Sequence
atgc intronic sequence ATGC exonic sequence...tatatctgcaaatatgcttttatttttttcccttctattgatgggattatgattgtaacattcagttgagttcatgaaaaattctattaatgctttgcagGGTTTACACCCAGTCACAAAATTCACTGAGGATTTTGATTTCATGGCAATGAATGAGAAGTTCAAAAAGGATGAAGTATGGGGCCATCTTGGTAAAAGTA
Basic information
species | Glycine max |
transcript | GLYMA01G22680.3 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G22680.3 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g30060.1 (Oryza sativa), 3'ss of exon 5
----tatatctgcaaatatgcttttatttttttcccttctattgatgggattatgattgtaacattcagttgagttcatgaaaaattctattaatgctttgcagGGTTTACACCCAGTCACAAAATTCACTGAGGATTTTGATTTCATGGCAATGAATGAGAAGTTCAAAAAGGATGAAGTATGGGGCCATCTTGGTAAAAGTA
|| | | | ||||| || | || | | || || | |||| | | | ||| || | || | | | || || | ||| | || || | || || || || ||||| || |||||||||||||||||||||||||| || || |||||||||||||||||||| |||||||| |
ttttgatgtattataggatgctgaaatctgttctgcatgaatc-atatg-ctatgttattgaaatt--gtaaaatttgtatacttattagtttcccctctccagCAATCACGTCCTATAACCAAGTTTACAGAGGACTTCGATTTCATGGCAATGAATGAGAAGTTTAACAAAGATGAAGTATGGGGCCATCTCGGTAAAAGCA
upper sequence: GLYMA01G22680.3 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g02090.1 (Oryza sativa), 3'ss of exon 5
tatatctgcaaatatgcttttatttttttccctt-ctattgatgggattatgattgtaacattcagttgagttcatgaaaaattcta---ttaatgctttgcagGGTTTACACCCAGTCACAAAATTCACTGAGGATTTTGATTTCATGGCAATGAATGAGAAGTTCAAAAAGGATGAAGTATGGGGCCATCTTGGTAAAAGTA
| ||| ||| |||||| | || | || | || | || ||| | | ||| || || | || | | || ||||||| || || |||| ||||| || ||||| || |||||||||||||| |||||||||||||| || || |||||||| ||||| ||||||||||| |
ttgatcatgtttcatgtttttatatgattatgatgctgcttattaaagagcatctg--gtattgattgaagt--attaatacttttgagtctgttgttttgcagTTTTCGCAGTCAGTAACAAATTTTACTGAAGAATTTGATTTCATGGCCATGAATGAGAAGTTTAACAAAGATGAAGTCTGGGGTCATCTTGGTAAGAAAT
upper sequence: GLYMA01G22680.3 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G341027_T01 (Zea mays), 3'ss of exon 5
tatatctgcaaatatgcttttatttt-tttcccttctattgatgggattatg-attgt-aacattcagttgagttcatgaaaaattctattaatg----ctttgcagGGTTTACACCCAGTCACAAAATTCACTGAGGATTTTGATTTCATGGCAATGAATGAGAAGTTCAAAAAGGATGAAGTATGGGGCCATCTTGGTAAAAGTA
|| |||| | | || | ||| | || |||| | ||| | |||| || | | || | | | | | | || | ||| | || || | || || ||||| ||||| |||||||||||||||||||||||||||||||| || ||||||||||||||||||||||||||||| |
-------cttaaaatgcctctgttctgttttcagtcccttgaggacattctttgttgtcgacttgcttttttttaaactgtagtcttcactgtcattctctctacagCAATCGCATCCCATAACCAAGTTCACAGAGGACTTTGATTTCATGGCAATGAATGAGAAGTTCAACAAAGATGAAGTATGGGGCCATCTTGGTAAAAGAA
upper sequence: GLYMA01G22680.3 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G132796_T01 (Zea mays), 3'ss of exon 5
-----tatatctgcaaatatgcttttatttttttcccttctattgatgggattatgattgtaacattcagttgagttcatgaaaaattctattaatgctttgcagGGTTTACACCCAGTCACAAAATTCACTGAGGATTTTGATTTCATGGCAATGAATGAGAAGTTCAAAAAGGATGAAGTATGGGGCCATCTTGGTAAAAGTA
||| || | | | || | | | | | || ||| || || | || || || | | || ||| |||||||||| || ||| | || ||| ||||||||| || |||||||||| ||| |||||||||||||| || || |||||||||||||||||||||||||| |
gagggagtatttgtataccttgggaaatgatgctaggattgaataatattgtta-aatagttaaat---gtcagatttgttgatgtttgtatct-tgctttgcagTTTTCACAGTCTGTAACAGCATTCACTGAAGAATTTGATTTCACGGCCATGAATGAGAAGTTTAACAAAGATGAAGTATGGGGCCATCTTGGTAAGAAAT
upper sequence: GLYMA01G22680.3 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G051622_T02 (Zea mays), 3'ss of exon 5
-tatatctgcaaatatgcttttatttttttcccttctattgatgggattatgattgtaacattcagt--tgagttcatgaaaaattctattaatgctttgcagGGTTTACACCCAGTCACAAAATTCACTGAGGATTTTGATTTCATGGCAATGAATGAGAAGTTCAAAAAGGATGAAGTATGGGGCCATCTTGGTAAAAGTA
||| || | | | || | | | | | || || | || | || ||| || | || || ||| | |||||||| || ||| |||| |||| ||||||||| || |||||||||| ||| |||||||||||||| || || |||||||| ||||| |||||||| || |
gagtatttgtataccttgggaaatgatgcttggattgaataatat--ttgttgttaaatagttaagtgtcagatttgttaatgtttgtatct-tcctttgcagTTTTCACAGTCAGTAACAACATTCACTGAAGAATTTGATTTCACGGCCATGAATGAGAAGTTTAACAAAGATGAAGTCTGGGGTCATCTTGGAAAGAAAT
upper sequence: GLYMA01G22680.3 (Glycine max), 3'ss of exon 4
lower sequence: AT1G26110.2 (Arabidopsis thaliana), 3'ss of exon 6
---------------tatatctgca-aatatgcttttatttttttccctt--ctattgatgggat-tatgattgtaacat---tcagttgagttcatgaaaaattctattaatgcttt------gcagGGTTTACACCCAGTCACAAAATTCACTGAGGATTTTGATTTCATGGCAATGAATGAGAAGTTCAAAAAGGATGAAGTATGGGGCCATCTTGGTAAAAGTA
|| || | ||| || |||| ||| || | | || ||| || | | ||| || ||| || | || ||| |||| ||| |||| | | ||||| ||| | ||||||||||| ||||||||||||| |||||||| || |||||||| ||||||||||||||||| |||||||| || ||||
gtactattcttctcactcatttgtagaatgtgacggcatttatttgtttttaccaaggaaaagatctaccagtttaaaatagctcatgaactttagccatgtatgctaataattcttcttgttggcagAGATCACACCAAGTAATGAAATTCACTGAAGATTTTGATTTCACAGCAATGAACGAAAAGTTCAATAAGGATGAAGTATGGGGTCATCTTGGGAAGAGTA
upper sequence: GLYMA01G22680.3 (Glycine max), 3'ss of exon 4
lower sequence: Vv01s0011g02820.t01 (Vitis vinifera), 3'ss of exon 5
tatatctgcaaatatgcttttatttttttcccttctattgatgggattat---gattgtaacattcagttgagttcatgaaaaattctattaatgctttgcagGGTTTACACCCAGTCACAAAATTCACTGAGGATTTTGATTTCATGGCAATGAATGAGAAGTTCAAAAAGGATGAAGTATGGGGCCATCTTGGTAAAAGTA
||| | | | || |||||| | | ||| | || | | | | | |||| |||| || ||| | ||| |||||||| | || ||||| |||||||||||||||||||||||||||||||||||||||||||| ||||| ||||||||||||||||| |||||||||||| |||
-ctat-tataggtttgattttatggggagaatatttgc-aatgagtttctccaaaattaattggaaatttgacggcatggaatatttaacatttgccttgcagGGCTCACGTCCAGTGACAAAATTCACTGAGGATTTTGATTTCATGGCAATGAATGAGAAATTCAAGAAGGATGAAGTATGGGGTCATCTTGGTAAAGGTA
upper sequence: GLYMA01G22680.3 (Glycine max), 3'ss of exon 4
lower sequence: PP1S198_51V6.2 (Physcomitrella patens), 3'ss of exon 7
----------------------------------------------------------------------------tatatctgcaaatatgcttttatttttttcccttctattgatgggattatgattgtaacattcagttgagtt---------------------catgaaaaattctattaatgctttgcagGGTTTACACCCAGTCACAAAATTCACTGAGGATTTTGATTTCATGGCAATGAATGAGAAGTTCAAAAAGGATGAAGTATGGGGCCATCTTGGTAAAAGTA
| || | || || | | ||| | | | | | | | | | | ||||| ||||||| ||||| || | | | | ||| | | |||| || |||||||||| ||||| || |||| || ||||||||||||||||| ||||| ||||| ||||| || || ||
gtaattttttatactttcctaaggttttaaggccccgtttgttcttgtttcaacttacaggttatactggcactaattgatatctaataattgtctcattgtgcactcgttaactctcaaaagttggcatccaacatcttcttgagttgttctgtgtctcattcctgatcatgacgaaacttgtaacttgtttcagCTGGCGAATCCCACGCA-GCAATTCACTGAAGATTTCGACTTCACAGCCATGAATGAGAAGTTCAACAAGGACGAAGTTTGGGGAACGCTCGGAGGAAAGG
upper sequence: GLYMA01G22680.3 (Glycine max), 3'ss of exon 4
lower sequence: EFJ13073 (Selaginella moellendorffii), 3'ss of exon 5
tatatctgcaaatatgcttttatttttttcccttctattgatgggattatgattgtaacattcagttgagttcatgaaaaattctattaatgctttgcagGGTTTACACCCAGTCACAAAATTCACTGAGGATTTTGATTTCATGGCAATGAATGAGAAGTTCAAAAAGGATGAAGTATGGGGCCATCTTGGTAAAAGTA---
| || | | | | | || | | || | || | || || || | | | | | | || || || || ||||| |||||||||||||| |||||||| |||||||| ||||| || || ||||| | ||||| ||
-------------------------------------------gtatgtttactcgagcttttcttctttcttgtggtat-ttattttgatatcatggacagCCTTC-TCAACGTACGAACTTTACGGAGGACTTTGATTTCATGGCGATGAATGAAAAGTTCAACAAGGACGAGGTTTGGGGTGAGCTTGGAGGAAAGGTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attatgattgtaacattcagttgagttcatgaaaaattctattaatgctttgcagGGTTTACACCCAGTCACAAAATTCACTGAGGATTTTGATTTCATGGCAATGAATGAGAAGTTCAAAAAGGATGAAGTATGGGGCCATCTTGGTAAAAGTA
tattaat putative branch site (score: 2)
ttcatgaaaaattcta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatatctgcaaatatgcttttatttttttcccttctattgatgggattatgattgtaacattcagttgagttcatgaaaaattctattaatgctttgcagGGTTTACACCCAGTCACAAAATTCACTGAGGATTTTGATTTCATGGCAATGAATGAGAAGTTCAAAAAGGATGAAGTATGGGGCCATCTTGGTAAAAGTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG