General information for g9652.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as HBS1-like protein.
Parent gene
- The parent gene g9652 is located on chr_1: 4486738..4487053 (+ strand)
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.t1 | TSS | g9652.t1 | 4483832 | 4483832 |
| chr_1 | g9652 | g9652.t1 | isoform | g9652.t1 | 4483931 | 4487053 |
| chr_1 | g9652 | g9652.t1 | exon | g9652.t1.exon1 | 4483931 | 4483970 |
| chr_1 | g9652 | g9652.t1 | cds | g9652.t1.CDS1 | 4483931 | 4483970 |
| chr_1 | g9652 | g9652.t1 | exon | g9652.t1.exon2 | 4484039 | 4484470 |
| chr_1 | g9652 | g9652.t1 | cds | g9652.t1.CDS2 | 4484039 | 4484470 |
| chr_1 | g9652 | g9652.t1 | exon | g9652.t1.exon3 | 4485409 | 4485942 |
| chr_1 | g9652 | g9652.t1 | cds | g9652.t1.CDS3 | 4485409 | 4485942 |
| chr_1 | g9652 | g9652.t1 | exon | g9652.t1.exon4 | 4485999 | 4486373 |
| chr_1 | g9652 | g9652.t1 | cds | g9652.t1.CDS4 | 4485999 | 4486373 |
| chr_1 | g9652 | g9652.t1 | exon | g9652.t1.exon5 | 4486431 | 4487053 |
| chr_1 | g9652 | g9652.t1 | cds | g9652.t1.CDS5 | 4486431 | 4487053 |
| chr_1 | g9652 | g9652.t1 | TTS | g9652.t1 | 4487132 | 4487132 |
Sequences
>g9652.t1 Gene=g9652 Length=2004
ATGTCACGACATAGAAATGTTAGGAATACGGCATACGATGATTATGACGACGACGATATT
GTTGGAAGTGTATCTGATGAGCCTGAATGCATATCTCCTACAGATGCTAAACAATGGATA
TTTGATAGAGCAAAGGGTCAATCTAGTTTAGAGCAGTTTCTTTCGAAAAATGAAGACATA
CAAGAGGAAGTAGAAGAGAATAATGATGATAGGAACATTTTTGATGGAAAAGTAAGACGA
GATTCAGAACATTATCAATTGCCTGATTTAAATGATATCGATAAAAGTAAACTGCTCTCA
TGCATGGAAGAAATCCGAAACATCATTGGAGAGACTTACTCAGATAAACGATTAGTGGAA
GCTATTATGTCCAATAATTTTAATTTTGACAAGGCACTCGATTGTCTACTTAATGGAGAA
AACAACAATACACAACAACAACGATCGAAAACTACAGAGACTATAGAGAAAGGCATTAGC
AATGTTTTGTATGAAAAGTCACAACAAATGAAACAGCAAAGGACTAAATTGACTATTAAA
ATAACTCCAGCATCGAAAATTAAGACATCAGGTTTTGAGATTAGTTCGCCAAAAGTGCAA
TCGCCAAAAACACAATCACCTTCTGGATCTGGAAGAAATTCTCCTGATGAAGAACAAAAC
AAATCAAATCGAACGAAAGAAGCATTAAGAAATGCGCGAGAACTTTATGAAAAGGAACGT
GGATCTGAAAAGGAACAACTTCATTTAGTTGTTATTGGTCATGTTGATGCAGGCAAATCT
ACAATGATGGGTCATTTATTATATGATCTAGGAAATGTTCCACAACGTTTGATGCATAAA
TATGAACAAGAGAGCAAAAAATTAGGTAAACAAAGTTTTGCTTTTGCTTGGGTGCTTGAT
GAAACAGGTGAAGAAAGAACGAGAGGTATCACAATGGATTGTGGTTTGCAGAGATTTGAA
ACCCCAACAAAACAAGTTACACTTCTTGATGCTCCTGGACATAAAGATTTCATACCTAAC
ATGATTTGTGGTGCAAATCAGGCTGATGTCGCAATACTCGTTGTTGATGCTACTCGTGGT
GAATTTGAAGCAGGTTTTGAGCAAGGAGGTCAAACAAGAGAGCATGCTTTACTTGTACGA
TCACTTGGTGTTAGTCAATTGTGTGTGGCTGTAAATAAATTAGACAACGAAAATTGGAGC
CAAGAACGTTTCAATGACATCATGACAAAACTCAAACAATTTTTGAAACAAGCAGGATTC
AAAGATTCCGAAGTTCATTATATACCTTGTTCAGGTCTTACAGGTGAAAACTTAGTTAAG
CCTTCGACTGAGCCCGCACTTAAAAGTTGGTATAATGGAAAAACATTATTAGAAGTTGTT
GATTCCTTTAAAGTTCCTGAAAGAGCAATAGACAAGCCATTCCGAATGTCTATTTCGGAT
GTTTTCAAAGGTGTTGGAAGTGCTGGTTTTTGTATTTCGGGAAGAATTGCATCAGGCCAT
GTCTGTGTGAATGATAAAGTTCTCATGTGTCCAAGTAGAGAACAATGTGTTGTCAAATAC
ATCACTATAGATGATGTTCAAGTTCAAACAGCATTTGCTGGTGATCAAGTTGCAATTACA
ATTACAGGCATTGATCCTTCAAATGTATCCGTTGGTTTTATATTATGCGACACACTTAAT
CCCGTTCCACTAGAAACAAAAATAAAAGCAAGAATAATTGTATTTAATGTCAAAACTCCA
ATAACTATAGGCTATCCTGTTTTATTACATCATCATTCGCTCGTAGAGCCAGCTATTATT
TCAAAGCTAAAAGCACAACTACACAAGGGTACAGGAGAAGTAATCAAAAAGAATCCTCGA
TGTTTAACTAATAACTCATGTGCACTAATTGAATTAAGTTTTCAACGTGCAATTGCAATT
GAAAAATATTCAGAATTAAAGGAAATGGGAAGAATAATGTTACGAGTTGGCGGAACAACG
ATTGCTGCTGGATTAGTTTTTTAA
>g9652.t1 Gene=g9652 Length=667
MSRHRNVRNTAYDDYDDDDIVGSVSDEPECISPTDAKQWIFDRAKGQSSLEQFLSKNEDI
QEEVEENNDDRNIFDGKVRRDSEHYQLPDLNDIDKSKLLSCMEEIRNIIGETYSDKRLVE
AIMSNNFNFDKALDCLLNGENNNTQQQRSKTTETIEKGISNVLYEKSQQMKQQRTKLTIK
ITPASKIKTSGFEISSPKVQSPKTQSPSGSGRNSPDEEQNKSNRTKEALRNARELYEKER
GSEKEQLHLVVIGHVDAGKSTMMGHLLYDLGNVPQRLMHKYEQESKKLGKQSFAFAWVLD
ETGEERTRGITMDCGLQRFETPTKQVTLLDAPGHKDFIPNMICGANQADVAILVVDATRG
EFEAGFEQGGQTREHALLVRSLGVSQLCVAVNKLDNENWSQERFNDIMTKLKQFLKQAGF
KDSEVHYIPCSGLTGENLVKPSTEPALKSWYNGKTLLEVVDSFKVPERAIDKPFRMSISD
VFKGVGSAGFCISGRIASGHVCVNDKVLMCPSREQCVVKYITIDDVQVQTAFAGDQVAIT
ITGIDPSNVSVGFILCDTLNPVPLETKIKARIIVFNVKTPITIGYPVLLHHHSLVEPAII
SKLKAQLHKGTGEVIKKNPRCLTNNSCALIELSFQRAIAIEKYSELKEMGRIMLRVGGTT
IAAGLVF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 21 | g9652.t1 | CDD | cd01883 | EF1_alpha | 248 | 467 | 8.093E-135 |
| 22 | g9652.t1 | CDD | cd16267 | HBS1-like_II | 473 | 557 | 1.69308E-38 |
| 23 | g9652.t1 | CDD | cd04093 | HBS1_C_III | 561 | 666 | 1.9094E-49 |
| 19 | g9652.t1 | Coils | Coil | Coil | 50 | 70 | - |
| 20 | g9652.t1 | Coils | Coil | Coil | 219 | 246 | - |
| 16 | g9652.t1 | Gene3D | G3DSA:1.10.8.10 | DNA helicase RuvA subunit | 90 | 145 | 1.9E-18 |
| 15 | g9652.t1 | Gene3D | G3DSA:3.40.50.300 | - | 216 | 466 | 1.2E-90 |
| 17 | g9652.t1 | Gene3D | G3DSA:2.40.30.10 | Translation factors | 470 | 560 | 2.7E-26 |
| 18 | g9652.t1 | Gene3D | G3DSA:2.40.30.10 | Translation factors | 561 | 667 | 1.2E-32 |
| 24 | g9652.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 190 | 226 | - |
| 25 | g9652.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 190 | 216 | - |
| 4 | g9652.t1 | PANTHER | PTHR23115:SF188 | HBS1-LIKE PROTEIN | 155 | 666 | 1.7E-244 |
| 5 | g9652.t1 | PANTHER | PTHR23115 | TRANSLATION FACTOR | 155 | 666 | 1.7E-244 |
| 8 | g9652.t1 | PRINTS | PR00315 | GTP-binding elongation factor signature | 248 | 261 | 4.5E-16 |
| 10 | g9652.t1 | PRINTS | PR00315 | GTP-binding elongation factor signature | 307 | 315 | 4.5E-16 |
| 7 | g9652.t1 | PRINTS | PR00315 | GTP-binding elongation factor signature | 327 | 337 | 4.5E-16 |
| 6 | g9652.t1 | PRINTS | PR00315 | GTP-binding elongation factor signature | 343 | 354 | 4.5E-16 |
| 9 | g9652.t1 | PRINTS | PR00315 | GTP-binding elongation factor signature | 387 | 396 | 4.5E-16 |
| 2 | g9652.t1 | Pfam | PF08938 | HBS1 N-terminus | 57 | 145 | 1.0E-16 |
| 3 | g9652.t1 | Pfam | PF00009 | Elongation factor Tu GTP binding domain | 247 | 462 | 3.0E-42 |
| 1 | g9652.t1 | Pfam | PF03143 | Elongation factor Tu C-terminal domain | 565 | 666 | 5.9E-14 |
| 26 | g9652.t1 | ProSiteProfiles | PS51722 | Translational (tr)-type guanine nucleotide-binding (G) domain profile. | 244 | 467 | 49.976 |
| 13 | g9652.t1 | SUPERFAMILY | SSF109732 | HBS1-like domain | 61 | 145 | 1.09E-21 |
| 12 | g9652.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 243 | 483 | 6.96E-62 |
| 14 | g9652.t1 | SUPERFAMILY | SSF50447 | Translation proteins | 465 | 561 | 1.85E-22 |
| 11 | g9652.t1 | SUPERFAMILY | SSF50465 | EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 567 | 666 | 1.3E-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
- This transcript has been annotated with K14416 (elongation factor 1 alpha-like protein)
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.
