATTTCATAGGCGAATTGTATAAAATTGAA
ATGCTTACTTCGAAAATCATGCGGTCATGCATTACACATTTACTTGATCCTTCCATGTGT
AGTGAAGAAACTCTTGAGTGTCTATGCAAATTACTAGAAACAATTGGAAAAAGATTAGAA
AAAACCGACAAGAACAGAATTGACCTCACAGATTATTTTCAAACTCTCGAGAAACTTGCT
GATAAAAAGAACCCAAGTGGAATAAGTGCAAGAATAAGGTTTATGATACAGGATGTTATA
GAATTGAGGATGAATAATTGGACACCACGCAAACCACGCCAAGGTAATAAACCTCTTACA
ATGGATGAAATCAAACAACAAGTTATTATGGAGCAAGCAATAAAAGAAATGGACAATAGA
GAAGCATTTCGTGAACAGGGAAATCGTCAAAATACACGCCGTACAGGAGCAGTCAATGAA
GAGGGCTGGAGTATGTCTTACTCTAAAAGTCGACCTGTGAAATTCGATCCTCTTAAGTTG
CCAACAAATGCAAGTGAAGACATCAAACTCGGACAGCCATCAAATTTTCAGAATTTCAGC
AATTTTCAGAGCAATCGTTTTGCTGGTTTGAAAGAAGAAGATCAAATGGAACAAGCTAAT
CGAAATTATAATGGACGATTCAGTGGTGGTGCTTCTTCTAATATGAATAGTCCAAATCGA
AATTCATTTGAAAACAGAAACAATCGTAACAATCGAGGTGGGAATCGATCTGCAGGATCA
AAAAGTTTGCAATCACCACAGTTACAGAAATATGGAACTAGTCGCAATAGTAATAACATG
GAACGACATCGGAATCCAAGTATGCAGTTTCATATGCAACGTCCGAATGATCTTCCAGTC
AAAGCATCACTGCCAACAAGAAAAATATCGGCTCCTGCTCGTCCTATGCAATATTCTGAA
GCATTTATTCAAGAGAGAAACCTCATTAATGATCCCAACAAAGTGTTCAATATAATGAAG
TCTTCTCTAACCGGATATCAGCATAATGAAATTACACTTGATGAAATAATGGAAAATTTA
AAGAAATTTCGTATCAGCAAAGATTCACTTGTACTACTCTACAATTGGGCTTTCGACCAA
CATGATAATGAACGTCTGCAATTGACCGAGATTATATGTGAAGGCGTTAGTGGAAATATA
ATTACTACAAAAGACTTGTTGGATGCTCTTAAAGAAACAATTGAATTGGCACAAGATTTA
GCATGCGACTTGCCACTAGTCTACAATTATATCGGACAATTTCTCGCGCTTCCTCTCACG
AAGAGAATTATATCACTGAAAGACTTGTATGATATTTCTAAATCACAAATTGATGAATTT
AGTAATGGCGAAGTCATTTTAAAAAATGTTTTTAAAATTATCGATGCACGTCACGGTAAA
GATGCGCTTTCTCAACTCTACTGTGAGGCCAATACCAATTTACAACTTTTCCTTGACACC
GCTAACACGCAGCTTAGCGAATTTTTAAAAGAAAATAATTTTGATTACCTCATGCAAATG
CAAGAAAATAACTCAATGGATAACTTTGATAAAGAATTAAAAGATCAACTAGAACAAAAA
TTAAAATCCGAATCGGATGTTGAAGCAATAATAATTTGGATAACAGAAAATATAAAAGAA
CATGATAATAAATTTATACGTGTTTTGATGGAGCTTTTATTGAAAAATTGCATAGAAAAA
ATGCATGATGGATCATATCGATTAGAACGTGAACGATTGGACTTTTTCGCACCATTACTC
ACACAATTTGTGGAAAAAAGCAAGGAAAAGCAAATTCAATGCTTACAAGTTATTCACCGT
TATATGAATGAACTCGAGCATCCTCAATCATGTTTAAATGATATTTTAACATGCTTATAT
GAAAATTTTGCTTTATCAAAGAGTGCATTTTTCAAGTGGCACGATGATGACGATCCACAT
GAGCAAGAAGGAAAAGGAGTTGCATTGAAAAGCATTCATCCGTTTATTCAATTTTTAAAA
ACTGAAAAGGATGAGAATGATGATGACTCTACAGGCGACGAAAATTAA

>g11510.t1 Gene=g11510 Length=1035
MDQSSSEELSHTFEIIDKKELLMTSTENDSDSLNNNNNINTDCDTNINDQMTTTIIAADK
ISEKNTDDDNGNNNTDNSNSKKYTRDQLIQMKQIASTMLPDLKREVKNLIFTETSALDNT
LNRKIRADAVIPNFMPLPGRNSAQRPKSEYAGNRKSQQGNKGQIITMRLTSNEEVKLNEA
KNAWKPSTLAQEEVVLSEEEKKTEELKKQFRGILNKLSPDNFLTLVGKLKTLQIDTVDRL
DECISLVFEKAITEPNYAPSYALLCKEVSDVFIVPLDPTNAQQQNAVFKKRLITQCQREF
EKHRDNELIKNTAERLKKIEAEEDPVKREELKNDFEYESMKVRKRAVGTVHFIGELYKIE
MLTSKIMRSCITHLLDPSMCSEETLECLCKLLETIGKRLEKTDKNRIDLTDYFQTLEKLA
DKKNPSGISARIRFMIQDVIELRMNNWTPRKPRQGNKPLTMDEIKQQVIMEQAIKEMDNR
EAFREQGNRQNTRRTGAVNEEGWSMSYSKSRPVKFDPLKLPTNASEDIKLGQPSNFQNFS
NFQSNRFAGLKEEDQMEQANRNYNGRFSGGASSNMNSPNRNSFENRNNRNNRGGNRSAGS
KSLQSPQLQKYGTSRNSNNMERHRNPSMQFHMQRPNDLPVKASLPTRKISAPARPMQYSE
AFIQERNLINDPNKVFNIMKSSLTGYQHNEITLDEIMENLKKFRISKDSLVLLYNWAFDQ
HDNERLQLTEIICEGVSGNIITTKDLLDALKETIELAQDLACDLPLVYNYIGQFLALPLT
KRIISLKDLYDISKSQIDEFSNGEVILKNVFKIIDARHGKDALSQLYCEANTNLQLFLDT
ANTQLSEFLKENNFDYLMQMQENNSMDNFDKELKDQLEQKLKSESDVEAIIIWITENIKE
HDNKFIRVLMELLLKNCIEKMHDGSYRLERERLDFFAPLLTQFVEKSKEKQIQCLQVIHR
YMNELEHPQSCLNDILTCLYENFALSKSAFFKWHDDDDPHEQEGKGVALKSIHPFIQFLK
TEKDENDDDSTGDEN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g11510.t1 CDD cd11559 W2_eIF4G1_like 871 999 1.22904E-22
11 g11510.t1 Coils Coil Coil 189 216 -
12 g11510.t1 Coils Coil Coil 302 322 -
10 g11510.t1 Gene3D G3DSA:1.25.40.180 - 197 448 8.5E-76
8 g11510.t1 Gene3D G3DSA:1.25.40.180 - 676 867 2.2E-23
9 g11510.t1 Gene3D G3DSA:1.25.40.180 - 871 1021 7.3E-33
22 g11510.t1 MobiDBLite mobidb-lite consensus disorder prediction 63 85 -
19 g11510.t1 MobiDBLite mobidb-lite consensus disorder prediction 71 85 -
17 g11510.t1 MobiDBLite mobidb-lite consensus disorder prediction 137 163 -
18 g11510.t1 MobiDBLite mobidb-lite consensus disorder prediction 146 163 -
16 g11510.t1 MobiDBLite mobidb-lite consensus disorder prediction 483 507 -
21 g11510.t1 MobiDBLite mobidb-lite consensus disorder prediction 489 506 -
20 g11510.t1 MobiDBLite mobidb-lite consensus disorder prediction 568 621 -
3 g11510.t1 PANTHER PTHR23253:SF63 EUKARYOTIC TRANSLATION INITIATION FACTOR 4G1, ISOFORM B-RELATED 26 1024 1.7E-119
4 g11510.t1 PANTHER PTHR23253 EUKARYOTIC TRANSLATION INITIATION FACTOR 4 GAMMA 26 1024 1.7E-119
1 g11510.t1 Pfam PF02854 MIF4G domain 209 446 1.8E-41
2 g11510.t1 Pfam PF02020 eIF4-gamma/eIF5/eIF2-epsilon 951 1029 8.3E-11
23 g11510.t1 ProSiteProfiles PS51366 MI domain profile. 670 794 9.522
24 g11510.t1 ProSiteProfiles PS51363 W2 domain profile. 863 1029 18.332
14 g11510.t1 SMART SM00543 if4_15 207 446 4.7E-35
15 g11510.t1 SMART SM00515 542_3 938 1025 4.4E-12
5 g11510.t1 SUPERFAMILY SSF48371 ARM repeat 199 448 3.22E-56
7 g11510.t1 SUPERFAMILY SSF48371 ARM repeat 710 858 9.59E-19
6 g11510.t1 SUPERFAMILY SSF48371 ARM repeat 869 993 8.9E-17

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