Sequence
atgc intronic sequence ATGC exonic sequence...tgttcaatatccaataccatgtggagggactagggagttaagttacttatgcacatctgaacagtgctctgattgggtgggaattggattttgggaacagGTTGATGGGGAAAGTTGCATCTGATAAGTGCCACAAGTGGGTCTTTAAAGAGCCCACAGAATGTGAACCAAATATCTCCAACTACTGGCAGAGCTCCTTT
Basic information
species | Glycine max |
transcript | GLYMA12G35490.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G35490.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G302293_T01 (Zea mays), 3'ss of exon 3
tgttcaatatccaataccatgtggagggactaggga-gttaagttacttatgcacatctgaacagtgctctgattgggtgggaat-tggattttgggaacagGTTGATGGGGAAAGTTGCATCTGATAAGTGCCACAAGTGGGTCTTTAAAGAGCCCACAGAATGTGAACCAAATATCTCCAACTACTGGCAGAGCTCCTTT
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atttcggaggcatacaatacatacatgagtcatggacgataatgtgctaatagacagacccatggg--tccgtttgatttggaccgtcgctcccgcatgcagGCTGATGGGAAAGGTGGCCTCTGATAAATGTCACAAATGGGTCTTCAAGGAACCTTCTGAATGCGAGCCCAACATCTCCAACTACTGGCAGAGCTCCTTC
upper sequence: GLYMA12G35490.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G132251_T01 (Zea mays), 3'ss of exon 3
----tgttcaatatccaataccatgtggagggactagggagttaagttacttatgcacatctgaacagtgctctgattgggtgggaattggattt--tgggaacagGTTGATGGGGAAAGTTGCATCTGATAAGTGCCACAAGTGGGTCTTTAAAGAGCCCACAGAATGTGAACCAAATATCTCCAACTACTGGCAGAGCTCCTTT
| | || ||| |||||| | | || | | || || | | | | | | | | || || || || || |||| ||||||| || || || |||||||| || ||||| |||||||| || || || | ||||| || || || ||||||||||||||||||||||| ||
agcttttggggcatgcaaacgcatgtgaa-----tcatgaatgatgt-gctcaagaccgtgggtctgattttgggttttggacccccttctccttcctgcatgcagGCTGATGGGAAAGGTGGCCTCTGATAAATGTCACAAATGGGTCTTCAAGGAACCTTCTGAATGCGAGCCCAACATCTCCAACTACTGGCAGAGCTCTTTC
upper sequence: GLYMA12G35490.2 (Glycine max), 3'ss of exon 2
lower sequence: AT5G53900.2 (Arabidopsis thaliana), 3'ss of exon 3
-----------------------------------------------------tgttcaatatccaataccatgtggagggactagggagttaagttac--ttatgcacatctgaacagtgctctgattgggtgggaattggat--tttgggaacagGTTGATGGGGAAAGTTGCATCTGATAAGTGCCACAAGTGGGTCTTTAAAGAGCCCACAGAATGTGAACCAAATATCTCCAACTACTGGCAGAGCTCCTTT
|| ||| || || | ||| || | ||| || |||| ||| | || | | |||| ||| | | | | ||| |||||||| |||||||| |||||||| || ||||||||||| || ||||| || | |||| |||||||||| | | || |||||||| || || |||
gtgggtactgggtaggtgttatatataagtaattatggaccaaaagataattagattatataaacacaccctaatcacttaacttatgattaaagatataattatttacaacacaa-gttattatgatcttgtgatgttcatgtgatatatctgcagATTGATGGGTAAAGTTGCTTCTGATAAATGTCACAAGTGGGTTTTCAAAGAACCATCTGAATCTGAACCAAATCTTGCTAATTACTGGCAAAGTTCTTTT
upper sequence: GLYMA12G35490.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv19s0014g02320.t01 (Vitis vinifera), 3'ss of exon 3
-----------------------------------------------------------------------------------tgttcaatatccaataccatgtggagggactagggagttaagttact---tatgcacatctgaaca-gtgctctgattgggtgggaattggattttgggaacagGTTGATGGGGAAAGTTGCATCTGATAAGTGCCACAAGTGGGTCTTTAAAGAGCCCACAGAATGTGAACCAAATATCTCCAACTACTGGCAGAGCTCCTTT
|||| | | | | || | | | || || | | || ||| | ||| |||| || || ||||| |||| || ||||||||||||||| ||||||||||||||||| || || ||||| || |||||||| |||| |||||||||||| ||||||||||||||||||| || |||
gtgggtactgggtaggtgtttttatttgatttcatctctctctccctctctttccctctctccctcattccctccctctctctctctcaacaatagggaggaagcagaaaagtgaaaaaataaaaataaaaaacaaaaattcctctacatgggctttgataggatg--aattgc-ttttatgagcagGTTGATGGGGAAGGTTGCATCTGATAAGTGTCATAAATGGGTTTTCAAAGAGCCTTCAGAGTGTGAACCAAATGTCTCCAACTACTGGCAGAGTTCTTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttatgcacatctgaacagtgctctgattgggtgggaattggattttgggaacagGTTGATGGGGAAAGTTGCATCTGATAAGTGCCACAAGTGGGTCTTTAAAGAGCCCACAGAATGTGAACCAAATATCTCCAACTACTGGCAGAGCTCCTTT
ctctgat putative branch site (score: 4)
atttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgttcaatatccaataccatgtggagggactagggagttaagttacttatgcacatctgaacagtgctctgattgggtgggaattggattttgggaacagGTTGATGGGGAAAGTTGCATCTGATAAGTGCCACAAGTGGGTCTTTAAAGAGCCCACAGAATGTGAACCAAATATCTCCAACTACTGGCAGAGCTCCTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT