Sequence
atgc intronic sequence ATGC exonic sequence...agacatttcaattttcctttcacataaaatattgaataagtgtaaatgttttttaaccttttctttttccatccatttctttttggaatcttgaaaacagAGATATGTGGGAGAAATCAATGAAAGGTCTATCAAGTTTGATTAGGAGATCAACACCATCTTCATTTGCTTATATATGTGAGAAGAATGGAGGATCTCTA
Basic information
species | Glycine max |
transcript | GLYMA07G02290.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G02290.1 (Glycine max), 3'ss of exon 8
lower sequence: AT3G21160.1 (Arabidopsis thaliana), 3'ss of exon 9
---------------------------------------------------------------------------------------------agacatttcaatt-ttcctttcacataaaatattgaataagtgtaaatgttttt---taaccttttctttttccatccatttctttttggaatcttgaaaacagAGATATGTGGGAGAAATCAATGAAAGGTCTATCAAGTTTGATTAGGAGATCAACACCATCTTCATTTGCTTATATATGTGAGAAGAATGGAGGATCTCTA
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gtaagtttaactctagtctactgagtgtatatatgtctgattgattcaagtccgctaagttcaaccagctgccatcacatttatctttctgcttgatatctatgttcttcttttcttttctggtctt---ttagtttcaacatctttagccgaacaataataatttgtactgttattacttgacatcttggcatcagAGATATGTGGGAGAAGTCAATGAATGGTCTGCTAAGCTTGGTTAAGAAATCAACACCTTTGTCGTTTACATATATCTGTGAGAAGAGTGGAAATTCTTTG
upper sequence: GLYMA07G02290.1 (Glycine max), 3'ss of exon 8
lower sequence: AT1G51590.1 (Arabidopsis thaliana), 3'ss of exon 9
agacatttcaattttcctttcacataaaatat-tgaataagtgtaaatgttttttaaccttttctttttccatccatttctttttggaatcttgaaaacagAGATATGTGGGAGAAATCAATGAAAGGTCTATCAAGTTTGATTAGGAGATCAACACCATCTTCATTTGCTTATATATGTGAGAAGAATGGAGGATCTCTA
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-------gtaagtaaagctcgacgctgtgtatatacacccaagtaattcaatatcagcaataaaggataaggactaaatctttcttaatgtattgaatcagAGATATGTGGGAGAAATCAATGAAAGGTTTGTTAAGCTTGGTCAAGAAATCAACACCTTCATCATTTACGTATATATGTGAGAAGAACGGAAATAATTTG
upper sequence: GLYMA07G02290.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv09s0054g00370.t01 (Vitis vinifera), 3'ss of exon 9
agacatttcaattttcctttca-cataaaatattgaataagtgtaaatgttttttaaccttt----tctttttccatcca---tttctttttggaatcttgaaaacagAGATATGTGGGAGAAATCAATGAAAGGTCTATCAAGTTTGATTAGGAGATCAACACCATCTTCATTTGCTTATATATGTGAGAAGAATGGAGGATCTCTA
|||||| ||| | || ||| | || || ||| || | ||| | ||| || ||| | | | || |||| | ||| || |||||| |||||||||| ||| ||||||||||| | ||| ||| | | ||| |||||||||| || || | |||||||||||||| ||||| | |||||
--------agattttcttttaaatatccaatgtctaaaaaatgtcaacagtctttccttcatagaatctattgatatcaaaattcttttattggtttgttggaagcagAGAAATGTGGGAGACATCTATGAAAGGTCTGTTAAGCTTGGTCCGAAGAACAACACCATCATCTTTCACATATATATGTGAGAAAAATGGGGATTCTCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgttttttaaccttttctttttccatccatttctttttggaatcttgaaaacagAGATATGTGGGAGAAATCAATGAAAGGTCTATCAAGTTTGATTAGGAGATCAACACCATCTTCATTTGCTTATATATGTGAGAAGAATGGAGGATCTCTA
ttttaac putative branch site (score: 2)
ttttcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agacatttcaattttcctttcacataaaatattgaataagtgtaaatgttttttaaccttttctttttccatccatttctttttggaatcttgaaaacagAGATATGTGGGAGAAATCAATGAAAGGTCTATCAAGTTTGATTAGGAGATCAACACCATCTTCATTTGCTTATATATGTGAGAAGAATGGAGGATCTCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - -cctttca
- - - - - - - - - - - -ataaaata