Sequence
atgc intronic sequence ATGC exonic sequencegtgagtttatttgtgtttgtgcgcgcacgcctgcatgcgtgtgctttttggttatccttgcttgtagatttgcttcatatacatggaatctgcttttgtttgtggaggggatttgactgttgctgtttgttggtaattgtagATGGCTCTTATTGCTCGAATCCAGCACCCTTACATTGTGGAATTCAAGGAGGCATGGGTTGAGAAG
Basic information
species | Glycine max |
transcript | GLYMA11G18340.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G18340.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g36960.1 (Oryza sativa), 3'ss of exon 2
gtgagtttatttgtgtttgtgcgcgcacgcctgcatgcgtgtgctttttggttatccttgcttgtagattt---gcttcatatacatgga-atctgcttttgtttgtggaggggatttgactgttgctgtttgttggtaattgtagATGGCTCTTATTGCTCGAATCCAGCACCCTTACATTGTGGAATTCAAGGAGGCATGGGTTGAGAAG
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------------------------------------gttagtggaatgtggaagtggaagcttgcaatccctaggctttgtttgttcggttgtttgctagtggtattattaggaatttgatcacgacgaaa----acgaattgcagATGGCTCTGATTGCTCGGTTGCAACACCCTTACATTGTTGAATTCAAAGAGGCTTGGGTTGAGAAG
upper sequence: GLYMA11G18340.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g64490.1 (Oryza sativa), 3'ss of exon 3
gtgagtttatttgtgtttgtgcgcgcacgcctgcatgcgtgtgctttttggttatccttgcttgtagatttgcttcatatacatggaatctgcttttgtttgtggaggggatttgactgttgctgtttgttggtaattgtagATGGCTCTTATTGCTCGAATCCAGCACCCTTACATTGTGGAATTCAAGGAGGCATGGGTTGAGAAG
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-----------------------------------------------------------gtcagtgaa---aatcaagaaaccttgggccc-ttttcgttcatcggttcatgctgcattgaacaatttaaaaatatatgcagATGGCCCTTATTGCTCGCCTGCAACATCCTTACATTGTTGAGTTCAAGGAAGCATGGGTTGAGAAG
upper sequence: GLYMA11G18340.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G137118_T02 (Zea mays), 3'ss of exon 3
gtgagtttatttgtgtttgtgcgcgcacgcctgcatgcgtgtgctttttggttatccttgcttgtagatttgcttcatatacatggaatctgcttttgtttgtggaggggatttgactgttgctgtttgttggtaattgtagATGGCTCTTATTGCTCGAATCCAGCACCCTTACATTGTGGAATTCAAGGAGGCATGGGTTGAGAAG
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--------------------------------------------------gttggtgaaatgtgatgctttatttctgattcatcggttgtgcctt-----gaagagtcagtaagggaaaagctg---------aattgcagATGGCTCTAATTGCTCGGCTGCAGCACCCTTACATTGTTGAATTCAAGGAGGCTTGGGTTGAGAAG
upper sequence: GLYMA11G18340.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G074262_T01 (Zea mays), 3'ss of exon 3
gtgagtttatttgtgtttgtgcgcgcacgcctgcatgcgtgtgctttttggttatccttgcttgtagatttgcttcatatacatggaatctgcttttgtttgtggaggggatttgactgttgctgtttgttggtaattgtagATGGCTCTTATTGCTCGAATCCAGCACCCTTACATTGTGGAATTCAAGGAGGCATGGGTTGAGAAG
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----------------------------gtcagcagaacagaaatttaca--cgccctttttcatttgtttgtttgtcat--------tttgcact-gtcttcggtga-------actgatagagcaaat-ggaaattgcagATGGCTCTTATTGCTCGCTTGCAACATCCTTACATCGTTGAGTTCAAGGAGGCATGGGTTGAGAAG
upper sequence: GLYMA11G18340.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0009g00690.t01 (Vitis vinifera), 3'ss of exon 2
gtgagtttatttgtgtttgtgcgcgcacgcctgcatgcgtgtgctttttggttatccttgcttgtagatttgcttcatatacatggaatctgcttttgtttgt--ggaggggatttgactgttgctgtttgttggtaatt------gtagATGGCTCTTATTGCTCGAATCCAGCACCCTTACATTGTGGAATTCAAGGAGGCATGGGTTGAGAAG
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---------------------------------------------ctttggcgatcctt-----cagtttgccttttgttttattgattatgttttcgcttatttggtctttgtttttttccccctacattttggcaatttggagtatagATGGCTCTAATTGCGAGAATCCAACACCCTTACATTGTTGAATTTAAGGAAGCATGGGTAGAGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atctgcttttgtttgtggaggggatttgactgttgctgtttgttggtaattgtagATGGCTCTTATTGCTCGAATCCAGCACCCTTACATTGTGGAATTCAAGGAGGCATGGGTTGAGAAG
atttgac putative branch site (score: 4)
ttttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtttatttgtgtttgtgcgcgcacgcctgcatgcgtgtgctttttggttatccttgcttgtagatttgcttcatatacatggaatctgcttttgtttgtggaggggatttgactgttgctgtttgttggtaattgtagATGGCTCTTATTGCTCGAATCCAGCACCCTTACATTGTGGAATTCAAGGAGGCATGGGTTGAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG