Sequence
atgc intronic sequence ATGC exonic sequence...ctatttctatgtcttataaacataggaaatgggtagtaccaatttgataacgattgttcttttaacaattccccgttgttcttgcatcttcatctggcagTCATACAGCCTCTATTGCAGCTGGAAGAAATGGAATTCCTGTGAGGATGCATGGACATGAATTTGGGAAAGCAAGTGGAATGGCTCCCCGTGCCAG
Basic information
species | Glycine max |
transcript | GLYMA15G17830.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G17830.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os06g48650.3 (Oryza sativa), 3'ss of exon 3
-----------------------------------------------------------------ctatttctatgtcttataaacataggaaatgggtagta--ccaatttgataacgattgt-tcttttaac-aattccccgttgttcttgcatcttcatctgg-cagTCATACAGCCTCTATTGCAGCTGGAAGAAATGGAATTCCTGTGAGGATGCATGGACATGAATTTGGGAAAGCAAGTGGAATGGCTCCCCGTGCCAG
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gtcatgctcctaattaatatatgttctgttctagtttcttataccaagaaaaatgccatacatgaaaattgttctgtccaaagaattagctattctggttgtgtttcatcttgagaagaatggcatgacttatctagttatctgatacaaagatgctttcccttaaacagTCATACAGCAGCAATTGCTGCTGGAAATAATGGGATTCCAGTACGAATGCATGGTCACGAATTTGGCAAAGCAAGTGGTATGGCTCCACGTGCTAG
upper sequence: GLYMA15G17830.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G19170.1 (Arabidopsis thaliana), 3'ss of exon 4
ctatttctatgtcttataaacataggaaatgggtagtaccaatttgataacgattgttcttttaacaattccccgttgttcttgcatcttcatctggcagTCATACAGCCTCTATTGCAGCTGGAAGAAATGGAATTCCTGTGAGGATGCATGGACATGAATTTGGGAAAGCAAGTGGAATGGCTCCCCGTGCCAG
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------gtttgtctt-taaa-gttgtctccaggtgttaggggga-gataatg-ctgttgtactaagcaaatctgattatgct-ggattttc-------agTCATACAGCAGCTATAGCAGCTGGGAATAACGGTATTCCGTTGAGGATGCATGGTTATGAATTTGGAAAAGCGAGTGGGATGGCTCCTCGTGCAAG
upper sequence: GLYMA15G17830.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G30020.1 (Arabidopsis thaliana), 3'ss of exon 4
--ctatttctatgtcttataaacataggaaatgggtagtaccaatttgataacgattgttcttttaacaattccccgttgttcttgc---atcttcatctggcagTCATACAGCCTCTATTGCAGCTGGAAGAAATGGAATTCCTGTGAGGATGCATGGACATGAATTTGGGAAAGCAAGTGGAATGGCTCCCCGTGCCAG
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gtttgtcttgttaattttttttaataatatctcagaactgcttattcctctgcacattttgatttgtatgcttctttttgttctaacgaaaaattggcctttcagTCACACAGCAGCTATTGCAGCTGGGAACAATGGTATTCCAGTGAGGATGCACGGTTATGAGTTTGGAAAAGCAAGCGGGATGGCTCCTCGTGCAAG
upper sequence: GLYMA15G17830.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv11s0103g00550.t01 (Vitis vinifera), 3'ss of exon 4
---ctatttctatgtcttataaacataggaaatgggtagtaccaatttgataacgattgttcttttaacaattccccgttgttcttgcatcttcatctggcagTCATACAGCCTCTATTGCAGCTGGAAGAAATGGAATTCCTGTGAGGATGCATGGACATGAATTTGGGAAAGCAAGTGGAATGGCTCCCCGTGCCAG
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atgatagtttgattttcttttaatattttgttcccatttactctgttttatt-tgattggg-tctggttcatttgttgtttcttgggaatactggac-aacagTCACACAGCAGCTATTGCAGCTGGAAATAATGGAATTCCAGTGAGAATGCATGGGTATGAATTTGGGAAAGCAAGTGGGATGGCTCCCCGTGCCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gataacgattgttcttttaacaattccccgttgttcttgcatcttcatctggcagTCATACAGCCTCTATTGCAGCTGGAAGAAATGGAATTCCTGTGAGGATGCATGGACATGAATTTGGGAAAGCAAGTGGAATGGCTCCCCGTGCCAG
ttttaac putative branch site (score: 2)
tcttcatct putative PPT
ttcttttaacaatt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctatttctatgtcttataaacataggaaatgggtagtaccaatttgataacgattgttcttttaacaattccccgttgttcttgcatcttcatctggcagTCATACAGCCTCTATTGCAGCTGGAAGAAATGGAATTCCTGTGAGGATGCATGGACATGAATTTGGGAAAGCAAGTGGAATGGCTCCCCGTGCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - ctatgtc