Gene loci information

Transcript annotation

  • This transcript has been annotated as Endonuclease III-like protein 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_1 g10945 g10945.t1 TSS g10945.t1 12935519 12935519
chr_1 g10945 g10945.t1 isoform g10945.t1 12935556 12936365
chr_1 g10945 g10945.t1 exon g10945.t1.exon1 12935556 12936365
chr_1 g10945 g10945.t1 cds g10945.t1.CDS1 12935556 12936365
chr_1 g10945 g10945.t1 TTS g10945.t1 12936496 12936496

Sequences

>g10945.t1 Gene=g10945 Length=810
ATGAGTAAGTCAAAAGCAAGTGGTAGCAAAGGCAATCGAAAGCATATTATAGTGAGTTAT
GAAGAAGGAAATAAAAGTGAAGTGAAAGATAAGAAAACAAAAGTAGAGCCAAAAAATTGG
CTACAAATTTATGAAAATATAAATGACATGAGGAAATTAAAACCAGCCCCAGTTGATAAA
ATGGGTTGTGAACAATGCGCAGACAATAAAATGGATATTGACACTCAACGATTTCAAACA
CTTGTAGCTTTAATGCTATCGGCTCAAACAAGAGATGAAGTAACATTCAGTGCTTGTCAG
CGATTAAAAGAATTTGGATTTACTGTCGAACATCTAGCTGAAGCAGATCAAAATAAATTG
GAAGAAGTTATCAAGCCAGTTGGATTCTATAGACAAAAGTCAAAACATATCATTCAATCA
TCAAAAATATTGCGGGATCAATATGACTCAAAAGTACCAAATGATTTAAAAGAATTACTG
AAATTGCCTGGTGTAGGAAAGAAAATGGCGAATATTGCTCTGGCAAGTTGTTTCGATAAT
GTTGTGGGAATTGGAGTTGACACTCACGTTCATCGTATTTCAAATCGTTTTGGCTGGGTA
AACTCAAAAACTCCTGAAGAAACACAAAAACAATTGGAAAGCTGGCTTCCTTATGAATAT
TGGCGTGATATAAATCTCACTTTGGTTGCATTTGGTCAAACAATTTGTCTTCCAAGACAT
CCAAAATGCATTGAATGTCTTAACAATAATATATGTCCAAGTGCATTCAAGGAGTCGCCA
AAGAAGACAAAAAGTCCTAAGAAAATGTGA

>g10945.t1 Gene=g10945 Length=269
MSKSKASGSKGNRKHIIVSYEEGNKSEVKDKKTKVEPKNWLQIYENINDMRKLKPAPVDK
MGCEQCADNKMDIDTQRFQTLVALMLSAQTRDEVTFSACQRLKEFGFTVEHLAEADQNKL
EEVIKPVGFYRQKSKHIIQSSKILRDQYDSKVPNDLKELLKLPGVGKKMANIALASCFDN
VVGIGVDTHVHRISNRFGWVNSKTPEETQKQLESWLPYEYWRDINLTLVAFGQTICLPRH
PKCIECLNNNICPSAFKESPKKTKSPKKM

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g10945.t1 CDD cd00056 ENDO3c 78 232 4.73669E-49
7 g10945.t1 Gene3D G3DSA:1.10.340.30 Hypothetical protein; domain 2 67 174 2.9E-31
8 g10945.t1 Gene3D G3DSA:1.10.1670.10 - 175 258 5.5E-27
5 g10945.t1 Hamap MF_03183 Endonuclease III-like protein 1 [NTHL1]. 36 258 41.127422
12 g10945.t1 MobiDBLite mobidb-lite consensus disorder prediction 1 33 -
13 g10945.t1 MobiDBLite mobidb-lite consensus disorder prediction 15 33 -
3 g10945.t1 PANTHER PTHR43286:SF1 ENDONUCLEASE III-LIKE PROTEIN 1 20 267 1.1E-102
4 g10945.t1 PANTHER PTHR43286 ENDONUCLEASE III-LIKE PROTEIN 1 20 267 1.1E-102
1 g10945.t1 Pfam PF00730 HhH-GPD superfamily base excision DNA repair protein 82 216 6.0E-25
2 g10945.t1 Pfam PF00633 Helix-hairpin-helix motif 148 171 1.2E-6
10 g10945.t1 SMART SM00478 endo3end 86 234 5.5E-55
11 g10945.t1 SMART SM00525 ccc3 235 255 0.0067
6 g10945.t1 SUPERFAMILY SSF48150 DNA-glycosylase 43 257 3.14E-64

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:0005634 nucleus CC
GO:0003906 DNA-(apurinic or apyrimidinic site) endonuclease activity MF
GO:0003677 DNA binding MF
GO:0006284 base-excision repair BP
GO:0006281 DNA repair BP
GO:0003824 catalytic activity MF
GO:0006285 base-excision repair, AP site formation BP
GO:0051539 4 iron, 4 sulfur cluster binding MF
GO:0019104 DNA N-glycosylase 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