Sequence
atgc intronic sequence ATGC exonic sequence...caacttgcctcttctgacgataaagttttatagtcttgagggttatagatgtcacaaatagctttcaataacctaaagtaaacatatgccatgtatgcagAATTCCAAAAACAATTGGTGTCTCAATTCCAATGAAGGCAACTTTCTTCATAACTTACATAATGGTGGATGGGTGGGCTGGATGTGCTGGTGAGATTTTA
Basic information
species | Glycine max |
transcript | GLYMA02G43910.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G43910.2 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os01g35050.3 (Oryza sativa), 3'ss of exon 9
caacttgcctcttctgacgataaagttttatagtcttgagggttatagatgtcacaaatagctttcaataacc----taaagtaaacatatgc-catgtatgcagAATTCCAAAAACAATTGGTGTCTCAATTCCAATGAAGGCAACTTTCTTCATAACTTACATAATGGTGGATGGGTGGGCTGGATGTGCTGGTGAGATTTTA
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-catgctcttcatttg-tgctacaatttccta---ttgtatttcctttctttttcgaagaaactcttatactccttttcaactgtacttatttgcctctttgcagAATACCAAGGACAATTGGTGAAGCAATTCCAATGAAAGCAACCTTTTTTATAACATATGTAATGGTTGATGGTTGGGCTGGGGTAGCTGGTGAAATTTTA
upper sequence: GLYMA02G43910.2 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G021194_T01 (Zea mays), 3'ss of exon 9
---caacttgcctcttctgacgataaagttttatagtcttgagggttatagatgt-cacaaatagctttcaataacctaaagtaaacatatgccatgtatgcagAATTCCAAAAACAATTGGTGTCTCAATTCCAATGAAGGCAACTTTCTTCATAACTTACATAATGGTGGATGGGTGGGCTGGATGTGCTGGTGAGATTTTA
| ||| | | || || | || || | | | || | | | | || ||| || || || | | | || || | |||||| |||| || ||||||| ||||||||||||||||||| || || ||||| || | |||||| ||||| |||||||| ||||||||||| ||
atttgaaggtcctgctattaccatggcatatttaagccctttcgtttctccttttgcgtgtatgaatttattta---tattgtctattttt-cctcgtttacagAATACCAAGGACGATTGGTGAAGCAATTCCAATGAAGGCAACCTTTTTTATAACATATACAATGGTTGATGGTTGGGCTGGGGTAGCTGGTGAGATATTG
upper sequence: GLYMA02G43910.2 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G064189_T01 (Zea mays), 3'ss of exon 2
----caacttgcctct--tctgacgataaagttttatagtcttgagggttatagatgtcacaaatagctttcaataacctaaagtaaacatatgccatgtatgcagAATTCCAAAAACAATTGGTGTCTCAATTCCAATGAAGGCAACTTTCTTCATAACTTACATAATGGTGGATGGGTGGGCTGGATGTGCTGGTGAGATTTTA
|| | || | ||| | || | |||| ||| | | | | || ||| || || || | | | || || | |||||| |||| || ||||||| ||||||||||||||||||| || || ||||| || | |||||| ||||| |||||||| ||||||||||| ||
tttctggtatgtcactaatttgaaggtata--tttaagccctttcgtttctccttttgcgtgtatgaatttattta---tattgtctattttt-cctcgtttacagAATACCAAGGACGATTGGTGAAGCAATTCCAATGAAGGCAACCTTTTTTATAACATATACAATGGTTGATGGTTGGGCTGGGGTAGCTGGTGAGATATTG
upper sequence: GLYMA02G43910.2 (Glycine max), 3'ss of exon 9
lower sequence: AT4G15430.1 (Arabidopsis thaliana), 3'ss of exon 9
caacttgcctcttctgacgataaagttttatagtcttgagggttatagatgtcacaaatagctttcaataacctaaagtaaacatatgccatgtatgcagAATTCCAAAAACAATTGGTGTCTCAATTCCAATGAAGGCAACTTTCTTCATAACTTACATAATGGTGGATGGGTGGGCTGGATGTGCTGGTGAGATTTTA
|| | || ||| | | || |||| | || | ||| || | | | | | ||| | ||||| ||||||||||||||||||||||| ||||||||||| || || ||||| ||||| ||||||||||||||||| |||||||| |||||||||||| ||
-------------------gtatgttctttagacctttctttgtctgcatttcactgagagatatca-tatctt----tctgactttttcatttctgcagTATTCCAAAAACAATTGGTGTCTCGATTCCAATGAAAGCGACCTTCTTTATAACATACATAATGGTGGATGGATGGGCTGGTGTTGCTGGTGAGATATTG
upper sequence: GLYMA02G43910.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv12s0059g01090.t01 (Vitis vinifera), 3'ss of exon 8
caacttgcctcttctgacgataaagttttatagtcttgagggttatagatgtcacaaatagctttcaata-acctaaagtaaacatatgccatgtat---gcagAATTCCAAAAACAATTGGTGTCTCAATTCCAATGAAGGCAACTTTCTTCATAACTTACATAATGGTGGATGGGTGGGCTGGATGTGCTGGTGAGATTTTA
| || || || | | || ||| || || | | | | | | ||| ||| |||| | | | || |||| || ||||| | || || ||||||||||||||||||||||||||||||||||||||||||||| ||||| ||||||||| | |||| |||||| ||
---aataccatttttgttactgga-ttaattagatctggatgtgacatcaagtgctactttgatctgatatgtttaatataaagtcaagtggttgattttgcagTATCCCAAAGATCATCGGAACCTCAATTCCAATGAAGGCAACTTTCTTCATAACTTACATAATGGTTGATGGATGGGCTGGAGTTTCTGGGGAGATTCTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagatgtcacaaatagctttcaataacctaaagtaaacatatgccatgtatgcagAATTCCAAAAACAATTGGTGTCTCAATTCCAATGAAGGCAACTTTCTTCATAACTTACATAATGGTGGATGGGTGGGCTGGATGTGCTGGTGAGATTTTA
taaagtaaacatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caacttgcctcttctgacgataaagttttatagtcttgagggttatagatgtcacaaatagctttcaataacctaaagtaaacatatgccatgtatgcagAATTCCAAAAACAATTGGTGTCTCAATTCCAATGAAGGCAACTTTCTTCATAACTTACATAATGGTGGATGGGTGGGCTGGATGTGCTGGTGAGATTTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - -cctcttc
- - - - - - - - - - - - - - - - - -ttgaggg
- - - - - - - - - - - - - - - - - - - - - - - - -tgtcaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atatgcc