Sequence
atgc intronic sequence ATGC exonic sequence...ttgatatgctcactgtcaaatcaaatgagtttgctttatttcaataatggtgtcatttcctgcaatattcgctctaaatcaagtttatctgtttatgtagATAGGATCCACTGAGTGGGTTGAACAAAACCTTATTAATCTTGGTTCCAAAGCTGTAGCATACCTTAATGTGGACTGTGCTGTGCAAGGTCCTGGTTTCT
Basic information
species | Glycine max |
transcript | GLYMA19G39080.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G39080.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G010353_T02 (Zea mays), 3'ss of exon 2
ttgatatgctcactgtcaaatcaaatgagtttgctttatttcaataatggtgt---catttcctgcaatattcgctctaaatca------agtttatctgtttatgtagATAGGATCCACTGAGTGGGTTGAACAAAACCTTATTAATCTTGGTTCCAAAGCTGTAGCATACCTTAATGTGGACTGTGCTGTGCAAGGTCCTGGTTTCT
| | ||| |||| | || || ||| | | | | | ||| || | || | || || | | | | | | |||| ||||| ||||| ||||||||| | |||||| |||| ||||||||||||||| ||| | ||||| || ||||||||||||||| || || |
-------gttag--atcaggtcaactttgtatgtgctatctaattgtcagcacatatacttcttgttacttttattgtatataatatgaaggctctttttcgtccccagATTGGATCAACTGAATGGGTTGAAGACAACCTTGAAGATCTGCATTCCAAAGCTGTAGCTTACTTGAATGTTGATTGTGCTGTGCAAGGTGTGGGATTTT
upper sequence: GLYMA19G39080.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv00s0285g00060.t01 (Vitis vinifera), 3'ss of exon 2
----ttgatatgctcactgtcaaatcaaatgagtttgctttatttcaataatggtgtcatttcctgcaatattcgctctaaatcaagtttatctgttta--tgtagATAGGATCCACTGAGTGGGTTGAACAAAACCTTATTAATCTTGGTTCCAAAGCTGTAGCATACCTTAATGTGGACTGTGCTGTGCAAGGTCCTGGTTTCT
||| | | || ||| | | | ||| | ||||| ||| | |||| |||| || | || ||| | || ||| | | |||||||||| ||||||||||| |||||||||||| | ||||| ||||| |||| |||||||||||||||||| |||||||| || ||||| || || ||||
ttatttgttctaaaagtaatccaattagctaggcttgttctatttgaatggttgtgt-attt-----aacactcaaaagtaatttacttgtgttgtgtggcttcagATAGGATCTACTGAGTGGGTCGAACAAAACCTTTTGAATCTGGGTTCTAAAGTTGTAGCATACCTTAATGTAGACTGTGCAGTTCAAGGACCAGGCTTCT
upper sequence: GLYMA19G39080.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv00s0319g00060.t01 (Vitis vinifera), 3'ss of exon 1
--ttgatatgctcactgtcaaatcaaatgagtttgctttatttcaataatggtgtcatttcctgcaatattcgctctaaatcaagtttatctgttta--tgtagATAGGATCCACTGAGTGGGTTGAACAAAACCTTATTAATCTTGGTTCCAAAGCTGTAGCATACCTTAATGTGGACTGTGCTGTGCAAGGTCCTGGTTTCT
||| | | || ||| | | | ||| | ||||| ||| | |||| || || | || ||| | || ||| | |||||||||| ||||||||||| |||||||||||| | ||||| ||||| ||| |||||||||||||||||| |||||||| || ||||| || || ||||
atttgttctaaaagtaatccaattagctaggcttgttctatttgaatggttgtgtgtatt----taacactcaaaagtaatttacttgtgttgtgtggcctcagATAGGATCTACTGAGTGGGTCGAACAAAACCTTTTGAATCTGGGTTCTGAAGTTGTAGCATACCTTAATGTAGACTGTGCAGTTCAAGGACCAGGCTTCT
upper sequence: GLYMA19G39080.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0032g00670.t01 (Vitis vinifera), 3'ss of exon 2
---ttgatatgctcactgtcaaatcaaatgagtttgctttatttcaataatggtgtcatttcctgcaatattcgctctaaatcaagtttatc-tgtttatgtagATAGGATCCACTGAGTGGGTTGAACAAAACCTTATTAATCTTGGTTCCAAAGCTGTAGCATACCTTAATGTGGACTGTGCTGTGCAAGGTCCTGGTTTCT
||| | | || ||| | | | ||| | ||||| ||| | |||| || || | || ||| | | | | | || | |||||||||| ||||||||||| |||||||||||| | ||||| ||||| |||| |||||||||||||||||| |||||||| || ||||| || || ||||
tatttgttctaaaagtaatccaattagctaggcttgttctatttgaatggttgtgtgtatt----taacactcaaagtaatttacttgtgttgcgtggtttcagATAGGATCTACTGAGTGGGTCGAACAAAACCTTTTGAATCTGGGTTCTAAAGTTGTAGCATACCTTAATGTAGACTGTGCAGTTCAAGGACCAGGCTTCT
upper sequence: GLYMA19G39080.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv00s0352g00020.t01 (Vitis vinifera), 3'ss of exon 2
--ttgatatgctcactgtcaaatcaaatgagtttgctttatttcaataatggtgtcatttcctgcaatattcgctctaaatcaagtttatctgttta--tgtagATAGGATCCACTGAGTGGGTTGAACAAAACCTTATTAATCTTGGTTCCAAAGCTGTAGCATACCTTAATGTGGACTGTGCTGTGCAAGGTCCTGGTTTCT
||| | | || ||| | | | ||| | ||||| ||| | |||| || || | || ||| | || ||| | |||||||||| ||||||||||| |||||||||||| | ||||| ||||| |||| |||||||||||||||||| |||||||| || ||||| || || ||||
atttgttctaaaagtaatccaattagctaggcttgttctatttgaatggttgtgtgtatt----taacactcaaaagtaatttacttgtgttgtgtggcctcagATAGGATCTACTGAGTGGGTCGAACAAAACCTTTTGAATCTGGGTTCTAAAGTTGTAGCATACCTTAATGTAGACTGTGCAGTTCAAGGACCAGGCTTCT
upper sequence: GLYMA19G39080.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv00s0327g00020.t01 (Vitis vinifera), 3'ss of exon 1
ttgatatgctcactgtcaaatcaaatgagtttgctttatttcaataatggtgt-cattt--cctgcaatattcgctctaaatcaagtttatctgtttatgtagATAGGATCCACTGAGTGGGTTGAACAAAACCTTATTAATCTTGGTTCCAAAGCTGTAGCATACCTTAATGTGGACTGTGCTGTGCAAGGTCCTGGTTTCT--
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--gttctaaaagtaatccaattagctaggcttgttctatttgaatggttgtgtgtatttaacactcaaaagtaattt---acttgtgttgtgtggcctcagatagGGGATCTACTGAGTGGGTCGAACAAAACCTTTTGAATCTGGGTTCTAAAGTTGTAGCATACCTTAATGTAGACTGTGCAGTTCAAGGACCAGGCTTCTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatggtgtcatttcctgcaatattcgctctaaatcaagtttatctgtttatgtagATAGGATCCACTGAGTGGGTTGAACAAAACCTTATTAATCTTGGTTCCAAAGCTGTAGCATACCTTAATGTGGACTGTGCTGTGCAAGGTCCTGGTTTCT
ctctaaa putative branch site (score: 3)
tctgttt putative PPT
taaatcaagtttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgatatgctcactgtcaaatcaaatgagtttgctttatttcaataatggtgtcatttcctgcaatattcgctctaaatcaagtttatctgtttatgtagATAGGATCCACTGAGTGGGTTGAACAAAACCTTATTAATCTTGGTTCCAAAGCTGTAGCATACCTTAATGTGGACTGTGCTGTGCAAGGTCCTGGTTTCT
- - tatgctc
- - - - - -actgtca
- - - - - - - - - - - - - - - -tgcttta
- - - - - - - - - - - - - - - - - - - - - - -aatggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaatcaag