Sequence
atgc intronic sequence ATGC exonic sequence...tagtgtggaaattgactgatgaagatattgatatgttttttttaacctttttgttttattttattgtttacatgttaaactcttaatttataatatgtagGAAAAAAGTTCTGGAATTTGTTTCACTTGCAACCTATGCGTGACCAAAAG
Basic information
species | Glycine max |
transcript | GLYMA16G19560.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G19560.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G58140.2 (Arabidopsis thaliana), 3'ss of exon 8
tagtgtggaaattgactgatgaagatattgatatgttttttttaacctttttgttttattttattgtttacatgttaaactcttaatttataatatgtagGAAAAAAGTTCTGGAATTTGTTTCACTTGCAACCTATGCGTGACCAAAAG
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----gtagttatcagatactgaacattttaaaacgatcatactgaaaagttt---ctatgtggttgtgt---cattaaaactctaaaccat----tgcagGAAAGAAATTCTGGAACTTATTCCACTTGCAACCTATGCGTGATCAGAAG
upper sequence: GLYMA16G19560.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv03s0038g04210.t01 (Vitis vinifera), 3'ss of exon 7
-----------------------tagtgtggaaat-tgactgatgaagatattgatatgttttttttaacctttttgttttatttt-----attgtttacatgttaaactc-ttaatt----------tataatatgtagGAAAAAAGTTCTGGAATTTGTTTCACTTGCAACCTATGCGTGACCAAAAG
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gtatggtgctaataatctgttcttagcttggagacatcacgttttactctctctctctctctctctctctctctctctctttttccccaaaacaattgctataccaaaatgattgattgcatggattacatgccttgcagGAAAGAAATTCTGGAATTTATTCCACTTGCAGCCCATGCGTGACCAAAAG
upper sequence: GLYMA16G19560.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ32904 (Selaginella moellendorffii), 3'ss of exon 8
tagtgtggaaattgactgatgaagatattgatatgttttttttaacctttttgttttattttattgtttacatgttaaactcttaatttataatatgtagGAAAAAAGTTCTGGAATTTGTTTCACTTGCAACCTATGCGTGACCAAAAG
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------------------------------gtatgcactatctgttcgtgaactctcctcctaatgttc----------ttgtcaattta------atagGGAAGCCTTTCTGGAATTTGTTTCACTTGCAACCCATGAGAGACAACAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctttttgttttattttattgtttacatgttaaactcttaatttataatatgtagGAAAAAAGTTCTGGAATTTGTTTCACTTGCAACCTATGCGTGACCAAAAG
tcttaat putative branch site (score: 3)
ttttattttattgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tagtgtggaaattgactgatgaagatattgatatgttttttttaacctttttgttttattttattgtttacatgttaaactcttaatttataatatgtagGAAAAAAGTTCTGGAATTTGTTTCACTTGCAACCTATGCGTGACCAAAAG
tagtgtg
- - - - - - - actgatg
- - - - - - - - - - - - - - tgatatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tacatgt