Sequence
atgc intronic sequence ATGC exonic sequencegttttgtatataagatacagccatcaaatattttgttcgtgctctttcatcaacaaatttaacctagacaatcatctttgcttgttttgagggataaaggataaaaggaatttgaactgtttaggtttgttctttttcttggtcaattaggctatcatggttaaagtgtgtcaatctgttttatgtggcagAGTGTTCCTGTGCAAGCTGGGCAAACTCCTCCACTATTGCAGTATTTTGGAACACTTCTAACAAGAGGAAAGCTGAATGCCTTTGAGTCATTGGAATTGT
Basic information
species | Glycine max |
transcript | GLYMA18G02960.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 11
gttttgtatataagatacagccatcaaatattttgttcgtgctctttcatcaacaaatttaacctagacaatcatctttgcttgttttgagggataaagg--ataaaaggaatttgaactgtttaggtttgttctttttcttggtcaattaggctatcatggttaaagtgtgtcaatctgttttatgtggcagAGTGTTCCTGTGCAAGCTGGGCAAACTCCTCCACTATTGCAGTATTTTGGAACACTTCTAACAAGAGGAAAGCTGAATGCCTTTGAGTCATTGGAATTGT
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-------------------------------------------------------------------------attttcatttactttcctgtgttgggactgtacaactaatcttaa-tgctta----tgctcttctgcttgac---ttagcttttt------------cgtttctgtgctttaaaatgcagAGTGTTCCTGTTCAAGCTGGGCAAACGCCTCCACTCTTGCAGTACTTTGGCACATTGCTAACTCGGGGGAAGCTCAATGCTTACGAGTCTCTTGAGCTAT
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 11
gttttgtatataagatacagccatcaaatattttgttcgtgctctttcatcaacaaatttaacctagacaatcatctttgcttgttttgagggataaagg--ataaaaggaatttgaactgtttaggtttgttctttttcttggtcaattaggctatcatggttaaagtgtgtcaatctgttttatgtggcagAGTGTTCCTGTGCAAGCTGGGCAAACTCCTCCACTATTGCAGTATTTTGGAACACTTCTAACAAGAGGAAAGCTGAATGCCTTTGAGTCATTGGAATTGT
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-------------------------------------------------------------------------attttcatttactttcctgtgttgggactgtacaactaatcttaa-tgctta----tgctcttctgcttg----acttagctttttcgtttc---tgtgc-------ttttaaatg-cagAGTGTTCCTGTTCAAGCTGGGCAAACGCCTCCACTCTTGCAGTACTTTGGCACATTGCTAACTCGGGGGAAGCTCAATGCTTACGAGTCTCTTGAGCTAT
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 9
gttttgtatataagatacagccatcaaatattttgttcgtgctctttcatcaacaaatttaacctagacaatcatctttgcttgttttgagggataaaggata--aaaggaatttgaactgtttaggtttgttctttttcttggtcaattaggctatcatggttaaagtgtgtcaatctgttttatgtggcagAGTGTTCCTGTGCAAGCTGGGCAAACTCCTCCACTATTGCAGTATTTTGGAACACTTCTAACAAGAGGAAAGCTGAATGCCTTTGAGTCATTGGAATTGT
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--------------------------------------------------------------------------------cctgctatcaggattcatgtacatttaatcaattctcagtgtataagttc---ctttctttgacttaataa--ttcttatgttta-------ttactttatcaaa-attgcagAGTGTTCCTGTGCAAGCTGGGCAAACACCCCCACTCTTGCAGTACTTTGGCACATTGCTAACTCGAGGGAAGCTCAATGCCTTTGAGTCTCTTGAGCTAT
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 11
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 11
gttttgtatataagatacagccatcaaatattttgttcgtgctctttcatcaacaaatttaacctagacaatcatctttgcttgttttgagggataaaggataaaaggaatttgaactgtttaggtttgttctttttcttggtcaattaggctatcatggttaaagtgtgtcaatctgttttatg---tggcagAGTGTTCCTGTGCAAGCTGGGCAAACTCCTCCACTATTGCAGTATTTTGGAACACTTCTAACAAGAGGAAAGCTGAATGCCTTTGAGTCATTGGAATTGT
| | | || | ||| || |||| || | | |||| | | | || || | || | ||| | || |||| | ||||||||||||||| ||||| ||||||||||||||| | || ||||||||||| || ||| | || ||||| ||||| ||| | | |||||| |||||| | |
-------------------------------------------------------------------------------gtatatgttccatattcaag----caaagaatc----ctctgtgaacatgttgtctataatgtatgtttgtaacaccagtctgaaactacaacatcacactttacaattttgcagAGTGTTCCTGTACAAGCAGGGCAAACTCCTCCATTGTTACAGTATTTTGGGACCCTTTTGACTAGAGGGAAGCTCAATTCATATGAGTCTTTGGAACTAT
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 11
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 11
gttttgtatataagatacagccatcaaatattttgttcgtgctctttcatcaacaaatttaacctagacaatcatctttgcttgttttgagggataaaggataaaaggaatttgaactgtttaggtttgttctttttcttggtcaattaggctatcatggttaaagtgtgtcaatctgttttatgtggcagAGTGTTCCTGTGCAAGCTGGGCAAACTCCTCCACTATTGCAGTATTTTGGAACACTTCTAACAAGAGGAAAGCTGAATGCCTTTGAGTCATTGGAATTGT
| || || | | | | || | | | || | || | | | | | | |||| || | | || | ||||||||||||||| |||||||| |||||||||||| | || ||||||||||| || ||| | || ||||| || || ||| | | ||||||| ||||| | |
------------------------------------------------------------------------------------------------gtgtctatttcatatccaagcaact-atgtgtaaacatgtttatttatgatgaaatgttggtaacaccaatttttcaa-ctctataattttgcagAGTGTTCCTGTACAAGCTGGACAAACTCCTCCATTGTTACAGTATTTTGGGACTCTTTTGACTAGAGGGAAACTCAATTCATATGAGTCACTGGAACTAT
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 11
gttttgtatataagatacagccatcaaatattttgttcgtgctctttcatcaacaaatttaacctagacaatcatctttgcttgttttgagggataaaggataaaaggaatttgaactgtttaggtttgttctttttcttggtcaattaggctatcatggttaaagtgtgtcaatctgttttatgtggcagAGTGTTCCTGTGCAAGCTGGGCAAACTCCTCCACTATTGCAGTATTTTGGAACACTTCTAACAAGAGGAAAGCTGAATGCCTTTGAGTCATTGGAATTGT
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---------------------------------------------------------------------------cttcctttattttttatttttttaaaaaaccattccctggaattttggggtgggaaagat------gctaaccactttgtcttcttctg---gtgtctaattttt-------gcagAGTGTTCCTATGCAATCTGGGCAGACTCCACCTTTGCTACAGTACTTTGGAACACTTCTAACTAGAGGAAAGCTCAATGCATTTGAGTCATTGGAATTAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttggtcaattaggctatcatggttaaagtgtgtcaatctgttttatgtggcagAGTGTTCCTGTGCAAGCTGGGCAAACTCCTCCACTATTGCAGTATTTTGGAACACTTCTAACAAGAGGAAAGCTGAATGCCTTTGAGTCATTGGAATTGT
tctgtttt CT-rich tract
tgttttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttttgtatataagatacagccatcaaatattttgttcgtgctctttcatcaacaaatttaacctagacaatcatctttgcttgttttgagggataaaggataaaaggaatttgaactgtttaggtttgttctttttcttggtcaattaggctatcatggttaaagtgtgtcaatctgttttatgtggcagAGTGTTCCTGTGCAAGCTGGGCAAACTCCTCCACTATTGCAGTATTTTGGAACACTTCTAACAAGAGGAAAGCTGAATGCCTTTGAGTCATTGGAATTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA