Sequence
atgc intronic sequence ATGC exonic sequencegtgagtttacattttgatttagactttgtttaagcttgtatatattgttgttagtcaatatttttaaataatgattctaaatattttcttcatttcttttctgtagAATCTCCTCCGCGGAGAGCCCCTCAAGCTTGTGGATGGTGGTCAATCCCAGAGGACTTTTGTGTATATTAAGGATGCTATTGAAGCCGTCTTATTGATGA
Basic information
species | Glycine max |
transcript | GLYMA17G05440.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G05440.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g73790.1 (Oryza sativa), 3'ss of exon 5
gtgagtttacattttgatttagactttgtttaagcttgtatatattgttgttagtcaatatttttaaataatgattctaaatattttcttcatttcttttctgtagAATCTCCTCCGCGGAGAGCCCCTCAAGCTTGTGGATGGTGGTCAATCCCAGAGGACTTTTGTGTATATTAAGGATGCTATTGAAGCCGTCTTATTGATGA
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--------gtatgtcaaccagtccctttctgagaataatatacctccat-ttcgttatggtcgttt--ttctcataagatgtatgtcgccaatgaattt---gcagAATCTCCTGCGTCGGGAGCCCCTGAAACTTGTTGATGGTGGCCAGTCCCAGAGAACTTTTGTTTACATTAAGGATGCCATTGAAGCTGTTCACTTGATGA
upper sequence: GLYMA17G05440.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G063949_T01 (Zea mays), 3'ss of exon 5
gtgagtttacattttgatttagactttgtttaagcttgtatatattgttgttagtcaatatttttaaataatgattctaaatattttcttcatttctt-ttctgtagAATCTCCTCCGCGGAGAGCCCCTCAAGCTTGTGGATGGTGGTCAATCCCAGAGGACTTTTGTGTATATTAAGGATGCTATTGAAGCCGTCTTATTGATGA
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----gtaagtgttcttgttt----cttggtgaggatcattatcttaattatttatgcaccatgttcagtctt--ctcagaagatgcacggtaccaatggttttgcagAATCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAGAGAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGA
upper sequence: GLYMA17G05440.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G27860.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgagtttacattttgatttagactttgtttaagcttgtatatattgttgttagtcaatatttttaaataatgattctaaatattttcttcatttcttttctgtagAATCTCCTCCGCGGAGAGCCCCTCAAGCTTGTGGATGGTGGTCAATCCCAGAGGACTTTTGTGTATATTAAGGATGCTATTGAAGCCGTCTTATTGATGA
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-----------------gtaagtgttcaaatccaagtatataacccaatgctagtctgtgtatatatgcaa-gcttttagttaatgcatctctatctatctttcagAATCTTCTACGTCGTGAGCCTCTCAAGCTTGTAGATGGTGGAGAATCACAGAGAACTTTCGTCTACATCAATGATGCTATTGAAGCTGTCCTTTTGATGA
upper sequence: GLYMA17G05440.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0061g01120.t01 (Vitis vinifera), 3'ss of exon 5
gtgagtttacattttgatttagactttgtttaagcttgtatatattgttgttagtcaatatttttaaataatgattctaaatattttcttcatttcttttctgtagAATCTCCTCCGCGGAGAGCCCCTCAAGCTTGTGGATGGTGGTCAATCCCAGAGGACTTTTGTGTATATTAAGGATGCTATTGAAGCCGTCTTATTGATGA
|| | || | | ||| | | | || || | || || || | ||| | | || |||| | |||||| | | ||||| || || || ||||| |||||||||||||||||||| ||||||||||| || ||||| || || ||||||||||||||||| ||||| |||||||
-----------gttagtttcaacatctgtcataacattta-gtagtattttttttc--tttttcttactactgatcttgctctttttctcc-------cacaatagAACCTTCTTCGTCATGAGCCACTCAAGCTTGTGGATGGTGGCCAATCCCAGAGAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGA
upper sequence: GLYMA17G05440.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 5
gtgagtttacattttgatttagactttgtttaagcttgtatatattgttgttagtcaatatttttaaataatgattctaaatattttcttcatttcttttctgtagAATCTCCTCCGCGGAGAGCCCCTCAAGCTTGTGGATGGTGGTCAATCCCAGAGGACTTTTGTGTATATTAAGGATGCTATTGAAGCCGTCTTATTGATGA
|| ||||| | | | || | | || | ||| |||| || | || ||||| || ||| | | |||| | || | |||||| || || || | ||||| |||||||||||||||||||| ||||||||||| || ||||| ||||| ||||||||||||||||| ||||| |||||||
gttagtttcaacatctgtcataacatggctt--gtttggtagtatttttttc-----attttttt------tgtctctgatcttgctctttttctcccacc-gtagAACCTTCTTCGTCGTGAGCCACTCAAGCTTGTGGATGGTGGCCAATCCCAGAGAACCTTTGTTTATATAAAGGATGCTATTGAAGCAGTCTTGTTGATGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagtcaatatttttaaataatgattctaaatattttcttcatttcttttctgtagAATCTCCTCCGCGGAGAGCCCCTCAAGCTTGTGGATGGTGGTCAATCCCAGAGGACTTTTGTGTATATTAAGGATGCTATTGAAGCCGTCTTATTGATGA
ttctaaa putative branch site (score: 2)
tattttcttcatttct CT-rich tract
aatatttttaaataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtttacattttgatttagactttgtttaagcttgtatatattgttgttagtcaatatttttaaataatgattctaaatattttcttcatttcttttctgtagAATCTCCTCCGCGGAGAGCCCCTCAAGCTTGTGGATGGTGGTCAATCCCAGAGGACTTTTGTGTATATTAAGGATGCTATTGAAGCCGTCTTATTGATGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC