Sequence
atgc intronic sequence ATGC exonic sequence...nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngatagtataatctgataatatcaacaaggttatccattagtaaatttactgaattgttgacatgatagGAGCCTGTTCTTCCCGGTTGTTTCCTGCGAGCCAGGGCCATTGGATTGATGCCTATGATTGACCAG
Basic information
species | Glycine max |
transcript | GLYMA16G01960.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G01960.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g36260.1 (Oryza sativa), 3'ss of exon 3
--nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngatagtataatctgataatatcaacaaggttatccattagtaaatttactgaattgttgacatgatagGAGCCTGTTCTTCCCGGTTGTTTCCTGCGAGCCAGGGCCATTGGATTGATGCCTATGATTGACCAG
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gtgaacagaattgacgcccttaattttctatatgactcacattttctg----catttgctaatttgtctaacgtacaacct--tgtgttgttcgca-accagGAACCAGTTCTTCCTGGTTCATTCCTCCGAGCCAGGGCCATTGGTCTCATGCCTATGATTGACCAG
upper sequence: GLYMA16G01960.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G01050.1 (Arabidopsis thaliana), 3'ss of exon 5
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngatagtataatctgataatatcaacaaggttatccattagtaaatttactgaattgttgacatgatagGAGCCTGTTCTTCCCGGTTGTTTCCTGCGAGCCAGGGCCATTGGATTGATGCCTATGATTGACCAG
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-gtattactctttctttctttctcatattatcccta-tactatttg-------caccaattttttgtattt-caaatatatattattatctttgtg-tagGAACCTGTGCTTCCGGGTTGTTTTCTGCGTGCCAGAGCCATTGGATTAATGCCTATGATTGACCAG
upper sequence: GLYMA16G01960.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G46860.1 (Arabidopsis thaliana), 3'ss of exon 4
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngatagtataatctgataatatcaacaaggttatccattagtaaatttactgaattgttgacatgatagGAGCCTGTTCTTCCCGGTTGTTTCCTGCGAGCCAGGGCCATTGGATTGATGCCTATGATTGACCAG
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---------gtaactgtgttttcacaaccatcaaaattatcatcaaatacca-cattgtgttgtaacctgagttagctt-ctgattcgt-------gtagGAACCAGTGCTTCCCGGATGTTTCCTCCGTGCTAGAGCCATTGGATTAATGCCCATGATTGATCAG
upper sequence: GLYMA16G01960.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G01480.1 (Arabidopsis thaliana), 3'ss of exon 5
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngatagtataatctgataatatcaacaaggttatccattagtaaatttactgaattgttgacatgatagGAGCCTGTTCTTCCCGGTTGTTTCCTGCGAGCCAGGGCCATTGGATTGATGCCTATGATTGACCAG
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---gtttgagtctaattctaacaacattcaccaaaagaa------aatgaaatggctgaaataatttcttatcaa--------agttgattatgt-acagGAGCCTGTGCTTCCGGGTTGTTTTCTTCGCGCCCGAGCTATTGGTTTAATGCCTATGATTGACCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gataatatcaacaaggttatccattagtaaatttactgaattgttgacatgatagGAGCCTGTTCTTCCCGGTTGTTTCCTGCGAGCCAGGGCCATTGGATTGATGCCTATGATTGACCAG
tgttgac putative branch site (score: 3)
attagtaaatttact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngatagtataatctgataatatcaacaaggttatccattagtaaatttactgaattgttgacatgatagGAGCCTGTTCTTCCCGGTTGTTTCCTGCGAGCCAGGGCCATTGGATTGATGCCTATGATTGACCAG
- - - - - - - - - - - - - - - - - - - - - - - - - -atcaaca