Sequence
atgc intronic sequence ATGC exonic sequence...tcaccattagacattgctttagtttgttattagaaattaacccatataaggtttcagcctatacataggataaatttctgacacttaatctctttttcagATCTTCCTCCAGACAAGGAGCCTCTGGACTGGAACACTAGGATGAAAATAGCAGCTGGAGCTGCAAAGGGATTGGAATATTTGCATGACAAGGCAAATCC
Basic information
species | Glycine max |
transcript | GLYMA13G28730.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G28730.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g30870.1 (Oryza sativa), 3'ss of exon 3
tcaccattagacattgctttagtttgttattagaaattaacccatataaggtttcagcctatacataggataaatttctgacacttaatctctttt---tcagATCTTCCTCCAGACAAGGAGCCTCTGGACTGGAACACTAGGATGAAAATAGCAGCTGGAGCTGCAAAGGGATTGGAATATTTGCATGACAAGGCAAATCC
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agactcttaagcgcattgtttgttcataagacgtatttagtttgtttaaa---ttaatttgcatgattcataaatggcaacgttttgtacttttgtgtgttagATATTCCACCTGACAAGGAACCTCTCGACTGGAATACACGGATGAAGATTGCTGCTGGTGCAGCCAAGGGCTTGGAATTCTTGCATGACAAGGCAAATCC
upper sequence: GLYMA13G28730.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G18610.1 (Arabidopsis thaliana), 3'ss of exon 4
tcaccattagacattgctttagtttgttattagaaattaacccatataaggtttcagcctatacataggataaatttctgacacttaa---tctctttttcagATCTTCCTCCAGACAAGGAGCCTCTGGACTGGAACACTAGGATGAAAATAGCAGCTGGAGCTGCAAAGGGATTGGAATATTTGCATGACAAGGCAAATCC
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---ttaatctgttcttccaaagctatttatggtgaataaatggaaatattagcttgtaatagttctatcaagtgcatgtaacgattaaaactttgattttcagATCTTCCACCTGATAAAGAGCCTCTAGACTGGAGTACTAGAATGACAATAGCGGCAGGAGCAGCAAAGGGACTGGAGTATCTGCATGATAAAGCGAATCC
upper sequence: GLYMA13G28730.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv05s0020g01770.t01 (Vitis vinifera), 3'ss of exon 3
tcaccattagacattgctttagtttgttattagaaattaacccat---ataaggtttcagcctatacataggataaatttctgacacttaatctct-ttttcagATCTTCCTCCAGACAAGGAGCCTCTGGACTGGAACACTAGGATGAAAATAGCAGCTGGAGCTGCAAAGGGATTGGAATATTTGCATGACAAGGCAAATCC
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--acaatttttcccaaaatca-ttcataatttcacattgtttgattagataagtccactttctgaaatcgcacttcattactt-tatttgctgcctgtcttcagATCTTCCACCAGACAAGGAGCCTCTGGACTGGAACACAAGGATGAAGATTGCTGCTGGTGCAGCTAAAGGTTTGGAGTATTTGCATGATAAAGCAAGCCC
upper sequence: GLYMA13G28730.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ23436 (Selaginella moellendorffii), 3'ss of exon 3
tcaccattagacattgctttagtttgttattagaaattaacccatataaggtttcagcctatacataggataaatttctgacacttaatctctttttcagATCTTCCTCCAGACAAGGAGCCTCTGGACTGGAACACTAGGATGAAAATAGCAGCTGGAGCTGCAAAGGGATTGGAATATTTGCATGACAAGGCAAATCC
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---------------------------------------gtttgtctattaatttagt-tgtttcctgcatacgaaactga---gtgagctttcgtgcagACGTGCCGGCTGACAAGGAACCGTTGGGCTGGAACACAAGGATGAAAATAGCTGCGGGAGCTGCCAGGGGACTGGAGTACCTACATGACAAAGCAAATCC
upper sequence: GLYMA13G28730.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ25419 (Selaginella moellendorffii), 3'ss of exon 3
tcaccattagacattgctttagtttgttattagaaattaacccatataaggtttcagcctatacataggataaatttctgacacttaatctctttttcagATCTTCCTCCAGACAAGGAGCCTCTGGACTGGAACACTAGGATGAAAATAGCAGCTGGAGCTGCAAAGGGATTGGAATATTTGCATGACAAGGCAAATCC
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-----------------------------------gtttgtctattaatttagttgtttcctacatacgaaa-----ctgag---tgagctttcgtgcagACGTGCCGGCTGACAAGGAACCGTTGGGCTGGAACACAAGGATGAAAATAGCTGCGGGAGCTGCCAGGGGACTGGAGTACCTGCATGACAAAGCAAATCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataaggtttcagcctatacataggataaatttctgacacttaatctctttttcagATCTTCCTCCAGACAAGGAGCCTCTGGACTGGAACACTAGGATGAAAATAGCAGCTGGAGCTGCAAAGGGATTGGAATATTTGCATGACAAGGCAAATCC
cttaatctctttttc CT-rich tract
ataaatttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcaccattagacattgctttagtttgttattagaaattaacccatataaggtttcagcctatacataggataaatttctgacacttaatctctttttcagATCTTCCTCCAGACAAGGAGCCTCTGGACTGGAACACTAGGATGAAAATAGCAGCTGGAGCTGCAAAGGGATTGGAATATTTGCATGACAAGGCAAATCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
tcaccat
- - - - - - - tgcttta
- - - - - - - - - - - - - - - - - - - -acccata