General information for g1758.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as RNA exonuclease 1-like protein.
Parent gene
- The parent gene g1758 is located on chr_3: 12875380..12876418 (+ 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_3 | g1758 | g1758.t1 | TSS | g1758.t1 | 12873111 | 12873111 |
| chr_3 | g1758 | g1758.t1 | isoform | g1758.t1 | 12873343 | 12876109 |
| chr_3 | g1758 | g1758.t1 | exon | g1758.t1.exon1 | 12873343 | 12873451 |
| chr_3 | g1758 | g1758.t1 | cds | g1758.t1.CDS1 | 12873343 | 12873451 |
| chr_3 | g1758 | g1758.t1 | exon | g1758.t1.exon2 | 12873514 | 12875910 |
| chr_3 | g1758 | g1758.t1 | cds | g1758.t1.CDS2 | 12873514 | 12875910 |
| chr_3 | g1758 | g1758.t1 | exon | g1758.t1.exon3 | 12876027 | 12876109 |
| chr_3 | g1758 | g1758.t1 | cds | g1758.t1.CDS3 | 12876027 | 12876109 |
| chr_3 | g1758 | g1758.t1 | TTS | g1758.t1 | 12876257 | 12876257 |
Sequences
>g1758.t1 Gene=g1758 Length=2589
ATGCTGCCTTCAACAGGATTATTTCGGAATATTTCATGTCCTTTTTATGAAGATGAAAAT
GAAGGATGTGTGAGGCCTTTTTGTCACTACTTACACGGACATAGGCGAATAGTGGAAACA
ACAAAACCGGTCTATCATGCAACTCCAATAACTCCTAAACCTGAAGAATCTAATAATATT
GCGAAAAAACCAAAACTTGAATATCTTCCTATTCCAATAAAGAAAACTGTTGCAACTTAT
ACACCAGCTGCTGTTAAGAATGATGATACATATGATCCAAATACAAATCAAGTGAACGAA
ACTGTGGCTTATGTTGCCTCAAAAATAGAAACTCCAAATGAGACATCAAGTGAAAAAGAA
TCAGAAGAAAAGAGTAAGAATAGCGATGAAAAAGATGAGAAAAAGAATAAATCAAGCAGC
TCATCATCACGACATCGATCACATAAAAGTTCTTCACATCGTGACTCGAATAGTTCAAGT
TCATCTTCATCACATAAGCACAAATCATCAAAAGATCGTCATAAATCCTCATCTTCATCA
AAAAGCAATAGTAAGGACCATAAATCAAGTCATAAACATAAAAGTAGAGATAAAGACAAG
CATGGGCATAGAGATAAAGACAAAAGTAATGAAAAGCATAGAGATAAAGAAAGGAAAAAG
GAAAAAGAGCAGAAAAAGAATGAATCAAAAGAAGTTGAAGAGATACCAGAAATCCCTATA
CTACATGATCTTAGTGAAGACGATGAAGATGACATTGAAGATCAATGCAGAATGATTTTT
GAAAGCTATGAACCATCACAAGAACCAACTAATGTACCAACATATACTCCAAGTACTTCA
AAAAATCCTGAAGAAAGTGATGATCAAATATACGGAGGCAAAAAACGACAAGCATATGAG
AATGCATCAAAAATTGTCAAAACTGCACCAGTTATTAGACAAAATCATTCACAAACTGCT
CTACAAACAGCTCAGATGAGGCACGATGTGGCTATTCAAAAAGCTATTGCAATGAAAAAA
GAGGCAGAAGAACAAATTGCTAAACTAACAGCTGATATAAAAGAAAAAGAGCAGACATTA
ACACCATTAATAAATCCATTAATACATGTTCGCCCACCACCATTAAAACGTCCATTAATT
ACTCCTATTTCTCAGAGAATGGCAATTGAAGCTGCAAAACGTAAAGTAATGGAATTAAAT
AAATCAATAGATCATAGTTTTCAAAAGTCTTCAACGCCTGCCCAAACATCTTCAAAAAGT
GGTAGCAGAGTGGCACATGTACCAACAAAAATTAACGATCTTGATATTAGTAAAATGGCA
CCACCGGTTATTGACTCACATCAAACAAAAATCTCATGCAATATTCGCACTCAACTCTAT
AAAATAATGGTTAAACATTGTCTCGAAATTTACTCTCTTCCTGCTGATGCATTTGAAAGG
GCACAAAATGAAGAGCATCAAGTTTTTAAAAAGTGTTCAATTGTACCAACTTATAAAACT
AGCTGTATGTTAGCAATTAATCGACTGAAAAAAGAAGCTGAAAATTGTGGAGCAAAGAAG
AATCCTAGATCAATATCACATGAAGTGTTACTCGCTGGTGCTGCTGGATCAAAAGTTTCT
TGGTCAATGAATAATAAGCAAAAAGTGGCAAATTCTGACTCTTCATTGTTAACAATTGAC
AATTGTTCAAGTTCTCAAGCTTATGATCTCGTTGCTGATTGTCTTCTTACTGAACAACAA
TTAAGAGAAAATGGATTTCCACGACAAACTGAAATAAAAGGAAGAGCTCAGTTTTTTACT
CCAAAGAAAGCGAAGCCGCAAAATGGGCGCGATGATGATTATTATTGTGCGCGATGCAAC
AAGGTCTTTAACGTTGAAATTTATGATGAAGTTCAGCGAGATTTATGTAATTATCACCCT
AAAAGATCAGGATATAGACGAGGTCATGCAGATAATTATTATTACTGTTGTCAATCAATA
GCCGGAAGTACAGGATGTTGTTACGCTGACTATCACGTATTTGATTATATCGATTATAAT
AATCTCGTTGGATATGTCAAAACAATGGATAAAGATGAAAATTATGTGTGCACAAAAAAA
GATATTTTTGCATTAGATTGTGAAATGTGCTATACAGTATGTGGTTTTGAATTGACACGT
TTGACAATTGTCGATTATGATGAGAAAGTTGTTTATGATAAATTCGTCCGACCACAAAAT
CGTGTAATTGACTATAATACAAGATACTCTGGAATAACGGAAGCAACTTTATCTTCAAAA
GATGCGTTAACACTTCCTGAAATTCAAGCAGTATTATTATCATTATTTCACTCGAGGACT
ATATTAATTGGACATTCACTTGAAAGTGATTTCAAGAGTCTAAAATTAATACACTCTACT
GTTGTTGATACATCTGTTTTGTATCCACATAAAATGGGATTTCCTAAAAAGAGAGCTTTA
AAAACATTATGCATTGAATATTTGAAAAAGATCATACAAGAAGATGACGCCGGTCACGAT
TCTGCTGAAGATTCAACAGTGTGCATTCAATTGGTAAAAAATTATTTGAGGAATCGTATT
GTCAATTGA
>g1758.t1 Gene=g1758 Length=862
MLPSTGLFRNISCPFYEDENEGCVRPFCHYLHGHRRIVETTKPVYHATPITPKPEESNNI
AKKPKLEYLPIPIKKTVATYTPAAVKNDDTYDPNTNQVNETVAYVASKIETPNETSSEKE
SEEKSKNSDEKDEKKNKSSSSSSRHRSHKSSSHRDSNSSSSSSSHKHKSSKDRHKSSSSS
KSNSKDHKSSHKHKSRDKDKHGHRDKDKSNEKHRDKERKKEKEQKKNESKEVEEIPEIPI
LHDLSEDDEDDIEDQCRMIFESYEPSQEPTNVPTYTPSTSKNPEESDDQIYGGKKRQAYE
NASKIVKTAPVIRQNHSQTALQTAQMRHDVAIQKAIAMKKEAEEQIAKLTADIKEKEQTL
TPLINPLIHVRPPPLKRPLITPISQRMAIEAAKRKVMELNKSIDHSFQKSSTPAQTSSKS
GSRVAHVPTKINDLDISKMAPPVIDSHQTKISCNIRTQLYKIMVKHCLEIYSLPADAFER
AQNEEHQVFKKCSIVPTYKTSCMLAINRLKKEAENCGAKKNPRSISHEVLLAGAAGSKVS
WSMNNKQKVANSDSSLLTIDNCSSSQAYDLVADCLLTEQQLRENGFPRQTEIKGRAQFFT
PKKAKPQNGRDDDYYCARCNKVFNVEIYDEVQRDLCNYHPKRSGYRRGHADNYYYCCQSI
AGSTGCCYADYHVFDYIDYNNLVGYVKTMDKDENYVCTKKDIFALDCEMCYTVCGFELTR
LTIVDYDEKVVYDKFVRPQNRVIDYNTRYSGITEATLSSKDALTLPEIQAVLLSLFHSRT
ILIGHSLESDFKSLKLIHSTVVDTSVLYPHKMGFPKKRALKTLCIEYLKKIIQEDDAGHD
SAEDSTVCIQLVKNYLRNRIVN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g1758.t1 | CDD | cd06145 | REX1_like | 703 | 853 | 1.13468E-82 |
| 7 | g1758.t1 | Coils | Coil | Coil | 206 | 233 | - |
| 6 | g1758.t1 | Coils | Coil | Coil | 332 | 359 | - |
| 5 | g1758.t1 | Gene3D | G3DSA:3.30.420.10 | - | 696 | 861 | 2.3E-47 |
| 12 | g1758.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 108 | 248 | - |
| 11 | g1758.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 113 | 140 | - |
| 13 | g1758.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 200 | 242 | - |
| 15 | g1758.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 262 | 291 | - |
| 14 | g1758.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 264 | 286 | - |
| 10 | g1758.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 404 | 425 | - |
| 2 | g1758.t1 | PANTHER | PTHR12801:SF138 | FI18136P1-RELATED | 327 | 857 | 1.9E-129 |
| 3 | g1758.t1 | PANTHER | PTHR12801 | RNA EXONUCLEASE REXO1 / RECO3 FAMILY MEMBER-RELATED | 327 | 857 | 1.9E-129 |
| 1 | g1758.t1 | Pfam | PF15870 | ElonginA binding-protein 1 | 441 | 602 | 1.7E-38 |
| 9 | g1758.t1 | SMART | SM00479 | exoiiiendus | 701 | 861 | 2.9E-32 |
| 4 | g1758.t1 | SUPERFAMILY | SSF53098 | Ribonuclease H-like | 702 | 858 | 1.04E-25 |
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:0003676 | nucleic acid binding | MF |
KEGG
Orthology
- This transcript has been annotated with K14570 (RNA exonuclease [EC:3.1.-.-])
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.
