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.t1 TTS g8373.t1 30060757 30060757
chr_2 g8373 g8373.t1 isoform g8373.t1 30061136 30066207
chr_2 g8373 g8373.t1 exon g8373.t1.exon1 30061136 30061166
chr_2 g8373 g8373.t1 cds g8373.t1.CDS1 30061136 30061166
chr_2 g8373 g8373.t1 exon g8373.t1.exon2 30061229 30061299
chr_2 g8373 g8373.t1 cds g8373.t1.CDS2 30061229 30061299
chr_2 g8373 g8373.t1 exon g8373.t1.exon3 30061565 30061688
chr_2 g8373 g8373.t1 cds g8373.t1.CDS3 30061565 30061688
chr_2 g8373 g8373.t1 exon g8373.t1.exon4 30061753 30061934
chr_2 g8373 g8373.t1 cds g8373.t1.CDS4 30061753 30061934
chr_2 g8373 g8373.t1 exon g8373.t1.exon5 30062323 30063782
chr_2 g8373 g8373.t1 cds g8373.t1.CDS5 30062323 30063782
chr_2 g8373 g8373.t1 exon g8373.t1.exon6 30064062 30064786
chr_2 g8373 g8373.t1 cds g8373.t1.CDS6 30064062 30064786
chr_2 g8373 g8373.t1 exon g8373.t1.exon7 30064844 30064913
chr_2 g8373 g8373.t1 cds g8373.t1.CDS7 30064844 30064913
chr_2 g8373 g8373.t1 exon g8373.t1.exon8 30064984 30065029
chr_2 g8373 g8373.t1 cds g8373.t1.CDS8 30064984 30065029
chr_2 g8373 g8373.t1 exon g8373.t1.exon9 30066145 30066207
chr_2 g8373 g8373.t1 cds g8373.t1.CDS9 30066145 30066207
chr_2 g8373 g8373.t1 TSS g8373.t1 NA NA

Sequences

>g8373.t1 Gene=g8373 Length=2772
ATGAGTGCAGCTCAGCAACAAGCACCTGCCTTATTACCACTAAAAAAGGGCATCGTTAAA
CAGGTTCTGTCTGGCGATTCTGTTATCATCAGAGGTCAACCGAAAAATGGACCACCTGCA
GAGAAGCAAATTAATTTTAGTAATGTAATTGCTCCAAAACTTGCTCGTCGTCCAACTAAT
CCATCTGAAGAAGGAACAAAAGATGAGCCGTGGGCATGGGAAGCCAGAGAATTCCTTCGT
CAAATGCTTGTTGGTGAAGAAGTTTATTTCCAATGTGAACGTAAACCGAATGCTACTCGT
GATTATGGTGTCATTTTCATCGGAAAAGATCCAAACAATTTGACTAATGTCACTGAACTT
GCTGTCTCGGAAGGTCTTATACAAGTCCGCCGTGAAAATGTTCGTACTACTCCTGAATTA
CAACGACTCATTGAACTAGAGGATCAAGCTAAGGCACAAGGAAAAGGTCGTTATAGTTCA
AACCCGCCAATTGTACGCAATATTGTGTGGCAAATCGAAAATCCCCGTCATTTTGTAGAC
TTGCAAGCAGGAAAACCTGTGAGGGCAATTATCGAACATGTGCGTGATGGCTCAACTGTT
AGAGCTTTCCTACTTCCCGGATTCCAATATGTTACATTAATGATCAGTGGAATCCGTTGC
CCTGGTTTTAAACTAGATAATGATGGAAGACCTGATCCATCTGTAGTTGTACCTTATGCT
GAAGAAGCCCGATACTTTGTAGAATCGAGACTTTTGCAACGCGATGTTGAAATTGTACTA
GAATCAAATAATAATTCAAACTTTGTTGGTACTATCTTGTTCCCGAAAGGTAATATTGCC
GAAGCACTTTTGCGTGAAGGATTTGCCAAATGTGTAGACTGGAGCATGGCATTTATGAAA
ACTGGTGTTGATAAGTTGCGTGCTGCTGAACGTCATGCTAAAAATAATCGAGTTCGTTTA
TGGAAAGATTATACGCCGCCAATTGCTCAATTTAGTGGCAAGGAGAAGGATTTCACTGGA
ACTGTCATCGAGGTTCATAATGGAGATGCAATTACTGTCAAAGTAAACAATAATCAAGTT
AAAAAAGTCTTTTTCTCAAGCATTCGTCCTCCTCGTGAAGCTGCAAAAGTTACTGATGAG
TCTGAAGGCAAACCTGCTCCTCCCGCAACTAATAAGTCTGGTCGTCCACTTTACGATGTA
CCATGGCTCTTTGAAGCTCGTGAATTCCTGCGTAAGAAATTAATTGGCAAGACTGTCAAG
TGTACACTTGATTATGTATCACCTGCGCGAGATAATTTCCCAGAAAAGTTCTGCTATACA
GTCACTATTGGTGGCTCAAATGTTGCTGAAGCATTGGTGAGCAAAGGTCTTGCACAAGTC
ATTCGTTATCGTCAAGATGATGATCAGCGTTCATCAAAGTACGATGATTTAATGGCTGCT
GAAACACAAGCGTCAAAACAACAAAAGGGTATTTTTGCAAAGAAAGATATTCCTGTGCAT
CGTATCAATGATTTGACAACAGCACCCGATTCATCACGTGTTAAACATCAATATTTGCCA
TCATGGCAACGTGCATTGCGTACTGAAGCTGTTGTTGAATTTGTAGCTAGTGGCTCTCGC
TTCCGTTTATTTATTCCAAAGGAATCTTGCTTAGTAACATTCCTTCTTGCTGGAATTTCC
TGCCCTCGTTCATCACGCCCAAGTGCTGATGGAAAAGGTGAAACAACTCCAGGTGAGCCA
TTTGGTGATGAAGCTTACAACTTTGTTAAGGAACGCATTTTGCAACGAGACGTAAGCGTA
CATGTTGATACCGTTGATAAAGCTGGCACTTCAGTAATTGGATGGCTTTGGCTTGAAAAT
AATGTTAATCTCTCTGTTGCACTTGTTGAAGAGGGCTTGGCTACCGTACATTTTACTGCC
GAAAAGTCTGAGCACTATCGTGTTTTGAAAGCTGCTGAAGATCAAGCAAAGGCTCAAAAG
AAGAATATCTGGAAAACATGGGTTGAACCAGTTGCTGAAGAGCCAAAAGTTCAAGATGGC
GATGACGATGTCGCTGAGAAAACTGAAGAAAAAGCTCCTGCAGAACGCAAAATGAAATTG
GAAGAGATTGTCGTTACTGAAGTGACGCCTGATCTTCATTTCTACGCTCAAAGCACCGAC
AGTGGTCCGAAATTAGAGCAGCTTATGTCGAAATTGAGACAAGAATTTAAATCATCCCCG
CCTGTTAGTGGCTCATACACGCCAAGAAGAGATGACTTGTGTGCAGCTAAATTCTCAGAA
GATGAGGAATGGTATCGTGCTAAAGTTATAAAAGTTGATAAAACTCAAGCAACGATCAAA
TACATCGATTATGGTAATACTGAGACCGTTCCAACAACTCGCCTCGCTGTTCTTCCTCCT
GCCTTTACATCTGATAGTGCTTTTGCAACTGAATATGCACTTGCATGGGCTGTTCTTCCA
CCTGATGAAGAAGATAAGATTGAAGCTTATAAGACATTCGCTCAAGATGTTCTCAACAGA
ACACTCAATTTGAATGTTGAGTTTGTAAACAATGGTCTCCCGAATGCTACATTATTTGAT
CCGAAAACAAAGGCCGATATTGGAAAGGGCTTGGTTCAAGATGGTTTTATCATTTGTGAA
AGACGTCCTGGAAGAAGATTTGCTAAGATTGTAAATGAATACAAGGAATTGGAACAACAA
GCTCGCAAATCTCACATTGGAATTTGGAAATACGGCGATATTACTGAAGATAATGCTGTT
GAGTTTGGTTAA

>g8373.t1 Gene=g8373 Length=923
MSAAQQQAPALLPLKKGIVKQVLSGDSVIIRGQPKNGPPAEKQINFSNVIAPKLARRPTN
PSEEGTKDEPWAWEAREFLRQMLVGEEVYFQCERKPNATRDYGVIFIGKDPNNLTNVTEL
AVSEGLIQVRRENVRTTPELQRLIELEDQAKAQGKGRYSSNPPIVRNIVWQIENPRHFVD
LQAGKPVRAIIEHVRDGSTVRAFLLPGFQYVTLMISGIRCPGFKLDNDGRPDPSVVVPYA
EEARYFVESRLLQRDVEIVLESNNNSNFVGTILFPKGNIAEALLREGFAKCVDWSMAFMK
TGVDKLRAAERHAKNNRVRLWKDYTPPIAQFSGKEKDFTGTVIEVHNGDAITVKVNNNQV
KKVFFSSIRPPREAAKVTDESEGKPAPPATNKSGRPLYDVPWLFEAREFLRKKLIGKTVK
CTLDYVSPARDNFPEKFCYTVTIGGSNVAEALVSKGLAQVIRYRQDDDQRSSKYDDLMAA
ETQASKQQKGIFAKKDIPVHRINDLTTAPDSSRVKHQYLPSWQRALRTEAVVEFVASGSR
FRLFIPKESCLVTFLLAGISCPRSSRPSADGKGETTPGEPFGDEAYNFVKERILQRDVSV
HVDTVDKAGTSVIGWLWLENNVNLSVALVEEGLATVHFTAEKSEHYRVLKAAEDQAKAQK
KNIWKTWVEPVAEEPKVQDGDDDVAEKTEEKAPAERKMKLEEIVVTEVTPDLHFYAQSTD
SGPKLEQLMSKLRQEFKSSPPVSGSYTPRRDDLCAAKFSEDEEWYRAKVIKVDKTQATIK
YIDYGNTETVPTTRLAVLPPAFTSDSAFATEYALAWAVLPPDEEDKIEAYKTFAQDVLNR
TLNLNVEFVNNGLPNATLFDPKTKADIGKGLVQDGFIICERRPGRRFAKIVNEYKELEQQ
ARKSHIGIWKYGDITEDNAVEFG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
23 g8373.t1 CDD cd00175 SNc 193 323 7.36084E-34
22 g8373.t1 CDD cd00175 SNc 534 665 1.27238E-34
21 g8373.t1 CDD cd04508 TUDOR 752 795 1.67637E-16
18 g8373.t1 Gene3D G3DSA:2.40.50.90 - 13 175 6.4E-38
17 g8373.t1 Gene3D G3DSA:2.40.50.90 - 176 334 3.3E-43
15 g8373.t1 Gene3D G3DSA:2.40.50.90 - 335 502 2.3E-50
16 g8373.t1 Gene3D G3DSA:2.40.50.90 - 508 664 1.9E-55
19 g8373.t1 Gene3D G3DSA:2.40.50.90 - 703 912 8.3E-70
14 g8373.t1 Gene3D G3DSA:2.30.30.140 - 719 809 8.3E-70
29 g8373.t1 MobiDBLite mobidb-lite consensus disorder prediction 674 695 -
6 g8373.t1 PANTHER PTHR12302:SF2 STAPHYLOCOCCAL NUCLEASE DOMAIN-CONTAINING PROTEIN 1 10 917 1.2E-284
7 g8373.t1 PANTHER PTHR12302 EBNA2 BINDING PROTEIN P100 10 917 1.2E-284
20 g8373.t1 PIRSF PIRSF017179 RISC-Tudor-SN 3 923 0.0
4 g8373.t1 Pfam PF00565 Staphylococcal nuclease homologue 44 156 1.2E-5
2 g8373.t1 Pfam PF00565 Staphylococcal nuclease homologue 215 323 3.7E-12
3 g8373.t1 Pfam PF00565 Staphylococcal nuclease homologue 388 492 7.7E-10
5 g8373.t1 Pfam PF00565 Staphylococcal nuclease homologue 554 665 3.6E-19
1 g8373.t1 Pfam PF00567 Tudor domain 697 815 3.2E-28
34 g8373.t1 ProSiteProfiles PS50830 Thermonuclease domain profile. 13 160 26.329
33 g8373.t1 ProSiteProfiles PS50830 Thermonuclease domain profile. 185 323 30.057
31 g8373.t1 ProSiteProfiles PS50830 Thermonuclease domain profile. 336 494 27.495
32 g8373.t1 ProSiteProfiles PS50830 Thermonuclease domain profile. 526 666 29.216
30 g8373.t1 ProSiteProfiles PS50304 Tudor domain profile. 747 805 17.937
28 g8373.t1 SMART SM00318 SNASE_2 13 160 7.5E-27
27 g8373.t1 SMART SM00318 SNASE_2 185 323 1.1E-42
25 g8373.t1 SMART SM00318 SNASE_2 336 494 9.7E-39
26 g8373.t1 SMART SM00318 SNASE_2 526 666 3.2E-39
24 g8373.t1 SMART SM00333 TUDOR_7 746 803 1.5E-16
10 g8373.t1 SUPERFAMILY SSF50199 Staphylococcal nuclease 15 163 1.16E-21
9 g8373.t1 SUPERFAMILY SSF50199 Staphylococcal nuclease 180 326 1.83E-28
12 g8373.t1 SUPERFAMILY SSF50199 Staphylococcal nuclease 331 498 3.79E-28
11 g8373.t1 SUPERFAMILY SSF50199 Staphylococcal nuclease 521 667 2.09E-29
13 g8373.t1 SUPERFAMILY SSF63748 Tudor/PWWP/MBT 723 815 4.81E-21
8 g8373.t1 SUPERFAMILY SSF50199 Staphylococcal nuclease 758 917 3.92E-14

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:0031047 gene silencing by RNA BP
GO:0016442 RISC complex CC

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