Gene loci information

Transcript annotation

  • This transcript has been annotated as Staphylococcal nuclease domain-containing 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_2 g8373 g8373.t4 isoform g8373.t4 30062334 30063272
chr_2 g8373 g8373.t4 exon g8373.t4.exon1 30062334 30063272
chr_2 g8373 g8373.t4 cds g8373.t4.CDS1 30062335 30063255
chr_2 g8373 g8373.t4 TSS g8373.t4 NA NA
chr_2 g8373 g8373.t4 TTS g8373.t4 NA NA

Sequences

>g8373.t4 Gene=g8373 Length=939
CAAAGTACGATGATTTAATGGCTGCTGAAACACAAGCGTCAAAACAACAAAAGGGTATTT
TTGCAAAGAAAGATATTCCTGTGCATCGTATCAATGATTTGACAACAGCACCCGATTCAT
CACGTGTTAAACATCAATATTTGCCATCATGGCAACGTGCATTGCGTACTGAAGCTGTTG
TTGAATTTGTAGCTAGTGGCTCTCGCTTCCGTTTATTTATTCCAAAGGAATCTTGCTTAG
TAACATTCCTTCTTGCTGGAATTTCCTGCCCTCGTTCATCACGCCCAAGTGCTGATGGAA
AAGGTGAAACAACTCCAGGTGAGCCATTTGGTGATGAAGCTTACAACTTTGTTAAGGAAC
GCATTTTGCAACGAGACGTAAGCGTACATGTTGATACCGTTGATAAAGCTGGCACTTCAG
TAATTGGATGGCTTTGGCTTGAAAATAATGTTAATCTCTCTGTTGCACTTGTTGAAGAGG
GCTTGGCTACCGTACATTTTACTGCCGAAAAGTCTGAGCACTATCGTGTTTTGAAAGCTG
CTGAAGATCAAGCAAAGGCTCAAAAGAAGAATATCTGGAAAACATGGGTTGAACCAGTTG
CTGAAGAGCCAAAAGTTCAAGATGGCGATGACGATGTCGCTGAGAAAACTGAAGAAAAAG
CTCCTGCAGAACGCAAAATGAAATTGGAAGAGATTGTCGTTACTGAAGTGACGCCTGATC
TTCATTTCTACGCTCAAAGCACCGACAGTGGTCCGAAATTAGAGCAGCTTATGTCGAAAT
TGAGACAAGAATTTAAATCATCCCCGCCTGTTAGTGGCTCATACACGCCAAGAAGAGATG
ACTTGTGTGCAGCTAAATTCTCAGAAGATGAGGAATGGTATCGTGCTAAAGTTATAAAAG
TTGATAAAACTCAAGCAACGATCAAATACATCGATTATG

>g8373.t4 Gene=g8373 Length=307
MAAETQASKQQKGIFAKKDIPVHRINDLTTAPDSSRVKHQYLPSWQRALRTEAVVEFVAS
GSRFRLFIPKESCLVTFLLAGISCPRSSRPSADGKGETTPGEPFGDEAYNFVKERILQRD
VSVHVDTVDKAGTSVIGWLWLENNVNLSVALVEEGLATVHFTAEKSEHYRVLKAAEDQAK
AQKKNIWKTWVEPVAEEPKVQDGDDDVAEKTEEKAPAERKMKLEEIVVTEVTPDLHFYAQ
STDSGPKLEQLMSKLRQEFKSSPPVSGSYTPRRDDLCAAKFSEDEEWYRAKVIKVDKTQA
TIKYIDY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g8373.t4 CDD cd00175 SNc 57 188 9.2528E-37
10 g8373.t4 CDD cd04508 TUDOR 275 307 6.66866E-11
9 g8373.t4 Gene3D G3DSA:2.40.50.90 - 30 187 2.1E-56
8 g8373.t4 Gene3D G3DSA:2.40.50.90 - 226 241 8.7E-30
7 g8373.t4 Gene3D G3DSA:2.30.30.140 - 242 307 8.7E-30
13 g8373.t4 MobiDBLite mobidb-lite consensus disorder prediction 197 218 -
3 g8373.t4 PANTHER PTHR12302:SF2 STAPHYLOCOCCAL NUCLEASE DOMAIN-CONTAINING PROTEIN 1 1 307 1.5E-92
4 g8373.t4 PANTHER PTHR12302 EBNA2 BINDING PROTEIN P100 1 307 1.5E-92
2 g8373.t4 Pfam PF00565 Staphylococcal nuclease homologue 77 188 5.4E-20
1 g8373.t4 Pfam PF00567 Tudor domain 220 307 1.2E-19
15 g8373.t4 ProSiteProfiles PS50830 Thermonuclease domain profile. 49 189 29.216
14 g8373.t4 ProSiteProfiles PS50304 Tudor domain profile. 270 307 14.492
12 g8373.t4 SMART SM00318 SNASE_2 49 189 3.2E-39
5 g8373.t4 SUPERFAMILY SSF50199 Staphylococcal nuclease 44 190 2.48E-30
6 g8373.t4 SUPERFAMILY SSF63748 Tudor/PWWP/MBT 247 307 2.78E-12

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

There are no GO annotations for this transcript.

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