Sequence
atgc intronic sequence ATGC exonic sequence...agcatccgttctcattcatttgccttgtttgggtagtcttatcatgttgacaagtgacttatggattaaagagagtacgtatacgtatattttgttgcagGTCAATCCAAAAGCTGCTGAATCATTGGCTAATCCTGAAGAATATCCAAATTTGTTTGAAGATTGGCAAGTTGCACTAGCTGTCGAATCTAAAGCTGTGG
Basic information
species | Glycine max |
transcript | GLYMA13G43680.2 |
intron # | 21 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G43680.1 (Glycine max), 3'ss of exon 21
lower sequence: LOC_Os02g11840.1 (Oryza sativa), 3'ss of exon 12
agcatccgttctcattcatttgcc-ttgtttgggtagtcttatc-atgttgacaagtgacttatgg-attaaagagagtacgtatacgtatattttgttgcagGTCAATCCAAAAGCTGCTGAATCATTGGCTAATCCTGAAGAATATCCAAATTTGTTTGAAGATTGGCAAGTTGCACTAGCTGTCGAATCTAAAGCTGTGG
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-tcttattttcagacttacgcgacactgtttaatttgtaggagctatgtgttttattatctcaccatgccttttttccttctcatgccattatctt--tatagGTAAACCCCAAAGCAGCAGAATCATTGGCAGATCCTGACGAGTACCCAAACTTGTTTGAAGACTGGCAAATTGCTCTCAATGTAGAAGCTAATGTCGCGC
upper sequence: GLYMA13G43680.1 (Glycine max), 3'ss of exon 21
lower sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 21
agcatccgttctcattcatttgccttgtttgggtagtcttatcatgttgacaagtgacttatggattaaagagagtacgtatacgtatattttgttgcagGTCAATCCAAAAGCTGCTGAATCATTGGCTAATCCTGAAGAATATCCAAATTTGTTTGAAGATTGGCAAGTTGCACTAGCTGTCGAATCTAAAGCTGTGG
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---gttcctttcaaatctttttaggttttagtgtaatgtggtcaaggagacaagt----tgtgggtttaagt---tacct-----tgcacttgaatacagGTTAATTCAAAAGCAGCAGAATCTTTGGCTGATCCTGAGGAGTACTCAAATCTTTTTGAAGATTGGCAAGTTGCTCTTTCTGTGGAAGCTAAAGCTGTAG
upper sequence: GLYMA13G43680.1 (Glycine max), 3'ss of exon 21
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 21
agcatccgttctcattcatttgccttgtttgggtagtcttatcatgttgacaagtgacttatggattaaagagagtacgtatacgtatattttgttg-cagGTCAATCCAAAAGCTGCTGAATCATTGGCTAATCCTGAAGAATATCCAAATTTGTTTGAAGATTGGCAAGTTGCACTAGCTGTCGAATCTAAAGCTGTGG
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----------gttattttcgcatcttttttttgt----ttactgtgtcaatgagaaa---attcatcatgtggctttaaattgcctttgacttgtcatcagGTTAATCCAAAAGCAGCTGAATCTTTAGCTGATCCTGAAGAGTACTCAAATCTTTTTGAGGATTGGCAAGTTGCTCTTTCTGTTGAAGCGAACACTGCAG
upper sequence: GLYMA13G43680.1 (Glycine max), 3'ss of exon 21
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 21
---agcatccgttctcattc--atttgccttgtttgggtagtcttatcatgttgacaagtgacttatggattaaagagagtacgtatacgtatattttgttgcagGTCAATCCAAAAGCTGCTGAATCATTGGCTAATCCTGAAGAATATCCAAATTTGTTTGAAGATTGGCAAGTTGCACTAGCTGTCGAATCTAAAGCTGTGG
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atatgcctgcttgggtagttggatctatttcatttaacttttcttgtgat-ttaaagaaagagacacatatctaatcctgtttgatca---acactatat-gcagGTTAATCCAAAAGCTGCTGAATCTTTGGCTGATCCTGAAGAGTATCCTAATTTATTTGAGGACTGGCAAGTTGGTCTTGCCATTGAATCTAAAGTTGCCG
upper sequence: GLYMA13G43680.1 (Glycine max), 3'ss of exon 21
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 21
agcatccgttctcattcatttgccttgtttgggtagtcttatcatgttgacaagtgac--ttatggattaaaga-gagtacgta-tacgt-atattttg--ttgcagGTCAATCCAAAAGCTGCTGAATCATTGGCTAATCCTGAAGAATATCCAAATTTGTTTGAAGATTGGCAAGTTGCACTAGCTGTCGAATCTAAAGCTGTGG
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-------catgtcataaatgaaccaagaaaagagataaggagaaaggaaaggagtgaaaattttgaacccttcttgactgcataatgcatgatgtcatgatttgcagGTGAGCAAAAAAGCTGCAGAATCATTGGCAGATCCTGAAGAGTACCCTAATTTGTTTGAGGACTGGCAGGTTGCTCTTGACATTGAATCTAAAATTTCAGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|26269606|gb|CA820669.1|CA820669EST: CAAGTAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGACCTCAATAAG GTCAATCCAAAAGCTGCTGAATCATTGGCTAATCCTGAATA-TATCCAAAT
genomic: CAAGTAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGACCTCAATAAGgtaatttctg ... tttgttgcagGTCAATCCAAAAGCTGCTGAATCATTGGCTAATCCTGAAGAATATCCAAAT
EST:
gi|151398221|gb|EV268099.1|EV268099EST: CAAGTAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGACCTCAATAAG GTCAATCCAAAAGCTGCTGAGTCATTGGCTAATCCTGAAGAATATCCAAAT
genomic: CAAGTAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGACCTCAATAAGgtaatttctg ... tttgttgcagGTCAATCCAAAAGCTGCTGAATCATTGGCTAATCCTGAAGAATATCCAAAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttgacaagtgacttatggattaaagagagtacgtatacgtatattttgttgcagGTCAATCCAAAAGCTGCTGAATCATTGGCTAATCCTGAAGAATATCCAAATTTGTTTGAAGATTGGCAAGTTGCACTAGCTGTCGAATCTAAAGCTGTGG
tgttgac putative branch site (score: 3)
ttttgtt putative PPT
tatacgtatatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agcatccgttctcattcatttgccttgtttgggtagtcttatcatgttgacaagtgacttatggattaaagagagtacgtatacgtatattttgttgcagGTCAATCCAAAAGCTGCTGAATCATTGGCTAATCCTGAAGAATATCCAAATTTGTTTGAAGATTGGCAAGTTGCACTAGCTGTCGAATCTAAAGCTGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG