Sequence
atgc intronic sequence ATGC exonic sequencegtccgtatttcgccactctctcgtcgttttccccgcaatgccttgccgcattgcccattctctcgtcgttttctgactctccgatacgctcgtcgtttttgcagTTGGCAAGTGTCGGAATCAACCCGCAATTCATCACTTTCACGCATGTCACCATGGAATCGGACAAGTACATTTGCGTCAGGGAAACCGCGCCGCAGAACA
Basic information
species | Glycine max |
transcript | GLYMA11G06720.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 1
gtccgtatttcgccactctctcgtcgttttccccgcaatgccttgccgcattgcccattctctcgtcgttttctgactctccgatacgctcgtcgtttttgcagTTGGCAAGTGTCGGAATCAACCCGCAATTCATCACTTTCACGCATGTCACCATGGAATCGGACAAGTACATTTGCGTCAGGGAAACCGCGCCGCAGAACA
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-----------gtaacaccttcgccacctcgtcctc----ctcttcttctccatccattcaccca-------ctgatcgttcgttgcttgcctgtcctccgcagCTCACCAGCCTGGGCATCGCGCCGCAGTTTGTCACGTTTACCCATGTCACCATGGAGTCGGAGAAGTACATCTGCGTCCGCGAGACCTCGCCGCAGAACA
upper sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 1
-----------------------------------------------gtccgtatt---tcgccactctctcgtcgttttccccgcaatgccttgccgcattgcccattctctcgtcg----tttt----ctgact-ctccgatacgctcgtcgtttttgcagTTGGCAAGTGTCGGAATCAACCCGCAATTCATCACTTTCACGCATGTCACCATGGAATCGGACAAGTACATTTGCGTCAGGGAAACCGCGCCGCAGAACA
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gtaagttctggagctcgatttgttcgttattgtttaaattcacttcagttcgtagtagatcttggattgttctggatctgtgttacagatcattgttgagttagttgttttttagtggataattttggtgttgattgttctgtttggttcggtggaattgcagTTGTCTAGTATCGGAATTAGTCCGCAATTCATGACATTTACGCATGTGACCATGGAGTCGGATAAGTATATTTGTGTTAGGGAGACGGCGCCGCAGAACA
upper sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 1
gtccgtatttcgccactctctcgtcgttttccccgcaatgccttgccgcattgcccattctctcgtcgttttctgactctccgatacgctcgtcgtttttgcagTTGGCAAGTGTCGGAATCAACCCGCAATTCATCACTTTCACGCATGTCACCATGGAATCGGACAAGTACATTTGCGTCAGGGAAACCGCGCCGCAGAACA
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------------------------------gtgcgtattttggttttggatttatttgctagaaatcagcattggattgtctaat---tttgt--tcttggcagCTCACGAGCTTGGGCATCAATCCCCAATGCATCACTTTCAACCATGTCACGATGGAATCCGAGAAGTACATATGCGTGAGAGAGACCACGCCGCAGAACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgcccattctctcgtcgttttctgactctccgatacgctcgtcgtttttgcagTTGGCAAGTGTCGGAATCAACCCGCAATTCATCACTTTCACGCATGTCACCATGGAATCGGACAAGTACATTTGCGTCAGGGAAACCGCGCCGCAGAACA
ttctgac putative branch site (score: 2)
tcgttttt putative PPT
ttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtccgtatttcgccactctctcgtcgttttccccgcaatgccttgccgcattgcccattctctcgtcgttttctgactctccgatacgctcgtcgtttttgcagTTGGCAAGTGTCGGAATCAACCCGCAATTCATCACTTTCACGCATGTCACCATGGAATCGGACAAGTACATTTGCGTCAGGGAAACCGCGCCGCAGAACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA