Sequence
atgc intronic sequence ATGC exonic sequence...cagatatgctcactatcaaatcaaatgagtttgctttatttcaataatggtgtcatttcctgcaatattctctcgaaatcaagtttatctgtttatgtagATAGGATCCACTGAGTGGGTTCAACAAAACCTTAATAATCTTCGTTCCAAAGCTGTAGCATACCTTAATGTGGACTGTGCTATGCAAGGTCTTGGTTGCT
Basic information
species | Glycine max |
transcript | GLYMA12G23220.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G23220.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv00s0285g00060.t01 (Vitis vinifera), 3'ss of exon 2
----cagatatgctcactatcaaatcaaatgagtttgctttatttcaataatggtgtcatttcctgcaatattctctcgaaatcaagtttatctgttta--tgtagATAGGATCCACTGAGTGGGTTCAACAAAACCTTAATAATCTTCGTTCCAAAGCTGTAGCATACCTTAATGTGGACTGTGCTATGCAAGGTCTTGGTTGCT
| | | ||| ||| | | | ||| | ||||| ||| | |||| |||| || | || | ||| | || ||| | | |||||||||| ||||||||||| ||||||||||| ||||| |||| |||| |||||||||||||||||| |||||||| | ||||| | || | ||
ttatttgttctaaaagtaatccaattagctaggcttgttctatttgaatggttgtgt-attt-----aacactcaaaagtaatttacttgtgttgtgtggcttcagATAGGATCTACTGAGTGGGTCGAACAAAACCTTTTGAATCTGGGTTCTAAAGTTGTAGCATACCTTAATGTAGACTGTGCAGTTCAAGGACCAGGCTTCT
upper sequence: GLYMA12G23220.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv00s0319g00060.t01 (Vitis vinifera), 3'ss of exon 1
--cagatatgctcactatcaaatcaaatgagtttgctttatttcaataatggtgtcatttcctgcaatattctctcgaaatcaagtttatctgttta--tgtagATAGGATCCACTGAGTGGGTTCAACAAAACCTTAATAATCTTCGTTCCAAAGCTGTAGCATACCTTAATGTGGACTGTGCTATGCAAGGTCTTGGTTGCT
| | | ||| ||| | | | ||| | ||||| ||| | |||| || || | || | ||| | || ||| | |||||||||| ||||||||||| ||||||||||| ||||| |||| ||| |||||||||||||||||| |||||||| | ||||| | || | ||
atttgttctaaaagtaatccaattagctaggcttgttctatttgaatggttgtgtgtatt----taacactcaaaagtaatttacttgtgttgtgtggcctcagATAGGATCTACTGAGTGGGTCGAACAAAACCTTTTGAATCTGGGTTCTGAAGTTGTAGCATACCTTAATGTAGACTGTGCAGTTCAAGGACCAGGCTTCT
upper sequence: GLYMA12G23220.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0032g00670.t01 (Vitis vinifera), 3'ss of exon 2
---cagatatgctcactatcaaatcaaatgagtttgctttatttcaataatggtgtcatttcctgcaatattctctcgaaatcaagtttatc-tgtttatgtagATAGGATCCACTGAGTGGGTTCAACAAAACCTTAATAATCTTCGTTCCAAAGCTGTAGCATACCTTAATGTGGACTGTGCTATGCAAGGTCTTGGTTGCT
| | | ||| ||| | | | ||| | ||||| ||| | |||| || || | || || | | | | | || | |||||||||| ||||||||||| ||||||||||| ||||| |||| |||| |||||||||||||||||| |||||||| | ||||| | || | ||
tatttgttctaaaagtaatccaattagctaggcttgttctatttgaatggttgtgtgtatt----taacactcaaagtaatttacttgtgttgcgtggtttcagATAGGATCTACTGAGTGGGTCGAACAAAACCTTTTGAATCTGGGTTCTAAAGTTGTAGCATACCTTAATGTAGACTGTGCAGTTCAAGGACCAGGCTTCT
upper sequence: GLYMA12G23220.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv00s0352g00020.t01 (Vitis vinifera), 3'ss of exon 2
--cagatatgctcactatcaaatcaaatgagtttgctttatttcaataatggtgtcatttcctgcaatattctctcgaaatcaagtttatctgttta--tgtagATAGGATCCACTGAGTGGGTTCAACAAAACCTTAATAATCTTCGTTCCAAAGCTGTAGCATACCTTAATGTGGACTGTGCTATGCAAGGTCTTGGTTGCT
| | | ||| ||| | | | ||| | ||||| ||| | |||| || || | || | ||| | || ||| | |||||||||| ||||||||||| ||||||||||| ||||| |||| |||| |||||||||||||||||| |||||||| | ||||| | || | ||
atttgttctaaaagtaatccaattagctaggcttgttctatttgaatggttgtgtgtatt----taacactcaaaagtaatttacttgtgttgtgtggcctcagATAGGATCTACTGAGTGGGTCGAACAAAACCTTTTGAATCTGGGTTCTAAAGTTGTAGCATACCTTAATGTAGACTGTGCAGTTCAAGGACCAGGCTTCT
upper sequence: GLYMA12G23220.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv00s0327g00020.t01 (Vitis vinifera), 3'ss of exon 1
cagatatgctcactatcaaatcaaatgagtttgctttatttcaataatggtgtcatttcctgcaatattctctcgaaatcaagtttatctgttta--tgtagATAGG--ATCCACTGAGTGGGTTCAACAAAACCTTAATAATCTTCGTTCCAAAGCTGTAGCATACCTTAATGTGGACTGTGCTATGCAAGGTCTTGGTTGCT--
| | | ||| ||| | | | ||| | ||||| ||| | |||| || || | || | ||| | || ||| | ||||||| ||| ||||||||||| ||||||||||| ||||| |||| |||| |||||||||||||||||| |||||||| | ||||| | || | ||
--gttctaaaagtaatccaattagctaggcttgttctatttgaatggttgtgtgtatt----taacactcaaaagtaatttacttgtgttgtgtggcctcagatagGGGATCTACTGAGTGGGTCGAACAAAACCTTTTGAATCTGGGTTCTAAAGTTGTAGCATACCTTAATGTAGACTGTGCAGTTCAAGGACCAGGCTTCTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatggtgtcatttcctgcaatattctctcgaaatcaagtttatctgtttatgtagATAGGATCCACTGAGTGGGTTCAACAAAACCTTAATAATCTTCGTTCCAAAGCTGTAGCATACCTTAATGTGGACTGTGCTATGCAAGGTCTTGGTTGCT
tctgttt CT-rich tract
aatattct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cagatatgctcactatcaaatcaaatgagtttgctttatttcaataatggtgtcatttcctgcaatattctctcgaaatcaagtttatctgtttatgtagATAGGATCCACTGAGTGGGTTCAACAAAACCTTAATAATCTTCGTTCCAAAGCTGTAGCATACCTTAATGTGGACTGTGCTATGCAAGGTCTTGGTTGCT
- - tatgctc
- - - - - - - - - - - - - - - -tgcttta
- - - - - - - - - - - - - - - - - - - - - - -aatggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaatcaag