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.t8 isoform g8373.t8 30064065 30066207
chr_2 g8373 g8373.t8 exon g8373.t8.exon1 30064065 30064786
chr_2 g8373 g8373.t8 cds g8373.t8.CDS1 30064066 30064786
chr_2 g8373 g8373.t8 exon g8373.t8.exon2 30064844 30064913
chr_2 g8373 g8373.t8 cds g8373.t8.CDS2 30064844 30064913
chr_2 g8373 g8373.t8 exon g8373.t8.exon3 30064984 30065029
chr_2 g8373 g8373.t8 cds g8373.t8.CDS3 30064984 30065029
chr_2 g8373 g8373.t8 exon g8373.t8.exon4 30066145 30066207
chr_2 g8373 g8373.t8 cds g8373.t8.CDS4 30066145 30066207
chr_2 g8373 g8373.t8 TSS g8373.t8 NA NA
chr_2 g8373 g8373.t8 TTS g8373.t8 NA NA

Sequences

>g8373.t8 Gene=g8373 Length=901
ATGAGTGCAGCTCAGCAACAAGCACCTGCCTTATTACCACTAAAAAAGGGCATCGTTAAA
CAGGTTCTGTCTGGCGATTCTGTTATCATCAGAGGTCAACCGAAAAATGGACCACCTGCA
GAGAAGCAAATTAATTTTAGTAATGTAATTGCTCCAAAACTTGCTCGTCGTCCAACTAAT
CCATCTGAAGAAGGAACAAAAGATGAGCCGTGGGCATGGGAAGCCAGAGAATTCCTTCGT
CAAATGCTTGTTGGTGAAGAAGTTTATTTCCAATGTGAACGTAAACCGAATGCTACTCGT
GATTATGGTGTCATTTTCATCGGAAAAGATCCAAACAATTTGACTAATGTCACTGAACTT
GCTGTCTCGGAAGGTCTTATACAAGTCCGCCGTGAAAATGTTCGTACTACTCCTGAATTA
CAACGACTCATTGAACTAGAGGATCAAGCTAAGGCACAAGGAAAAGGTCGTTATAGTTCA
AACCCGCCAATTGTACGCAATATTGTGTGGCAAATCGAAAATCCCCGTCATTTTGTAGAC
TTGCAAGCAGGAAAACCTGTGAGGGCAATTATCGAACATGTGCGTGATGGCTCAACTGTT
AGAGCTTTCCTACTTCCCGGATTCCAATATGTTACATTAATGATCAGTGGAATCCGTTGC
CCTGGTTTTAAACTAGATAATGATGGAAGACCTGATCCATCTGTAGTTGTACCTTATGCT
GAAGAAGCCCGATACTTTGTAGAATCGAGACTTTTGCAACGCGATGTTGAAATTGTACTA
GAATCAAATAATAATTCAAACTTTGTTGGTACTATCTTGTTCCCGAAAGGTAATATTGCC
GAAGCACTTTTGCGTGAAGGATTTGCCAAATGTGTAGACTGGAGCATGGCATTTATGAAA
A

>g8373.t8 Gene=g8373 Length=300
MSAAQQQAPALLPLKKGIVKQVLSGDSVIIRGQPKNGPPAEKQINFSNVIAPKLARRPTN
PSEEGTKDEPWAWEAREFLRQMLVGEEVYFQCERKPNATRDYGVIFIGKDPNNLTNVTEL
AVSEGLIQVRRENVRTTPELQRLIELEDQAKAQGKGRYSSNPPIVRNIVWQIENPRHFVD
LQAGKPVRAIIEHVRDGSTVRAFLLPGFQYVTLMISGIRCPGFKLDNDGRPDPSVVVPYA
EEARYFVESRLLQRDVEIVLESNNNSNFVGTILFPKGNIAEALLREGFAKCVDWSMAFMK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g8373.t8 Gene3D G3DSA:2.40.50.90 - 13 174 0.0000000
10 g8373.t8 Gene3D G3DSA:2.40.50.90 - 175 300 0.0000000
3 g8373.t8 PANTHER PTHR12302:SF2 STAPHYLOCOCCAL NUCLEASE DOMAIN-CONTAINING PROTEIN 1 10 299 0.0000000
4 g8373.t8 PANTHER PTHR12302 EBNA2 BINDING PROTEIN P100 10 299 0.0000000
1 g8373.t8 Pfam PF00565 Staphylococcal nuclease homologue 44 156 0.0000017
2 g8373.t8 Pfam PF00565 Staphylococcal nuclease homologue 215 292 0.0000004
12 g8373.t8 ProSiteProfiles PS50830 Thermonuclease domain profile. 13 160 26.3290000
11 g8373.t8 ProSiteProfiles PS50830 Thermonuclease domain profile. 185 300 22.5620000
8 g8373.t8 SMART SM00318 SNASE_2 13 160 0.0000000
7 g8373.t8 SMART SM00318 SNASE_2 185 300 0.0000000
5 g8373.t8 SUPERFAMILY SSF50199 Staphylococcal nuclease 15 163 0.0000000
6 g8373.t8 SUPERFAMILY SSF50199 Staphylococcal nuclease 180 297 0.0000000

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

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. There were no conditions that were differentially expressed