Sequence
atgc intronic sequence ATGC exonic sequencegtatctggatttttttttgtaataactctgatgcaagttctttctaaaattgaatattaaataataaaaattggctaaggtattctggtttggcaaggaataatagtaatacgatggactattttataagttttgagcttacctgatgaagtatgtggttgttctttcagCCTAGTACATTTTTCACTGAGCAGTTGACAGCATTTGAGGTATGGCTTGACCATGGTTCTGAACATAAGAAACCACCAGAACAGTTGCCTATAGTTCTTC
Basic information
species | Glycine max |
transcript | GLYMA09G41510.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G41510.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os11g01872.1 (Oryza sativa), 3'ss of exon 8
gtatctggatttttttttgtaataactctgatgcaagttctttctaaaattgaatattaaataataaaaattggctaaggtattctggtttggcaaggaataata-gtaatacgatggactattttataagttttgagcttacctgatgaagtatgtggttgttctt-tcagCCTAGTACATTTTTCACTGAGCAGTTGACAGCATTTGAGGTATGGCTTGACCATGGTTCTGAACATAAGAAACCACCAGAACAGTTGCCTATAGTTCTTC
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---------------------------gtgctattaaccgtctttgcttttt----ttgaatgatctaa--tactttggacatcaacattttgttggcattgttatgttgtttga-gaattatcacttcagtacca---tcactttgtt---catttccttactcaaaccagCCGAGTCCATTTTTCACGGAGCAATTGACAGCATTTGAAGTTTGGCTTGATCATGGCTCTGAAGACAAGAAACCCCCAGAACAGCTACCTATTGTTCTTC
upper sequence: GLYMA09G41510.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G01770.1 (Arabidopsis thaliana), 3'ss of exon 9
gtatctggatttttttttgtaataactctgatgcaagttctttctaaaattgaatattaaataataaaaattggctaaggtattctggtttggcaaggaata-atagtaatacgatgg-actattttataagttttgagcttacctgatgaagtatgtggttgttcttt---cagCCTAGTACATTTTTCACTGAGCAGTTGACAGCATTTGAGGTATGGCTTGACCATGGTTCTGAACATAAGAAACCACCAGAACAGTTGCCTATAGTTCTTC
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----------------------------------------------------------------------------------gtttgttttgtccattattatatttccttgtaattgtatgatttggtatgatgtctgtcttgttgataatgcttgttactctcctttatctagCCAAGTTCATTTTTCACTGAGCAACTGACAGCTTTTGAGGTCTGGCTGGATCATGGATCTGAGCATAAGAAGCCACCAGAGCAGTTACCTATTGTTCTTC
upper sequence: GLYMA09G41510.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv08s0058g00890.t01 (Vitis vinifera), 3'ss of exon 9
--gtatctggatttttttttgtaata-actctgatgcaagttctttctaaaattgaatattaaataataaaaattggctaaggtattctggtttggcaaggaataatagtaatacgatggactattttataagttttgagcttacctgatgaagtatgtggttgttctttcagCCTAGTACATTTTTCACTGAGCAGTTGACAGCATTTGAGGTATGGCTTGACCATGGTTCTGAACATAAGAAACCACCAGAACAGTTGCCTATAGTTCTTC
| | | || ||||| || || | ||| | | | | | || || || | ||| || ||| | | | | | || | | | | || | ||| | | || | ||| | || |||||||| ||| | || |||||||||||| |||| || |||||||||||||| || ||||| || ||||| |||||||||||||| |||||||| || |||||||
gtgcacatttccttaagtttgtgttatacaattatgaatctcttattttgggtttgc--ttgggtacttgaaacgagc------atttagagtacctagaagaatgttgtgctg-gttttatcatctcatatgcccagttacgacattgatgtctatacaatgtttttttcagCCAAGTCCTTTCTTCACTGAGCAGCTGACTGCTTTTGAGGTATGGCTAGATCATGGATCAGAACACAAGAAACCACCAGAGCAGTTGCCAATTGTTCTTC
upper sequence: GLYMA09G41510.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S199_73V6.1 (Physcomitrella patens), 3'ss of exon 9
gtatctggatttttttttgtaataactctgatgcaagttctttctaaaattgaatattaaataataaaaattggct-aaggtattctggtttggcaaggaataatagtaatacgatggactattttataagttttgagcttacctgatgaagtatgtggttgttctttcagCCTAGTACATTTTTCACTGAGCAGTTGACAGCATTTGAGGTATGGCTTGACCATGGTTCTGAACATAAGAAACCACCAGAACAGTTGCCTATAGTTCTTC
||| || | || | | |||| |||| | | || | | || | | || ||| | || | | | || || || ||||||||| | |||||||| ||||| |||||||| ||||| || ||| | |||||||||||||| | ||||| |||||||| ||| | ||||| ||||| |
--------------------------------------------------------------------tgttgtcttgatgtttctttgtttttatccatgtaatttttttttgaatgctagtagcattc-tctggatactacttactgt--tttttccttcttattgcagCCTAGTCCTTTTTTCACAGAGCAATTGACAGCCTTTGAAGTGTGGTTGGACCATGGTTCTGAGCGGAAGAAGCCACCAGAGCAGCTCCCTATCGTTCTGC
upper sequence: GLYMA09G41510.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S124_156V6.1 (Physcomitrella patens), 3'ss of exon 9
gtatctggatttttttttgtaataactctgatgcaagttctttctaaaattgaatattaaataataaaaattggctaaggtattctggtttggcaaggaataatagtaatacgatggactattttataagttttgagcttacctgatgaagtatgtggttgttcttt--cagCCTAGTACATTTTTCACTGAGCAGTTGACAGCATTTGAGGTATGGCTTGACCATGGTTCTGAACATAAGAAACCACCAGAACAGTTGCCTATAGTTCTTC
| | | ||| | | | || ||| || | | | | | | | || ||| | || || | | | | |||| | ||||||||| | |||||||| ||||| |||||||| || ||||| ||||| || |||||||||||| ||||| ||||| || || | ||||| |||||||
------------------------------------------------------------------tttttcgtttttaaaatttt--tatatcatttaattattatt-tgtgtcgaaatcagtagcaaatttgaaa---acaagacttgatttttagcctttctattgcagCCTAGTCCTTTTTTCACAGAGCAATTGACAGCTTTCGAGGTGTGGCTGGAGCATGGTTCTGAAAGGAAGAAGCCACCTGAGCAACTTCCTATCGTTCTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggactattttataagttttgagcttacctgatgaagtatgtggttgttctttcagCCTAGTACATTTTTCACTGAGCAGTTGACAGCATTTGAGGTATGGCTTGACCATGGTTCTGAACATAAGAAACCACCAGAACAGTTGCCTATAGTTCTTC
ttgttctttc CT-rich tract
attttataagttttga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatctggatttttttttgtaataactctgatgcaagttctttctaaaattgaatattaaataataaaaattggctaaggtattctggtttggcaaggaataatagtaatacgatggactattttataagttttgagcttacctgatgaagtatgtggttgttctttcagCCTAGTACATTTTTCACTGAGCAGTTGACAGCATTTGAGGTATGGCTTGACCATGGTTCTGAACATAAGAAACCACCAGAACAGTTGCCTATAGTTCTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA