Sequence
atgc intronic sequence ATGC exonic sequence...tgattgattatatttcttctattcttcagaatatcttacaatgctgaatataggtttgacctgaatttgtagtgtatattctatgttaatggctttccagATGACAAAGGCTGATTTTGTTCGAAACAACCGAGGAATAGATGATGGGAAGGATTTACCAGAGGAATATCTTGGGGCAATTTATGACCAAATTGTTAAAA
Basic information
species | Glycine max |
transcript | GLYMA02G48200.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G48200.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G092586_T01 (Zea mays), 3'ss of exon 4
tgattgattatatttcttctattcttcagaatatcttacaatgctgaatataggtttgacctgaatttgtagtgtatattctatgttaatggctttccagATGACAAAGGCTGATTTTGTTCGAAACAACCGAGGAATAGATGATGGGAAGGATTTACCAGAGGAATATCTTGGGGCAATTTATGACCAAATTGTTAAAA
| | |||| || | ||| | | | | || || | ||| ||| ||| | | | | | || |||| ||| | | | |||||| | ||||| |||||| | || ||||| |||||||||||||||||||||||||| ||||| || ||||| | || | |||||||| ||||| || |
-gtatacttatgattttattatcatacgggaatgtctataaag--aaatttagtttt---ttaactctatcaaaggtaatctaagtt--ttcttgtgcagATGTCTAAGGCAGATTTTATGCGCAACAATCGAGGAATAGATGATGGGAAGGATTTGCCAGAAGATTATCTGAGTGCGCTGTATGACCAGATTGTCAACA
upper sequence: GLYMA02G48200.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G365185_T01 (Zea mays), 3'ss of exon 4
tgattgattatatttcttctattcttcagaatatcttacaatgctgaatataggtttgacctgaatttgtagtgtatattctatgttaatggctttccagATGACAAAGGCTGATTTTGTTCGAAACAACCGAGGAATAGATGATGGGAAGGATTTACCAGAGGAATATCTTGGGGCAATTTATGACCAAATTGTTAAAA
| | | || | | ||| ||||| | || ||| ||| | | || | | |||||| | || |||| || |||| || |||||||||||||||||||| |||||||| ||||| ||||| || || | |||||||||||||| ||||
-----------------------------gtaaacaaatgataataagcata--tttgattcaagatt--agtttatttatgagatttccaa-tgtgcagATGTCTAAATCTGACTTCATTCGCAATAACCGAGGAATAGATGATGGAAAGGATTTGCCAGAAACTTATCTGGGTACACTATATGACCAAATTGTCAAAA
upper sequence: GLYMA02G48200.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G38200.1 (Arabidopsis thaliana), 3'ss of exon 4
---------------------------------------------------------------------------tgattgattatatttcttct------att--cttcagaatatcttaca------atgct-----gaatataggtttgacctgaatttgtagtgtatattctatg-ttaatggctttccagATGACAAAGGCTGATTTTGTTCGAAACAACCGAGGAATAGATGATGGGAAGGATTTACCAGAGGAATATCTTGGGGCAATTTATGACCAAATTGTTAAAA
| ||| ||| | | | || ||| || ||||| || | ||||| | || |||| | | | | | || || | | | || || ||| | || ||||||| |||||||||||| | |||| |||||||| || |||||||| || ||| | ||||| || |||||||| || ||||||||||| |||| | ||
gtttgtcttcttggctgtcacaatttattcaatccatgactgatagcttttggagtgtatgggcatgtgttaacttttttggctatttctgtgctcagaaaattgcttttgaaatattctaaattggagatgctttttggtgtaaaggtctttacagtgtatttaacgtctgctttctggtttatgacaatc-agATGACCAAGGCTGATTTTATCAGAAATAACCGAGGCATTGATGATGGCAAAGATCTCCCAGAAGAGTATCTTGGTGCGCTTTATGACCAAGTTGTCATAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaatataggtttgacctgaatttgtagtgtatattctatgttaatggctttccagATGACAAAGGCTGATTTTGTTCGAAACAACCGAGGAATAGATGATGGGAAGGATTTACCAGAGGAATATCTTGGGGCAATTTATGACCAAATTGTTAAAA
tgttaat putative branch site (score: 3)
ctttcc putative PPT
tatattctatgttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgattgattatatttcttctattcttcagaatatcttacaatgctgaatataggtttgacctgaatttgtagtgtatattctatgttaatggctttccagATGACAAAGGCTGATTTTGTTCGAAACAACCGAGGAATAGATGATGGGAAGGATTTACCAGAGGAATATCTTGGGGCAATTTATGACCAAATTGTTAAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - caatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - acctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtagtg