Gene loci information

Transcript annotation

  • This transcript has been annotated as HBS1-like protein.

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 g9652 g9652.t6 TSS g9652.t6 4483832 4483832
chr_1 g9652 g9652.t6 isoform g9652.t6 4483931 4487053
chr_1 g9652 g9652.t6 exon g9652.t6.exon1 4483931 4484470
chr_1 g9652 g9652.t6 cds g9652.t6.CDS1 4484302 4484470
chr_1 g9652 g9652.t6 exon g9652.t6.exon2 4485409 4485942
chr_1 g9652 g9652.t6 cds g9652.t6.CDS2 4485409 4485942
chr_1 g9652 g9652.t6 exon g9652.t6.exon3 4485999 4486373
chr_1 g9652 g9652.t6 cds g9652.t6.CDS3 4485999 4486373
chr_1 g9652 g9652.t6 exon g9652.t6.exon4 4486431 4487053
chr_1 g9652 g9652.t6 cds g9652.t6.CDS4 4486431 4487053
chr_1 g9652 g9652.t6 TTS g9652.t6 4487132 4487132

Sequences

>g9652.t6 Gene=g9652 Length=2072
ATGTCACGACATAGAAATGTTAGGAATACGGCATACGATGGTAAATATATTAAAATCATT
AAATTTTGCTTATTATACATTAAAACAATATTTTTAAAATTCATTTAGATTATGACGACG
ACGATATTGTTGGAAGTGTATCTGATGAGCCTGAATGCATATCTCCTACAGATGCTAAAC
AATGGATATTTGATAGAGCAAAGGGTCAATCTAGTTTAGAGCAGTTTCTTTCGAAAAATG
AAGACATACAAGAGGAAGTAGAAGAGAATAATGATGATAGGAACATTTTTGATGGAAAAG
TAAGACGAGATTCAGAACATTATCAATTGCCTGATTTAAATGATATCGATAAAAGTAAAC
TGCTCTCATGCATGGAAGAAATCCGAAACATCATTGGAGAGACTTACTCAGATAAACGAT
TAGTGGAAGCTATTATGTCCAATAATTTTAATTTTGACAAGGCACTCGATTGTCTACTTA
ATGGAGAAAACAACAATACACAACAACAACGATCGAAAACTACAGAGACTATAGAGAAAG
GCATTAGCAATGTTTTGTATGAAAAGTCACAACAAATGAAACAGCAAAGGACTAAATTGA
CTATTAAAATAACTCCAGCATCGAAAATTAAGACATCAGGTTTTGAGATTAGTTCGCCAA
AAGTGCAATCGCCAAAAACACAATCACCTTCTGGATCTGGAAGAAATTCTCCTGATGAAG
AACAAAACAAATCAAATCGAACGAAAGAAGCATTAAGAAATGCGCGAGAACTTTATGAAA
AGGAACGTGGATCTGAAAAGGAACAACTTCATTTAGTTGTTATTGGTCATGTTGATGCAG
GCAAATCTACAATGATGGGTCATTTATTATATGATCTAGGAAATGTTCCACAACGTTTGA
TGCATAAATATGAACAAGAGAGCAAAAAATTAGGTAAACAAAGTTTTGCTTTTGCTTGGG
TGCTTGATGAAACAGGTGAAGAAAGAACGAGAGGTATCACAATGGATTGTGGTTTGCAGA
GATTTGAAACCCCAACAAAACAAGTTACACTTCTTGATGCTCCTGGACATAAAGATTTCA
TACCTAACATGATTTGTGGTGCAAATCAGGCTGATGTCGCAATACTCGTTGTTGATGCTA
CTCGTGGTGAATTTGAAGCAGGTTTTGAGCAAGGAGGTCAAACAAGAGAGCATGCTTTAC
TTGTACGATCACTTGGTGTTAGTCAATTGTGTGTGGCTGTAAATAAATTAGACAACGAAA
ATTGGAGCCAAGAACGTTTCAATGACATCATGACAAAACTCAAACAATTTTTGAAACAAG
CAGGATTCAAAGATTCCGAAGTTCATTATATACCTTGTTCAGGTCTTACAGGTGAAAACT
TAGTTAAGCCTTCGACTGAGCCCGCACTTAAAAGTTGGTATAATGGAAAAACATTATTAG
AAGTTGTTGATTCCTTTAAAGTTCCTGAAAGAGCAATAGACAAGCCATTCCGAATGTCTA
TTTCGGATGTTTTCAAAGGTGTTGGAAGTGCTGGTTTTTGTATTTCGGGAAGAATTGCAT
CAGGCCATGTCTGTGTGAATGATAAAGTTCTCATGTGTCCAAGTAGAGAACAATGTGTTG
TCAAATACATCACTATAGATGATGTTCAAGTTCAAACAGCATTTGCTGGTGATCAAGTTG
CAATTACAATTACAGGCATTGATCCTTCAAATGTATCCGTTGGTTTTATATTATGCGACA
CACTTAATCCCGTTCCACTAGAAACAAAAATAAAAGCAAGAATAATTGTATTTAATGTCA
AAACTCCAATAACTATAGGCTATCCTGTTTTATTACATCATCATTCGCTCGTAGAGCCAG
CTATTATTTCAAAGCTAAAAGCACAACTACACAAGGGTACAGGAGAAGTAATCAAAAAGA
ATCCTCGATGTTTAACTAATAACTCATGTGCACTAATTGAATTAAGTTTTCAACGTGCAA
TTGCAATTGAAAAATATTCAGAATTAAAGGAAATGGGAAGAATAATGTTACGAGTTGGCG
GAACAACGATTGCTGCTGGATTAGTTTTTTAA

>g9652.t6 Gene=g9652 Length=566
MEEIRNIIGETYSDKRLVEAIMSNNFNFDKALDCLLNGENNNTQQQRSKTTETIEKGISN
VLYEKSQQMKQQRTKLTIKITPASKIKTSGFEISSPKVQSPKTQSPSGSGRNSPDEEQNK
SNRTKEALRNARELYEKERGSEKEQLHLVVIGHVDAGKSTMMGHLLYDLGNVPQRLMHKY
EQESKKLGKQSFAFAWVLDETGEERTRGITMDCGLQRFETPTKQVTLLDAPGHKDFIPNM
ICGANQADVAILVVDATRGEFEAGFEQGGQTREHALLVRSLGVSQLCVAVNKLDNENWSQ
ERFNDIMTKLKQFLKQAGFKDSEVHYIPCSGLTGENLVKPSTEPALKSWYNGKTLLEVVD
SFKVPERAIDKPFRMSISDVFKGVGSAGFCISGRIASGHVCVNDKVLMCPSREQCVVKYI
TIDDVQVQTAFAGDQVAITITGIDPSNVSVGFILCDTLNPVPLETKIKARIIVFNVKTPI
TIGYPVLLHHHSLVEPAIISKLKAQLHKGTGEVIKKNPRCLTNNSCALIELSFQRAIAIE
KYSELKEMGRIMLRVGGTTIAAGLVF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
20 g9652.t6 CDD cd01883 EF1_alpha 147 366 5.80057E-136
21 g9652.t6 CDD cd16267 HBS1-like_II 372 456 9.27854E-39
22 g9652.t6 CDD cd04093 HBS1_C_III 460 565 1.88324E-49
19 g9652.t6 Coils Coil Coil 118 145 -
16 g9652.t6 Gene3D G3DSA:1.10.8.10 DNA helicase RuvA subunit 1 44 1.8E-11
15 g9652.t6 Gene3D G3DSA:3.40.50.300 - 115 365 8.3E-91
18 g9652.t6 Gene3D G3DSA:2.40.30.10 Translation factors 369 459 2.1E-26
17 g9652.t6 Gene3D G3DSA:2.40.30.10 Translation factors 460 566 9.1E-33
23 g9652.t6 MobiDBLite mobidb-lite consensus disorder prediction 89 125 -
24 g9652.t6 MobiDBLite mobidb-lite consensus disorder prediction 89 115 -
4 g9652.t6 PANTHER PTHR23115:SF188 HBS1-LIKE PROTEIN 43 565 1.7E-243
5 g9652.t6 PANTHER PTHR23115 TRANSLATION FACTOR 43 565 1.7E-243
10 g9652.t6 PRINTS PR00315 GTP-binding elongation factor signature 147 160 2.2E-16
9 g9652.t6 PRINTS PR00315 GTP-binding elongation factor signature 206 214 2.2E-16
6 g9652.t6 PRINTS PR00315 GTP-binding elongation factor signature 226 236 2.2E-16
7 g9652.t6 PRINTS PR00315 GTP-binding elongation factor signature 242 253 2.2E-16
8 g9652.t6 PRINTS PR00315 GTP-binding elongation factor signature 286 295 2.2E-16
2 g9652.t6 Pfam PF08938 HBS1 N-terminus 1 44 4.0E-8
3 g9652.t6 Pfam PF00009 Elongation factor Tu GTP binding domain 146 361 2.1E-42
1 g9652.t6 Pfam PF03143 Elongation factor Tu C-terminal domain 464 565 4.6E-14
25 g9652.t6 ProSiteProfiles PS51722 Translational (tr)-type guanine nucleotide-binding (G) domain profile. 143 366 49.976
13 g9652.t6 SUPERFAMILY SSF109732 HBS1-like domain 1 44 2.48E-10
12 g9652.t6 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 142 382 4.67E-62
14 g9652.t6 SUPERFAMILY SSF50447 Translation proteins 364 460 1.43E-22
11 g9652.t6 SUPERFAMILY SSF50465 EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain 466 565 1.01E-26

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:0005525 GTP binding MF
GO:0003924 GTPase activity 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