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.t2 TTS g7495.t2 23998111 23998111
chr_2 g7495 g7495.t2 isoform g7495.t2 23998297 23999276
chr_2 g7495 g7495.t2 exon g7495.t2.exon1 23998297 23998759
chr_2 g7495 g7495.t2 cds g7495.t2.CDS1 23998297 23998759
chr_2 g7495 g7495.t2 exon g7495.t2.exon2 23998818 23998913
chr_2 g7495 g7495.t2 cds g7495.t2.CDS2 23998818 23998913
chr_2 g7495 g7495.t2 exon g7495.t2.exon3 23998971 23999276
chr_2 g7495 g7495.t2 cds g7495.t2.CDS3 23998971 23999188
chr_2 g7495 g7495.t2 TSS g7495.t2 23999319 23999319

Sequences

>g7495.t2 Gene=g7495 Length=865
ATGGATGCTGTAACTGTGATTGATAACTTTTTTGGTGTTTATTTGCTTGTTAATAACAAT
GACAATCCAAAGTACAAGGGTAGATGTTATGTCGGTATGTAAATTTTTAAAAATATATTA
TGACATTTTAAATTTAAATGTGTATTCTATAGGTTTTACTGTAAATCCCACAAGAAGAAT
CACACAACATAATAGAGGAAAAAAATTCGGTGGCGCTAATCAAACTTCACGTATTCCAGG
ACCTTGGACAATGGTATTAATAGTTCACGACTTTCCTGATAATATTTCTGCACTTCGATT
TGAATGGGCTTGGCAAGAACCAAAGAACTCACGTCGCTTGAAAGTAATTGACAGTATTCA
ACGACGAAAACCCAATGAATCACATTTCAATTTTCATTTTAGAATTTTAACAGAAATGAT
TAATACACCACCATGGAATAGATTACCTTTAAAAATTCGATGGTTAGAGTCTGATTATTG
TATTGACTTTCCTTCAGATCGTTTTCCAAAACACATGTCAATTAAACATGGTGCCATCAA
AGCTTTTAAAAAAACAGTCAGTCAAACACAAGAACAAAAAGAGCTGATGGATGCAGTAAG
AACTCGTAAAGAATGTCATTTGTGTATGGAAAAAATTCAAAATCTTGACACAGATCGTGT
TTTATGCATTAATCCACGATGTAAACTTGTAGCTCATACAAAATGTCTCGCGCGCATATG
TTTAGAACCAAACCACTATTTGCCTATAGCTGGTAAATGTCCTTTATGTGATTGTAACTT
TTTATGGAATGATATAATTCGAAAGAAAAATGGATTTTCTGTTCCATTCGTTAATATCGA
TGACGAAGAGGAATTTGATATTTAA

>g7495.t2 Gene=g7495 Length=258
MSVCKFLKIYYDILNLNVYSIGFTVNPTRRITQHNRGKKFGGANQTSRIPGPWTMVLIVH
DFPDNISALRFEWAWQEPKNSRRLKVIDSIQRRKPNESHFNFHFRILTEMINTPPWNRLP
LKIRWLESDYCIDFPSDRFPKHMSIKHGAIKAFKKTVSQTQEQKELMDAVRTRKECHLCM
EKIQNLDTDRVLCINPRCKLVAHTKCLARICLEPNHYLPIAGKCPLCDCNFLWNDIIRKK
NGFSVPFVNIDDEEEFDI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g7495.t2 Gene3D G3DSA:3.40.1440.10 - 11 105 0.00000
6 g7495.t2 Gene3D G3DSA:3.30.40.10 Zinc/RING finger domain 172 242 0.00000
4 g7495.t2 Hamap MF_03100 Structure-specific endonuclease subunit [SLX1]. 2 249 21.53244
2 g7495.t2 PANTHER PTHR20208:SF10 STRUCTURE-SPECIFIC ENDONUCLEASE SUBUNIT SLX1 21 242 0.00000
3 g7495.t2 PANTHER PTHR20208 STRUCTURE-SPECIFIC ENDONUCLEASE SUBUNIT SLX1 21 242 0.00000
1 g7495.t2 Pfam PF01541 GIY-YIG catalytic domain 19 83 0.00000
7 g7495.t2 ProSiteProfiles PS50164 GIY-YIG domain profile. 1 87 10.92700

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