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.t4 TSS g12163.t4 21431704 21431704
chr_1 g12163 g12163.t4 isoform g12163.t4 21431927 21433028
chr_1 g12163 g12163.t4 exon g12163.t4.exon1 21431927 21433028
chr_1 g12163 g12163.t4 cds g12163.t4.CDS1 21431997 21433028
chr_1 g12163 g12163.t4 TTS g12163.t4 21433085 21433085

Sequences

>g12163.t4 Gene=g12163 Length=1102
AAGTAAATTTGTGAAATCTTTATTTGAAAATGGTTGTAAAGCAAATGATTATATCTTATT
TTATTTAGGTATGTCTCTGTACCAATTTCTTATCGCTGTACGGGCTGAAGGAGCACAATT
AACAGATGCAAATGGAGAAACAACATCACATTTGATGGGAATATTTTACAGAACAATTCG
ACTTTTGGAAAATGGCATAAAGCCGGTTTATGTTTTTGACGGTAAGCCTCCAGATATGAA
GAGTGGAGAACTTGTAAAACGTGCAGAAAGACGTGAAGAAGCACAAAAAGCTTTAGAAAA
AGCAACAGAAGCAGGAGATCAAGTTGAAATGGACAAAATGAATCGACGTTTAGTAAAAGT
TACAAAAGAACACAATAATGAAGCAAAAGAATTGCTTAAACTCATGGGTGTTCCATATAT
TGATGCTGCATCTGAAGCTGAAGCTCAATGTTCAGCTATGGTCAAAGGTGGAAAAGTTTT
TGGAGTTGCGACTGAAGATATGGATGCATTGACTTTCGGTGCAAATGTTCTTCTTCGTCA
TATGACATTCAGTGAAGCAAGGAAAATGCCAGTACAAGAAATTCACTATGAGAAAGTCTT
AAAAGGTCTCGAATTGGAACCAAATGAGTTCATCGATCTTTGCATTTTAATGGGTTGCGA
TTATTGCGATACAATCAGAGGAATTGGACCAAAGAGAGCTTATGAGTTGATTCAAAAATA
CAAATCAATTGAAGAGATTGTGAAGAACATTGATAAGAAGAAATATGAGGTGCCAGAAAA
TTGGAATTATGAACGAGCACGTGAGCTTTTCAAGGAACCAGAAATTACTGATATCGAAAC
AATTGAGCTCAAATGGACACAGCCTGATGAAGACGGTTTAGTCAAGTATTTATGTGGTGA
TAAGCAATTCAATGAAGAGCGTGTTCGTGCAGGAGCTCAGAAAATTCAAAAATCTCTCAA
AACTGCAACACAAGGACGTCTCGATAGTTTCTTTAAAGTTATTCCATCAAGCACTCCTCC
ATCACTAAAACGTAAAGTAGATGACAAGAAAAGTTCTGGAAGTGCTAAAAAAGTAAAGGG
TAGTGGAAGGAAGCCTAAATAA

>g12163.t4 Gene=g12163 Length=343
MSLYQFLIAVRAEGAQLTDANGETTSHLMGIFYRTIRLLENGIKPVYVFDGKPPDMKSGE
LVKRAERREEAQKALEKATEAGDQVEMDKMNRRLVKVTKEHNNEAKELLKLMGVPYIDAA
SEAEAQCSAMVKGGKVFGVATEDMDALTFGANVLLRHMTFSEARKMPVQEIHYEKVLKGL
ELEPNEFIDLCILMGCDYCDTIRGIGPKRAYELIQKYKSIEEIVKNIDKKKYEVPENWNY
ERARELFKEPEITDIETIELKWTQPDEDGLVKYLCGDKQFNEERVRAGAQKIQKSLKTAT
QGRLDSFFKVIPSSTPPSLKRKVDDKKSSGSAKKVKGSGRKPK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
20 g12163.t4 CDD cd09867 PIN_FEN1 1 294 1.17323E-120
19 g12163.t4 CDD cd09907 H3TH_FEN1-Euk 186 254 7.21351E-45
13 g12163.t4 Coils Coil Coil 61 107 -
12 g12163.t4 Gene3D G3DSA:3.40.50.1010 - 1 322 1.5E-135
5 g12163.t4 Hamap MF_00614 Flap endonuclease 1 [fen]. 1 309 135.582275
26 g12163.t4 MobiDBLite mobidb-lite consensus disorder prediction 316 343 -
3 g12163.t4 PANTHER PTHR11081:SF51 FLAP ENDONUCLEASE 1 1 339 2.9E-147
4 g12163.t4 PANTHER PTHR11081 FLAP ENDONUCLEASE FAMILY MEMBER 1 339 2.9E-147
6 g12163.t4 PRINTS PR00853 Xeroderma pigmentosum group G/yeast RAD superfamily signature 45 64 7.4E-33
9 g12163.t4 PRINTS PR00853 Xeroderma pigmentosum group G/yeast RAD superfamily signature 109 126 7.4E-33
8 g12163.t4 PRINTS PR00853 Xeroderma pigmentosum group G/yeast RAD superfamily signature 130 150 7.4E-33
7 g12163.t4 PRINTS PR00853 Xeroderma pigmentosum group G/yeast RAD superfamily signature 187 202 7.4E-33
2 g12163.t4 Pfam PF00752 XPG N-terminal domain 1 71 1.3E-19
1 g12163.t4 Pfam PF00867 XPG I-region 110 197 1.2E-29
15 g12163.t4 Phobius SIGNAL_PEPTIDE Signal peptide region 1 14 -
16 g12163.t4 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
17 g12163.t4 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 10 -
18 g12163.t4 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 11 14 -
14 g12163.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 15 343 -
25 g12163.t4 ProSitePatterns PS00841 XPG protein signature 1. 43 57 -
22 g12163.t4 SMART SM00485 xpgn3 1 71 2.8E-21
23 g12163.t4 SMART SM00475 53exo3 10 261 5.4E-4
21 g12163.t4 SMART SM00484 xpgineu 110 182 3.5E-30
24 g12163.t4 SMART SM00279 HhH_4 184 217 9.6E-15
10 g12163.t4 SUPERFAMILY SSF88723 PIN domain-like 1 197 1.08E-60
11 g12163.t4 SUPERFAMILY SSF47807 5’ to 3’ exonuclease, C-terminal subdomain 182 316 8.37E-44

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

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