Gene loci information

Transcript annotation

  • This transcript has been annotated as Exonuclease 1.

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_3 g2143 g2143.t14 isoform g2143.t14 15574620 15576592
chr_3 g2143 g2143.t14 exon g2143.t14.exon1 15574620 15574757
chr_3 g2143 g2143.t14 exon g2143.t14.exon2 15574818 15576592
chr_3 g2143 g2143.t14 cds g2143.t14.CDS1 15574835 15576592
chr_3 g2143 g2143.t14 TSS g2143.t14 NA NA
chr_3 g2143 g2143.t14 TTS g2143.t14 NA NA

Sequences

>g2143.t14 Gene=g2143 Length=1913
ATGGGAATTACAGGACTAATTAAGTTTGTTGACGATGCTATAACAACCTCAAGAATCAGC
ACATTAAACGGCTCAACTGTAGCTGTTGATTCTTATTATTTATTACATAAAGGAAGTTAT
TCTTGTGCTGATCGATTGGAATAAAATCAACAGCAATGATTTCTTATGCAATGAAATATG
TGAGAATGCTATTGAGTCACAGAATTTCTATCGTAATGGTGTTTGATGGCAAAAATTTAA
AAGCAAAAGCATTGACAGAAAAACGAAGACGAGAAGATAGAGAAAGTGCTAAAACAAAAG
CAACTGAATTACTAAGAGCAGGTAAAGTTGAAGAGGCTCGAAAAGAATTTACGAAGGCTG
TAAATATTACACATGATCATGCTCTTGAATTGATGGCAGAATGCCGCAAACTTGGTGTTG
ATTGCATTGTGGCAATGTATGAAGCAGATGCTCAACTCGCCTACCTCAATAAAATTGGTA
TAGTACAATATGTTATATCTGAAGATAGTGATTTAATATTGTTTGGGTGCAAAAACATAG
TCTATAAATTATCTCTTGATGAAAGCTGCCAGATTTATGATTCAAATCGACTTCATTTAG
CAATGAAAAAACCTAAAGATAAATTTTCATTTGAAACTTTTCGTCGTCTATGCATATTAT
CAGGTTGTGATTACATCGATAGCTTACCAGGAATAGGTTTAGTAAAAGCCTCAAAATTTT
TTGATATGACTAATGAAACTGATATGAAAATAGCATTATATCGAGTTCCGTCATATTTAA
AACTTAAGAAAGCTAATGTCACACCAGAATATGTAGATAATTTTTTAATAGCTGAAGCTA
CATTTAAGTATATGTATGTATTTGATCCAATCAAAAAAGAAATGGTACGACTGAATGAAA
TCGAAAATGAAGATGATCTCAAGTATTGTGTTAATGCTGGTGAATTATTGGATAAAGAGA
CTGCCTATCAATTAGCATTAGGAAATTTAAATCCGAGAACTATGGAGAAAGTTAATGACT
ATGATCCGTTTAAACACACATTTACGCGAAAAAGTATTTGGAGGACTACAAACATTGCAA
CAAATAATGATAAATCTATGCCGTCAACTATTCAAAAACGAATTCCTTCAATGTTCTTGA
ATACAAAACCAAAAGCCGAAGTGAAACCAGAAGTATATAAAATATTCAAGGAAGAAACGA
ATATGGAAGAAATTTTAATTGATGAACTTGTTCAATCATATACCAATAATTTACAAGAAA
AATCTGAAAATAATGCTAAAAAGAGATCACGTTTAGATTCTTTGAAGACTGAAGATAAAC
CTTCTGTATCATCTCACAATCCGTTTGCTAAAAAAATTAAATATGATAAAAATCAAGATG
ACCTAAATGATAGTAGCCTTAAAGGAGAAGATGCACATAATTTATCATTATTGGGTAACA
TAAAAGAAAAGATCAATGCACAAAGCCCCGAGAATACTGTTCAAAAAAGTAGATTTTTTC
AAGAATTTGTATCTTCTCATCATGTGCCAAAAGATATTATTTTAGAAAATTATTTAGATA
ATACTGATGATAATATTCCAATAATTACTGAACAGAAGGAACCAGACGAAATTAATCCAA
ATGAATTTATTTTCTTCCCAGAACAAATTGAAATTGGTGATGGAAAAAATTACAAATATG
ATTCGTGTACTCAATCATTTAGATCGAAAGTAAAAGAAAGTCCAAAGAAAATTGTATTAG
CATTTGACAAATGGAGGTCTAAATATGAAAATAAGAAAATTGATGATGAAAAAAATAACA
AGAAAGTTTCGAATCCTAAATCAAAAACGGAAGGTCCAAAGCCAATTGTTTTGGCATTTG
ACAAATGGAAGACCAAATATGAGAATAAGAAGCAATCAAATTGGCAAAAATAA

>g2143.t14 Gene=g2143 Length=585
MISYAMKYVRMLLSHRISIVMVFDGKNLKAKALTEKRRREDRESAKTKATELLRAGKVEE
ARKEFTKAVNITHDHALELMAECRKLGVDCIVAMYEADAQLAYLNKIGIVQYVISEDSDL
ILFGCKNIVYKLSLDESCQIYDSNRLHLAMKKPKDKFSFETFRRLCILSGCDYIDSLPGI
GLVKASKFFDMTNETDMKIALYRVPSYLKLKKANVTPEYVDNFLIAEATFKYMYVFDPIK
KEMVRLNEIENEDDLKYCVNAGELLDKETAYQLALGNLNPRTMEKVNDYDPFKHTFTRKS
IWRTTNIATNNDKSMPSTIQKRIPSMFLNTKPKAEVKPEVYKIFKEETNMEEILIDELVQ
SYTNNLQEKSENNAKKRSRLDSLKTEDKPSVSSHNPFAKKIKYDKNQDDLNDSSLKGEDA
HNLSLLGNIKEKINAQSPENTVQKSRFFQEFVSSHHVPKDIILENYLDNTDDNIPIITEQ
KEPDEINPNEFIFFPEQIEIGDGKNYKYDSCTQSFRSKVKESPKKIVLAFDKWRSKYENK
KIDDEKNNKKVSNPKSKTEGPKPIVLAFDKWKTKYENKKQSNWQK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g2143.t14 CDD cd09857 PIN_EXO1 2 148 2.16464E-72
12 g2143.t14 Coils Coil Coil 359 386 -
10 g2143.t14 Gene3D G3DSA:3.40.50.1010 - 1 152 5.6E-50
11 g2143.t14 Gene3D G3DSA:1.10.150.20 5’ to 3’ exonuclease 155 233 5.8E-25
19 g2143.t14 MobiDBLite mobidb-lite consensus disorder prediction 367 405 -
17 g2143.t14 MobiDBLite mobidb-lite consensus disorder prediction 370 388 -
16 g2143.t14 MobiDBLite mobidb-lite consensus disorder prediction 541 563 -
18 g2143.t14 MobiDBLite mobidb-lite consensus disorder prediction 541 556 -
2 g2143.t14 PANTHER PTHR11081:SF8 EXONUCLEASE 1 2 549 5.6E-89
3 g2143.t14 PANTHER PTHR11081 FLAP ENDONUCLEASE FAMILY MEMBER 2 549 5.6E-89
5 g2143.t14 PRINTS PR00853 Xeroderma pigmentosum group G/yeast RAD superfamily signature 19 38 8.8E-22
4 g2143.t14 PRINTS PR00853 Xeroderma pigmentosum group G/yeast RAD superfamily signature 83 100 8.8E-22
6 g2143.t14 PRINTS PR00853 Xeroderma pigmentosum group G/yeast RAD superfamily signature 104 124 8.8E-22
7 g2143.t14 PRINTS PR00853 Xeroderma pigmentosum group G/yeast RAD superfamily signature 162 177 8.8E-22
1 g2143.t14 Pfam PF00867 XPG I-region 85 172 2.1E-22
14 g2143.t14 SMART SM00484 xpgineu 84 148 3.5E-18
15 g2143.t14 SMART SM00279 HhH_4 159 192 2.1E-6
8 g2143.t14 SUPERFAMILY SSF88723 PIN domain-like 3 172 1.88E-43
9 g2143.t14 SUPERFAMILY SSF47807 5’ to 3’ exonuclease, C-terminal subdomain 158 296 3.44E-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 gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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