Sequence
atgc intronic sequence ATGC exonic sequencegtgattcctctccctctctttttcactctacgctacttcttctctttcatattgttgtattttaactgcgttttctctgtttcttgttcagCCTTTCAAGAGGTATGTTGAGATTGGGAGGGTTTCCCAAATCAACTACGGCAAGGAATATGGCAGGCTCGTCGTCATTGTCGATGTCATTGACCAGAACA
Basic information
species | Glycine max |
transcript | GLYMA03G06380.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G06380.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os04g43540.1 (Oryza sativa), 3'ss of exon 1
gtgattcctctccctctctttttcactctacgctacttcttctctttcatattgttgtattttaactgcgttttctctgtttcttgttcagCCTTTCAAGAGGTATGTTGAGATTGGGAGGGTTTCCCAAATCAACTACGGCAAGGAATATGGCAGGCTCGTCGTCATTGTCGATGTCATTGACCAGAACA
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gtagggag-ctgtcgcgaaatcttgcccgtcgtctcgtcggtatgtgctgatgcgcgcgttgttactgtgcttgtgctgtg-------cagCCGTTCAAGAGGTTCGTGGAGATCGGGCGGGTGGCCCTGGTGAACTACGGCAAGGACTACGGCCGCCTCGTCGTCATTGTCGATGTCGTCGACCAGAACA
upper sequence: GLYMA03G06380.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g40880.1 (Oryza sativa), 3'ss of exon 1
-----------------------gtgattcctctccctctctttttcact--ctacgctacttcttctctttcatattgt-----tgtattttaactgcgttttctc-tgtttcttgttcagCCTTTCAAGAGGTATGTTGAGATTGGGAGGGTTTCCCAAATCAACTACGGCAAGGAATATGGCAGGCTCGTCGTCATTGTCGATGTCATTGACCAGAACA
| | | || | | || | | | | | | | || |||| ||| ||| | | | ||||| | || | | || ||||| |||||||||| || ||||| ||| |||| ||| | |||||||||||||| || ||| | ||||||||||| || |||||| | |||||||||
gtaggtggatcgccgtgggctcgtcgtcttgccgccgttgccgttccggtggtggtggtggtggtggtgctttggattgcgcgcgtgtgtttgaccggggtttttttgtgcctttcgtgcagCCGTTCAAGAGGTTCGTGGAGATCGGGCGGGTGGCCCTGGTGAACTACGGCAAGGACTACGGCCGCCTCGTCGTCATCGTTGATGTCGTCGACCAGAACC
upper sequence: GLYMA03G06380.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G028883_T01 (Zea mays), 3'ss of exon 1
gtg-attcctctccctctctttttcactctacgctacttcttctctttcatattgttgtattttaac--tgcgt---tttctctgtttc--ttgttcagCCTTTCAAGAGGTATGTTGAGATTGGGAGGGTTTCCCAAATCAACTACGGCAAGGAATATGGCAGGCTCGTCGTCATTGTCGATGTCATTGACCAGAACA
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gtatatgtctcccgatatcattcccgcatcaaggggtcttgtctttttgttgttgttgttggctaatgatgcgcacctgttgatgttgcggttccgcagCCGTTCAAGAGGTTCGTGGAGATCGGGCGAGTGGCCCTTGTAAACTACGGCAAGGAGTATGGCCGCCTCGTCGTCATCGTCGACGTCGTCGACCAGAACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcttctctttcatattgttgtattttaactgcgttttctctgtttcttgttcagCCTTTCAAGAGGTATGTTGAGATTGGGAGGGTTTCCCAAATCAACTACGGCAAGGAATATGGCAGGCTCGTCGTCATTGTCGATGTCATTGACCAGAACA
ttttaac putative branch site (score: 2)
cgttttctctgtttct putative PPT
tttcatattgttgtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgattcctctccctctctttttcactctacgctacttcttctctttcatattgttgtattttaactgcgttttctctgtttcttgttcagCCTTTCAAGAGGTATGTTGAGATTGGGAGGGTTTCCCAAATCAACTACGGCAAGGAATATGGCAGGCTCGTCGTCATTGTCGATGTCATTGACCAGAACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA