Gene loci information

Transcript annotation

  • This transcript has been annotated as Flap endonuclease 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 g12163 g12163.t3 TSS g12163.t3 21431704 21431704
chr_1 g12163 g12163.t3 isoform g12163.t3 21431819 21433028
chr_1 g12163 g12163.t3 exon g12163.t3.exon1 21431819 21431924
chr_1 g12163 g12163.t3 cds g12163.t3.CDS1 21431819 21431924
chr_1 g12163 g12163.t3 exon g12163.t3.exon2 21431995 21432734
chr_1 g12163 g12163.t3 cds g12163.t3.CDS2 21431995 21432734
chr_1 g12163 g12163.t3 exon g12163.t3.exon3 21432808 21433028
chr_1 g12163 g12163.t3 cds g12163.t3.CDS3 21432808 21432954
chr_1 g12163 g12163.t3 TTS g12163.t3 21433085 21433085

Sequences

>g12163.t3 Gene=g12163 Length=1067
ATGGGAATTACTGGACTTGCCAAATTAATTGCTGATATTGCGCCATGGGCAATTAAAGAA
ACAGAAATCAAAAATTATTTTGGAAGAAAAATTGCAATTGATGCAAGTATGTCTCTGTAC
CAATTTCTTATCGCTGTACGGGCTGAAGGAGCACAATTAACAGATGCAAATGGAGAAACA
ACATCACATTTGATGGGAATATTTTACAGAACAATTCGACTTTTGGAAAATGGCATAAAG
CCGGTTTATGTTTTTGACGGTAAGCCTCCAGATATGAAGAGTGGAGAACTTGTAAAACGT
GCAGAAAGACGTGAAGAAGCACAAAAAGCTTTAGAAAAAGCAACAGAAGCAGGAGATCAA
GTTGAAATGGACAAAATGAATCGACGTTTAGTAAAAGTTACAAAAGAACACAATAATGAA
GCAAAAGAATTGCTTAAACTCATGGGTGTTCCATATATTGATGCTGCATCTGAAGCTGAA
GCTCAATGTTCAGCTATGGTCAAAGGTGGAAAAGTTTTTGGAGTTGCGACTGAAGATATG
GATGCATTGACTTTCGGTGCAAATGTTCTTCTTCGTCATATGACATTCAGTGAAGCAAGG
AAAATGCCAGTACAAGAAATTCACTATGAGAAAGTCTTAAAAGGTCTCGAATTGGAACCA
AATGAGTTCATCGATCTTTGCATTTTAATGGGTTGCGATTATTGCGATACAATCAGAGGA
ATTGGACCAAAGAGAGCTTATGAGTTGATTCAAAAATACAAATCAATTGAAGAGATTGTG
AAGAACATTGATAAGAAGAAATATGAGGTGCCAGAAAATTGGAATTATGAACGAGCACGT
GAGCTTTCAAGTATTTATGTGGTGATAAGCAATTCAATGAAGAGCGTGTTCGTGCAGGAG
CTCAGAAAATTCAAAAATCTCTCAAAACTGCAACACAAGGACGTCTCGATAGTTTCTTTA
AAGTTATTCCATCAAGCACTCCTCCATCACTAAAACGTAAAGTAGATGACAAGAAAAGTT
CTGGAAGTGCTAAAAAAGTAAAGGGTAGTGGAAGGAAGCCTAAATAA

>g12163.t3 Gene=g12163 Length=330
MGITGLAKLIADIAPWAIKETEIKNYFGRKIAIDASMSLYQFLIAVRAEGAQLTDANGET
TSHLMGIFYRTIRLLENGIKPVYVFDGKPPDMKSGELVKRAERREEAQKALEKATEAGDQ
VEMDKMNRRLVKVTKEHNNEAKELLKLMGVPYIDAASEAEAQCSAMVKGGKVFGVATEDM
DALTFGANVLLRHMTFSEARKMPVQEIHYEKVLKGLELEPNEFIDLCILMGCDYCDTIRG
IGPKRAYELIQKYKSIEEIVKNIDKKKYEVPENWNYERARELSSIYVVISNSMKSVFVQE
LRKFKNLSKLQHKDVSIVSLKLFHQALLHH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g12163.t3 CDD cd09867 PIN_FEN1 4 222 1.23204E-130
15 g12163.t3 CDD cd09907 H3TH_FEN1-Euk 222 282 9.04957E-40
14 g12163.t3 Coils Coil Coil 97 143 -
13 g12163.t3 Gene3D G3DSA:3.40.50.1010 - 2 323 6.0E-125
5 g12163.t3 Hamap MF_00614 Flap endonuclease 1 [fen]. 1 330 117.00209
3 g12163.t3 PANTHER PTHR11081:SF51 FLAP ENDONUCLEASE 1 1 283 3.1E-134
4 g12163.t3 PANTHER PTHR11081 FLAP ENDONUCLEASE FAMILY MEMBER 1 283 3.1E-134
9 g12163.t3 PRINTS PR00853 Xeroderma pigmentosum group G/yeast RAD superfamily signature 28 42 1.2E-40
7 g12163.t3 PRINTS PR00853 Xeroderma pigmentosum group G/yeast RAD superfamily signature 81 100 1.2E-40
6 g12163.t3 PRINTS PR00853 Xeroderma pigmentosum group G/yeast RAD superfamily signature 145 162 1.2E-40
10 g12163.t3 PRINTS PR00853 Xeroderma pigmentosum group G/yeast RAD superfamily signature 166 186 1.2E-40
8 g12163.t3 PRINTS PR00853 Xeroderma pigmentosum group G/yeast RAD superfamily signature 223 238 1.2E-40
2 g12163.t3 Pfam PF00752 XPG N-terminal domain 1 107 3.8E-34
1 g12163.t3 Pfam PF00867 XPG I-region 146 233 1.1E-29
21 g12163.t3 ProSitePatterns PS00841 XPG protein signature 1. 79 93 -
18 g12163.t3 SMART SM00485 xpgn3 1 107 4.7E-56
19 g12163.t3 SMART SM00475 53exo3 29 305 1.6E-4
17 g12163.t3 SMART SM00484 xpgineu 146 218 3.5E-30
20 g12163.t3 SMART SM00279 HhH_4 220 253 9.6E-15
11 g12163.t3 SUPERFAMILY SSF88723 PIN domain-like 2 233 9.81E-72
12 g12163.t3 SUPERFAMILY SSF47807 5’ to 3’ exonuclease, C-terminal subdomain 218 290 1.38E-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:0003677 DNA binding MF
GO:0003824 catalytic activity MF
GO:0016788 hydrolase activity, acting on ester bonds 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