Sequence
atgc intronic sequence ATGC exonic sequence...cacggattgatcttggattgagaagagataaatttatttcgtggagacacaacacgagcattcataagattatctaagatgtgtagttctctttgtgtagGTTGTTCGCTGGGGCCGTTCTGTATATGCAAATATTCAGAAATTTATTCAGTTCCAACTCACTGTTAATGTTGCTGCTCTTGTAATAAATGTAGTGGCAG
Basic information
species | Glycine max |
transcript | GLYMA13G44990.1 |
intron # | 27 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G44990.1 (Glycine max), 3'ss of exon 27
lower sequence: LOC_Os02g08010.1 (Oryza sativa), 3'ss of exon 9
cacggattgatcttggattgagaagagataaatttatttcgtggagacacaacacgagcattcataagattatctaagatgtgtagttctctttgtgtagGTTGTTCGCTGGGGCCGTTCTGTATATGCAAATATTCAGAAATTTATTCAGTTCCAACTCACTGTTAATGTTGCTGCTCTTGTAATAAATGTAGTGGCAG
|| ||| |||| ||| | | |||| || || | | ||||| | | |||| ||| |||| || |||||||| ||||| || ||||||||||| || || |||||||| ||||| || ||||| |||||||| |||||| |||| ||||| || || |
-----gttaggg--aagttggagcttaataatcttacacaattaa--tttaacaaatgccttaacat--ttatcca---tatgtaacgttct------agGTGGTCCGCTGGGGTCGTTCGGTTTATGCAAATATCCAAAAGTTTATTCAATTCCAGCTTACTGTAAATGTTGCGGCTCTTATAATCAATGTGGTTGCTG
upper sequence: GLYMA13G44990.1 (Glycine max), 3'ss of exon 27
lower sequence: GRMZM5G893864_T01 (Zea mays), 3'ss of exon 5
cacggattgatcttggattgagaagagataaatttatttcgtggagacacaacacgagcattcataagattatctaagatgtgtagttctctttgtgt---agGTTGTTCGCTGGGGCCGTTCTGTATATGCAAATATTCAGAAATTTATTCAGTTCCAACTCACTGTTAATGTTGCTGCTCTTGTAATAAATGTAGTGGCAG
|| | | || |||| | || | | | |||| | | | || || ||| | |||| | ||| | | |||| ||||||||||| || ||||| ||||||||||| || || |||||||||||||| || || || |||||||| |||||||| || ||||| || || |
-----gtttggcctatttttagaatctaaggatcttgataatacgcgcacatgcctaatac----aacgttgtcttacatgttctttatcttttatattctagGTGGTTCGCTGGGGTCGCTCTGTTTATGCAAATATCCAAAAGTTTATTCAGTTCCAGCTTACCGTAAATGTTGCAGCTCTTGTCATCAATGTTGTTGCTG
upper sequence: GLYMA13G44990.1 (Glycine max), 3'ss of exon 27
lower sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 25
cacggattgatct--tggattgagaagagataaatttatttcgtggagacacaacacgagcattcataagattatctaagatgtgtagt---tctctttgtgtagGTTGTTCGCTGGGGCCGTTCTGTATATGCAAATATTCAGAAATTTATTCAGTTCCAACTCACTGTTAATGTTGCTGCTCTTGTAATAAATGTAGTGGCAG
|| ||| | || | | ||| | || | | ||| | | ||| || | || ||||| | | | | | | | |||||||||| |||||||||||||| ||||| || ||||||||||| || || ||||| || ||||| |||||||| || ||| |||| ||||| || ||||
-----gttagtctactacatcaaatatagaaacatgtgatcttct---acattatcctt-catctttatgcttttctaatcaataaactctgtttactcttccagGTTGTTCGTTGGGGCCGTTCTGTGTATGCTAACATTCAGAAATTCATACAATTCCAGCTTACTGTGAATGTTGCCGCACTTATAATCAATGTTGTAGCAG
upper sequence: GLYMA13G44990.1 (Glycine max), 3'ss of exon 27
lower sequence: Vv09s0018g02130.t01 (Vitis vinifera), 3'ss of exon 27
cacggattgatcttggattgagaagagataaatttatttcgtggagacacaacacgagcattcataagattatctaagatgtgtagttctctttg---tgtagGTTGTTCGCTGGGGCCGTTCTGTATATGCAAATATTCAGAAATTTATTCAGTTCCAACTCACTGTTAATGTTGCTGCTCTTGTAATAAATGTAGTGGCAG
| | | || |||||| |||| | | || || | | | ||| | | | | || || | |||| ||||||||||||||||||| |||||||| |||||||||||||| |||||||| |||||||| ||||||||||||||||| |||||| | |||||||| || |||
--ttgccatgtatgcatttatgaagaggcttatttgaaaattcccagtaattcatatttatacctg-gtgtatatgacaattttatttgtttttgccatgtagGTTGTTCGCTGGGGGCGTTCTGTCTATGCAAATATTCAAAAATTTATCCAGTTCCAGCTCACTGTTAATGTTGCAGCTCTTATTATAAATGTTGTTGCAT
upper sequence: GLYMA13G44990.1 (Glycine max), 3'ss of exon 27
lower sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 22
cacggattgatcttggattgagaagagataaatttatttcgtggagacacaacacgagcattcataagattatctaagatgtgtagttctctttgtgtagGTTGTTCGCTGGGGCCGTTCTGTATATGCAAATATTCAGAAATTTATTCAGTTCCAACTCACTGTTAATGTTGCTGCTCTTGTAATAAATGTAGTGGCAG
| | | |||| || | || | | | ||| | | |||| || ||||||| |||||||| || || || ||||| ||||||||||| ||||| |||||||| || ||||| ||||||| ||| || || | || || ||||| |
-------------------------------------------gtaagataaca--gcttttggtgcgagtctgaaggat-cgaaattct-----tgcagGTTGTACGCTGGGGTCGGTCCGTGTATGCCAATATTCAGAAGTTTATCCAGTTCCAGCTGACTGTAAATGTTGTTGCGCTGGTTCTCAACGTCGTGGCCG
upper sequence: GLYMA13G44990.1 (Glycine max), 3'ss of exon 27
lower sequence: EFJ25508 (Selaginella moellendorffii), 3'ss of exon 23
cacggattgatcttggattgagaagagataaatttatttcgtggagacacaacacgagcattcataagattatctaagatgtgtagttctctttgtgtagGTTGTTCGCTGGGGCCGTTCTGTATATGCAAATATTCAGAAATTTATTCAGTTCCAACTCACTGTTAATGTTGCTGCTCTTGTAATAAATGTAGTGGCAG
| | | |||| || | || | | | ||| | | |||| || ||||||| |||||||| || || || ||||| ||||||||||| ||||| |||||||| || ||||| ||||| | ||| || || | || || ||||| |
-------------------------------------------gtaagataaca--gcttttggtgcgagtctgaaggat-cgaaattct-----tgcagGTTGTACGCTGGGGTCGGTCCGTGTATGCCAATATTCAGAAGTTTATCCAGTTCCAGCTGACTGTAAATGTAGTTGCGCTGGTTCTCAACGTCGTGGCCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gacacaacacgagcattcataagattatctaagatgtgtagttctctttgtgtagGTTGTTCGCTGGGGCCGTTCTGTATATGCAAATATTCAGAAATTTATTCAGTTCCAACTCACTGTTAATGTTGCTGCTCTTGTAATAAATGTAGTGGCAG
ttctctttgt CT-rich tract
attcataagattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cacggattgatcttggattgagaagagataaatttatttcgtggagacacaacacgagcattcataagattatctaagatgtgtagttctctttgtgtagGTTGTTCGCTGGGGCCGTTCTGTATATGCAAATATTCAGAAATTTATTCAGTTCCAACTCACTGTTAATGTTGCTGCTCTTGTAATAAATGTAGTGGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - -cacaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcattca