General information for g2143.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Exonuclease 1.
Parent gene
- The parent gene g2143 is located on chr_3: 15576592..15577976 (+ 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 | g2143 | g2143.t1 | isoform | g2143.t1 | 15574620 | 15576592 |
| chr_3 | g2143 | g2143.t1 | exon | g2143.t1.exon1 | 15574620 | 15574757 |
| chr_3 | g2143 | g2143.t1 | cds | g2143.t1.CDS1 | 15574620 | 15574757 |
| chr_3 | g2143 | g2143.t1 | exon | g2143.t1.exon2 | 15574811 | 15576592 |
| chr_3 | g2143 | g2143.t1 | cds | g2143.t1.CDS2 | 15574811 | 15576592 |
| chr_3 | g2143 | g2143.t1 | TSS | g2143.t1 | NA | NA |
| chr_3 | g2143 | g2143.t1 | TTS | g2143.t1 | NA | NA |
Sequences
>g2143.t1 Gene=g2143 Length=1920
ATGGGAATTACAGGACTAATTAAGTTTGTTGACGATGCTATAACAACCTCAAGAATCAGC
ACATTAAACGGCTCAACTGTAGCTGTTGATTCTTATTATTTATTACATAAAGGAAGTTAT
TCTTGTGCTGATCGATTGGTACAAGGAATAAAATCAACAGCAATGATTTCTTATGCAATG
AAATATGTGAGAATGCTATTGAGTCACAGAATTTCTATCGTAATGGTGTTTGATGGCAAA
AATTTAAAAGCAAAAGCATTGACAGAAAAACGAAGACGAGAAGATAGAGAAAGTGCTAAA
ACAAAAGCAACTGAATTACTAAGAGCAGGTAAAGTTGAAGAGGCTCGAAAAGAATTTACG
AAGGCTGTAAATATTACACATGATCATGCTCTTGAATTGATGGCAGAATGCCGCAAACTT
GGTGTTGATTGCATTGTGGCAATGTATGAAGCAGATGCTCAACTCGCCTACCTCAATAAA
ATTGGTATAGTACAATATGTTATATCTGAAGATAGTGATTTAATATTGTTTGGGTGCAAA
AACATAGTCTATAAATTATCTCTTGATGAAAGCTGCCAGATTTATGATTCAAATCGACTT
CATTTAGCAATGAAAAAACCTAAAGATAAATTTTCATTTGAAACTTTTCGTCGTCTATGC
ATATTATCAGGTTGTGATTACATCGATAGCTTACCAGGAATAGGTTTAGTAAAAGCCTCA
AAATTTTTTGATATGACTAATGAAACTGATATGAAAATAGCATTATATCGAGTTCCGTCA
TATTTAAAACTTAAGAAAGCTAATGTCACACCAGAATATGTAGATAATTTTTTAATAGCT
GAAGCTACATTTAAGTATATGTATGTATTTGATCCAATCAAAAAAGAAATGGTACGACTG
AATGAAATCGAAAATGAAGATGATCTCAAGTATTGTGTTAATGCTGGTGAATTATTGGAT
AAAGAGACTGCCTATCAATTAGCATTAGGAAATTTAAATCCGAGAACTATGGAGAAAGTT
AATGACTATGATCCGTTTAAACACACATTTACGCGAAAAAGTATTTGGAGGACTACAAAC
ATTGCAACAAATAATGATAAATCTATGCCGTCAACTATTCAAAAACGAATTCCTTCAATG
TTCTTGAATACAAAACCAAAAGCCGAAGTGAAACCAGAAGTATATAAAATATTCAAGGAA
GAAACGAATATGGAAGAAATTTTAATTGATGAACTTGTTCAATCATATACCAATAATTTA
CAAGAAAAATCTGAAAATAATGCTAAAAAGAGATCACGTTTAGATTCTTTGAAGACTGAA
GATAAACCTTCTGTATCATCTCACAATCCGTTTGCTAAAAAAATTAAATATGATAAAAAT
CAAGATGACCTAAATGATAGTAGCCTTAAAGGAGAAGATGCACATAATTTATCATTATTG
GGTAACATAAAAGAAAAGATCAATGCACAAAGCCCCGAGAATACTGTTCAAAAAAGTAGA
TTTTTTCAAGAATTTGTATCTTCTCATCATGTGCCAAAAGATATTATTTTAGAAAATTAT
TTAGATAATACTGATGATAATATTCCAATAATTACTGAACAGAAGGAACCAGACGAAATT
AATCCAAATGAATTTATTTTCTTCCCAGAACAAATTGAAATTGGTGATGGAAAAAATTAC
AAATATGATTCGTGTACTCAATCATTTAGATCGAAAGTAAAAGAAAGTCCAAAGAAAATT
GTATTAGCATTTGACAAATGGAGGTCTAAATATGAAAATAAGAAAATTGATGATGAAAAA
AATAACAAGAAAGTTTCGAATCCTAAATCAAAAACGGAAGGTCCAAAGCCAATTGTTTTG
GCATTTGACAAATGGAAGACCAAATATGAGAATAAGAAGCAATCAAATTGGCAAAAATAA
>g2143.t1 Gene=g2143 Length=639
MGITGLIKFVDDAITTSRISTLNGSTVAVDSYYLLHKGSYSCADRLVQGIKSTAMISYAM
KYVRMLLSHRISIVMVFDGKNLKAKALTEKRRREDRESAKTKATELLRAGKVEEARKEFT
KAVNITHDHALELMAECRKLGVDCIVAMYEADAQLAYLNKIGIVQYVISEDSDLILFGCK
NIVYKLSLDESCQIYDSNRLHLAMKKPKDKFSFETFRRLCILSGCDYIDSLPGIGLVKAS
KFFDMTNETDMKIALYRVPSYLKLKKANVTPEYVDNFLIAEATFKYMYVFDPIKKEMVRL
NEIENEDDLKYCVNAGELLDKETAYQLALGNLNPRTMEKVNDYDPFKHTFTRKSIWRTTN
IATNNDKSMPSTIQKRIPSMFLNTKPKAEVKPEVYKIFKEETNMEEILIDELVQSYTNNL
QEKSENNAKKRSRLDSLKTEDKPSVSSHNPFAKKIKYDKNQDDLNDSSLKGEDAHNLSLL
GNIKEKINAQSPENTVQKSRFFQEFVSSHHVPKDIILENYLDNTDDNIPIITEQKEPDEI
NPNEFIFFPEQIEIGDGKNYKYDSCTQSFRSKVKESPKKIVLAFDKWRSKYENKKIDDEK
NNKKVSNPKSKTEGPKPIVLAFDKWKTKYENKKQSNWQK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g2143.t1 | CDD | cd09857 | PIN_EXO1 | 1 | 202 | 3.42548E-98 |
| 14 | g2143.t1 | Coils | Coil | Coil | 413 | 440 | - |
| 12 | g2143.t1 | Gene3D | G3DSA:3.40.50.1010 | - | 1 | 206 | 1.2E-68 |
| 13 | g2143.t1 | Gene3D | G3DSA:1.10.150.20 | 5’ to 3’ exonuclease | 209 | 287 | 6.5E-25 |
| 20 | g2143.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 422 | 459 | - |
| 21 | g2143.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 424 | 442 | - |
| 19 | g2143.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 595 | 610 | - |
| 22 | g2143.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 595 | 617 | - |
| 3 | g2143.t1 | PANTHER | PTHR11081:SF8 | EXONUCLEASE 1 | 1 | 603 | 1.7E-107 |
| 4 | g2143.t1 | PANTHER | PTHR11081 | FLAP ENDONUCLEASE FAMILY MEMBER | 1 | 603 | 1.7E-107 |
| 6 | g2143.t1 | PRINTS | PR00853 | Xeroderma pigmentosum group G/yeast RAD superfamily signature | 24 | 38 | 4.4E-26 |
| 8 | g2143.t1 | PRINTS | PR00853 | Xeroderma pigmentosum group G/yeast RAD superfamily signature | 73 | 92 | 4.4E-26 |
| 9 | g2143.t1 | PRINTS | PR00853 | Xeroderma pigmentosum group G/yeast RAD superfamily signature | 137 | 154 | 4.4E-26 |
| 7 | g2143.t1 | PRINTS | PR00853 | Xeroderma pigmentosum group G/yeast RAD superfamily signature | 158 | 178 | 4.4E-26 |
| 5 | g2143.t1 | PRINTS | PR00853 | Xeroderma pigmentosum group G/yeast RAD superfamily signature | 216 | 231 | 4.4E-26 |
| 2 | g2143.t1 | Pfam | PF00752 | XPG N-terminal domain | 1 | 98 | 2.4E-15 |
| 1 | g2143.t1 | Pfam | PF00867 | XPG I-region | 139 | 226 | 2.3E-22 |
| 17 | g2143.t1 | SMART | SM00485 | xpgn3 | 1 | 99 | 5.1E-26 |
| 16 | g2143.t1 | SMART | SM00484 | xpgineu | 138 | 202 | 3.5E-18 |
| 18 | g2143.t1 | SMART | SM00279 | HhH_4 | 213 | 246 | 2.1E-6 |
| 10 | g2143.t1 | SUPERFAMILY | SSF88723 | PIN domain-like | 2 | 226 | 2.1E-56 |
| 11 | g2143.t1 | SUPERFAMILY | SSF47807 | 5’ to 3’ exonuclease, C-terminal subdomain | 212 | 350 | 4.04E-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:0003677 | DNA binding | MF |
| GO:0006281 | DNA repair | BP |
| GO:0035312 | 5’-3’ exodeoxyribonuclease activity | MF |
| GO:0003824 | catalytic activity | MF |
| GO:0004518 | nuclease activity | MF |
KEGG
Orthology
- This transcript has been annotated with K10746 (exonuclease 1 [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.
