Gene loci information

Transcript annotation

  • This transcript has been annotated as Structure-specific endonuclease subunit SLX1-like protein.

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_2 g7495 g7495.t1 TTS g7495.t1 23998111 23998111
chr_2 g7495 g7495.t1 isoform g7495.t1 23998297 23999276
chr_2 g7495 g7495.t1 exon g7495.t1.exon1 23998297 23998759
chr_2 g7495 g7495.t1 cds g7495.t1.CDS1 23998297 23998759
chr_2 g7495 g7495.t1 exon g7495.t1.exon2 23998818 23998913
chr_2 g7495 g7495.t1 cds g7495.t1.CDS2 23998818 23998913
chr_2 g7495 g7495.t1 exon g7495.t1.exon3 23998971 23999124
chr_2 g7495 g7495.t1 cds g7495.t1.CDS3 23998971 23999124
chr_2 g7495 g7495.t1 exon g7495.t1.exon4 23999183 23999276
chr_2 g7495 g7495.t1 cds g7495.t1.CDS4 23999183 23999276
chr_2 g7495 g7495.t1 TSS g7495.t1 23999319 23999319

Sequences

>g7495.t1 Gene=g7495 Length=807
ATGGATGCTGTAACTGTGATTGATAACTTTTTTGGTGTTTATTTGCTTGTTAATAACAAT
GACAATCCAAAGTACAAGGGTAGATGTTATGTCGGTTTTACTGTAAATCCCACAAGAAGA
ATCACACAACATAATAGAGGAAAAAAATTCGGTGGCGCTAATCAAACTTCACGTATTCCA
GGACCTTGGACAATGGTATTAATAGTTCACGACTTTCCTGATAATATTTCTGCACTTCGA
TTTGAATGGGCTTGGCAAGAACCAAAGAACTCACGTCGCTTGAAAGTAATTGACAGTATT
CAACGACGAAAACCCAATGAATCACATTTCAATTTTCATTTTAGAATTTTAACAGAAATG
ATTAATACACCACCATGGAATAGATTACCTTTAAAAATTCGATGGTTAGAGTCTGATTAT
TGTATTGACTTTCCTTCAGATCGTTTTCCAAAACACATGTCAATTAAACATGGTGCCATC
AAAGCTTTTAAAAAAACAGTCAGTCAAACACAAGAACAAAAAGAGCTGATGGATGCAGTA
AGAACTCGTAAAGAATGTCATTTGTGTATGGAAAAAATTCAAAATCTTGACACAGATCGT
GTTTTATGCATTAATCCACGATGTAAACTTGTAGCTCATACAAAATGTCTCGCGCGCATA
TGTTTAGAACCAAACCACTATTTGCCTATAGCTGGTAAATGTCCTTTATGTGATTGTAAC
TTTTTATGGAATGATATAATTCGAAAGAAAAATGGATTTTCTGTTCCATTCGTTAATATC
GATGACGAAGAGGAATTTGATATTTAA

>g7495.t1 Gene=g7495 Length=268
MDAVTVIDNFFGVYLLVNNNDNPKYKGRCYVGFTVNPTRRITQHNRGKKFGGANQTSRIP
GPWTMVLIVHDFPDNISALRFEWAWQEPKNSRRLKVIDSIQRRKPNESHFNFHFRILTEM
INTPPWNRLPLKIRWLESDYCIDFPSDRFPKHMSIKHGAIKAFKKTVSQTQEQKELMDAV
RTRKECHLCMEKIQNLDTDRVLCINPRCKLVAHTKCLARICLEPNHYLPIAGKCPLCDCN
FLWNDIIRKKNGFSVPFVNIDDEEEFDI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g7495.t1 CDD cd10455 GIY-YIG_SLX1 10 88 0.0000000
6 g7495.t1 Gene3D G3DSA:3.40.1440.10 - 8 115 0.0000000
7 g7495.t1 Gene3D G3DSA:3.30.40.10 Zinc/RING finger domain 182 252 0.0000000
4 g7495.t1 Hamap MF_03100 Structure-specific endonuclease subunit [SLX1]. 6 259 24.7662240
2 g7495.t1 PANTHER PTHR20208:SF10 STRUCTURE-SPECIFIC ENDONUCLEASE SUBUNIT SLX1 5 252 0.0000000
3 g7495.t1 PANTHER PTHR20208 STRUCTURE-SPECIFIC ENDONUCLEASE SUBUNIT SLX1 5 252 0.0000000
1 g7495.t1 Pfam PF01541 GIY-YIG catalytic domain 11 93 0.0000000
10 g7495.t1 ProSiteProfiles PS50164 GIY-YIG domain profile. 9 97 18.0700000
9 g7495.t1 SMART SM00465 uri_9 10 114 0.0079000
5 g7495.t1 SUPERFAMILY SSF82771 GIY-YIG endonuclease 10 88 0.0000111

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:0006281 DNA repair BP
GO:0033557 Slx1-Slx4 complex CC
GO:0017108 5’-flap endonuclease 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