Sequence
atgc intronic sequence ATGC exonic sequence...acatatcttttgtcagatgattgtgcaagagtgctatatgaagcaagaccaatttatctgatcaattctcaattgccttatgttgctccctgtttttcagTGTGGTGTAGGAGAACGGATGAACTTGTTGATGGTCCTAATGCTTCACAAATTACGCCAACTGCTTAGAAATAGGTGGGAATCAAGATTGGAAGAACTTT
Basic information
species | Glycine max |
transcript | GLYMA14G39050.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G39050.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G17230.1 (Arabidopsis thaliana), 3'ss of exon 3
---acatatcttttgtcagatgattgtgcaagagtgctatatgaagcaagaccaatttatctgatcaattctcaattgccttatgttgctccctgttttt--cagTGTGGTGTAGGAGAACGGATGAACTTGTTGATGGTCCTAATGCTTCACAAATTACGCCAACTGCTTAGAAATAGGTGGGAATCAAGATTGGAAGAACTTT-
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aggacata-ctagtatccaaagcatatg---gggaattttaaagttgttttcttatatgtttgattggtt-tgaatttgatagttttactctgtcttttgtgcagTTTGGTGTAGAAGAACTGATGAACTTGTGGATGGGCCAAATGCTTCACATATAACTCCCATGGCTTT-AGATAGATGGGAAGCAAGGTTAGAAGATCTTTT
upper sequence: GLYMA14G39050.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv04s0079g00680.t01 (Vitis vinifera), 3'ss of exon 3
acatatcttttgtcag-atg-attgtgcaagagtgctata-tgaagcaagaccaatttatctgatcaattctcaattgccttatgttgctccctgttttt---cagTGTGGTGTAGGAGAACGGATGAACTTGTTGATGGTCCTAATGCTTCACAAATTACGCCAACTGCTTAGAAATAGGTGGGAATCAAGATTGGAAGAACTTT-
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----gaattttgtaaatatgcacaatacacaagttcaatactgaaacaaagacgagaggatttat--attctcttttgtttcttatgattctctctccatgaacagTGTGGTGTCGGAGAACAGATGAGCTTGTTGATGGGCCTAATGCATCACACATAACCCCAACAGCCTTGGA-TAGGTGGGAGTCAAGGTTGGAAGATCTTTT
upper sequence: GLYMA14G39050.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S196_120V6.1 (Physcomitrella patens), 3'ss of exon 3
---acatatcttttgtcagatgattgtgcaagagtgctatatgaagcaagaccaatttatctgatcaattctcaattgccttatgttgctccctgttt--ttcagTGTGGTGTAGGAGAACGGATGAACTTGTTGATGGTCCTAATGCTTCACAAATTACGCCAACTGCTTAGAAATAGGTGGGAATCAAGATTGGAAGAACTTT-
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ggcacttgtcacttgcct--caaatgt---agaaccttaaatgagtaagaatccgaaaaggtcgaatatgctcccctgggttaaacctctacttgctcaatgcagTATGGTGCAGGAGGACGGATGAACTTGTGGATGGCCCTAATGCATCTCGCATCACCCCCACTGCCCTTGA-CCGCTGGGAAGATAGGTTGGAGGATATTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agaccaatttatctgatcaattctcaattgccttatgttgctccctgtttttcagTGTGGTGTAGGAGAACGGATGAACTTGTTGATGGTCCTAATGCTTCACAAATTACGCCAACTGCTTAGAAATAGGTGGGAATCAAGATTGGAAGAACTTT
atctgat putative branch site (score: 4)
ttgctccctgtttttc putative PPT
aatttatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acatatcttttgtcagatgattgtgcaagagtgctatatgaagcaagaccaatttatctgatcaattctcaattgccttatgttgctccctgtttttcagTGTGGTGTAGGAGAACGGATGAACTTGTTGATGGTCCTAATGCTTCACAAATTACGCCAACTGCTTAGAAATAGGTGGGAATCAAGATTGGAAGAACTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC