Sequence
atgc intronic sequence ATGC exonic sequencegtgcaaattgcttgttttgctcagttgcaacttgcatgttgttatcttactttttgaataatctctctctatcctgttatgtctctgctgagttgcataagattgcaatccaaatgctatgaaggtacttccatcttacatatggtgtttgtttttcgtccagTCATTGGCTCGGATGAACAAGAAAGATTCATGGCTTTTCTGGTGGACGCTTTACCTTACA
Basic information
| species | Glycine max |
| transcript | GLYMA19G41530.1 |
| intron # | 2 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G41530.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g22870.1 (Oryza sativa), 3'ss of exon 3
gtgcaaattgcttgttttgctcagttgcaacttgcatgttgttatcttactttttgaataatctctctctatcctgttatgtctctgctgagttgcataagattgcaatccaaatgctatgaaggtacttccatcttacatatggtgtttgtttttcgtccagTCATTGGCTCGGATGAACAAGAAAGATTCATGGCTTTTCTGGTGGACGCTTTACCTTACA
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--------------------------------------------------------------------------------gtttgcgttc-gtctctcagtatacttgtgacattttggtgcaattgcttatccctaaattagtgtatccgttttgc-tgcagTCTCTTGCTAGGATGAACAAGAAGGACTCATGGCTGTTCTGGTGGACTCTGTACTTGACT
upper sequence: GLYMA19G41530.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G048117_T01 (Zea mays), 3'ss of exon 3
gtgcaaattgcttgttttgctcagttgcaacttgcatgttgttatcttactttttgaataatctctctctatcctgttatgtctctgc-tgagttgcataagattgcaatccaaatgctatg-aaggtacttccatcttacatatggtgtttgtttttcgtccagTCATTGGCTCGGATGAACAAGAAAGATTCATGGCTTTTCTGGTGGACGCTTTACCTTACA
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--------------------------------------------------------------------------------gtctgtgcctgctttgcctgtgatgttaattgtattcgtgtgtgaaattgttgcaggttgtaact--tgaatgttccctg--cagTCTCTCGCTCGGATGAACAAGAAGGATTCATGGCTGTTCTGGTGGACTCTTTACTTGACT
upper sequence: GLYMA19G41530.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G09330.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgcaaattgcttgttttgctcagttgcaacttgcatgttgttatcttactttttgaataatctctctctatcctgttatgtctctgctgagttgcataagattgcaatccaaatgctatgaaggtacttccatcttacatatggtgtttgtttttc-gtccagTCATTGGCTCGGATGAACAAGAAAGATTCATGGCTTTTCTGGTGGACGCTTTACCTTACA
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----------------------------------------gttagctt--ttcttcacttattcacaaggatatgggttcagc-ctgtcgagaaatgtggggttgtgtttccctttccgttttttttttgtatactcatgtgttttcatcatttttctatacagTCTTTGGCTCGGATGAACAAGAAAGACTCATGGCTTTTCTGGTGGACACTTTACCTTGCA
upper sequence: GLYMA19G41530.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S6_365V6.1 (Physcomitrella patens), 3'ss of exon 3
gtgcaaattgcttgttttgctcagttgcaacttgcatgttgttatcttactttttgaataatctctctctatcctgttatgtctctgctgagttgcataagattgcaatccaaatgctatgaaggtacttccatcttacatatggtgtttgtttttcgtccagTCATTGGCTCGGATGAACAAGAAAGATTCATGGCTTTTCTGGTGGACGCTTTACCTTACA
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--------------------------------------------tccaagttattgagggattgatgtagtttctattcaaaatgaattc-gtagtaagagattgc-----agatgttgacttaagattgg----ttatggatgacgtctg---------cagACCTTGGAGACATTGAACAAGAAAGATGCTTGGCTATTCTGGTGGACGCTGTACCTTACT
upper sequence: GLYMA19G41530.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S6_199V6.1 (Physcomitrella patens), 3'ss of exon 1
gtgcaaattgcttgttttgctcagttgcaacttgcatgttgttatcttactttttgaataatctctctctatcctgttatgtctctgctgagttgcataagattgcaat---ccaaatgctatgaaggtacttccatcttacatatggtgtttgtttttcgtccagTCATTGGCTCGGATGAACAAGAAAGATTCATGGCTTTTCTGGTGGACGCTTTACCTTACA
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---------------------------------------------------------------gctctaagttattggatgactgttttcgtttatgttaaagtgcaatgtgccggaagagattgcggc-cgttgacttaggattgattattaatgttttctgcagACCTTGGAGACGTTGAACAAGAAAGATGCTTGGCTATTCTGGTGGACGCTGTATCTCACT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccaaatgctatgaaggtacttccatcttacatatggtgtttgtttttcgtccagTCATTGGCTCGGATGAACAAGAAAGATTCATGGCTTTTCTGGTGGACGCTTTACCTTACA
atcttac putative branch site (score: 3)
tttgtttttcgtcc putative PPT
tttgttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcaaattgcttgttttgctcagttgcaacttgcatgttgttatcttactttttgaataatctctctctatcctgttatgtctctgctgagttgcataagattgcaatccaaatgctatgaaggtacttccatcttacatatggtgtttgtttttcgtccagTCATTGGCTCGGATGAACAAGAAAGATTCATGGCTTTTCTGGTGGACGCTTTACCTTACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
