Sequence
atgc intronic sequence ATGC exonic sequence...ctaataatgatttcattcttatggagaataagaagcacacataaaaacattttttgtttaggcgggacaaatataattaagttttatttatccattgtagTATGGAGACTATTACTCTTGGGGACAAACGAATTGGAATCAAGACTAGTGTTCTAGAGGAAAAAGCTACAGCATGTAACATGCTTTGTTGCTATGCTGAT
Basic information
species | Glycine max |
transcript | GLYMA05G28950.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G28950.2 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os03g49420.2 (Oryza sativa), 3'ss of exon 6
---ctaataatgatttcattcttatggagaataagaagcacacataaaaacattttttgtttaggcgggacaaatataattaagttttatttatccattgtagTATGGAGACTATTACTCTTGGGGACAAACGAATTGGAATCAAGACTAGTGTTCTAGAGGAAAAAGCTACAGCATGTAACATGCTTTGTTGCTATGCTGAT
|||| || | | | || | | | || | || | | | || | | | | | | || | || ||| | ||||||||||| || || ||||| ||||||| ||| || ||| | || ||||||||||| || |||||||| ||||| ||||| |||||||||
catttaatttgaatgttgatatcctgttg--ttgtctgattctatgatcttatgatatctgtaaa-attttgtgttttacctggctgcctgcataaaatgcagTGTTGAGACTATTACGCTAGGAGACAAGAGAATTGGCATCCGAACCAGTCTGCTGGAGGAAAAAGCAACGGCATGTAATATGCTATGTTGTTATGCTGAT
upper sequence: GLYMA05G28950.2 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G033619_T01 (Zea mays), 3'ss of exon 6
ctaataatgatttcattcttatggagaat----aagaagcacacataaaaacattttttgtttaggcgggacaaatataattaagttttatttatccattgtagTATGGAGACTATTACTCTTGGGGACAAACGAATTGGAATCAAGACTAGTGTTCTAGAGGAAAAAGCTACAGCATGTAACATGCTTTGTTGCTATGCTGAT
|| | | | || || | | ||| || | || | | || | || | ||| | | | | | | | || ||| | ||||||||||| || || || || | || || ||| |||||| | |||||||| ||||||||||||||||||||||| |||||||| ||||||
--aacgctaagaggttggataagggaactcttggagatgctcccagtctcaggctcttgttctatctactagcaattgtactcactggcagca--ctactgcagTGTCGAGACTATTACACTAGGTGATAAGAGGATCGGCATCCGAACTAGTCTACTAGAGGAGAAAGCTACAGCATGTAACATGCTGTGTTGCTACGCTGAT
upper sequence: GLYMA05G28950.2 (Glycine max), 3'ss of exon 9
lower sequence: AT5G19820.1 (Arabidopsis thaliana), 3'ss of exon 7
ctaataatgatttcattcttatggagaataagaagcacacataaaaacattttttgtttaggcgggacaaatataattaagttttatttatccat-----tgtagTATGGAGACTATTACTCTTGGGGACAAACGAATTGGAATCAAGACTAGTGTTCTAGAGGAAAAAGCTACAGCATGTAACATGCTTTGTTGCTATGCTGAT
|| || || | | | |||| | | || |||| | || | |||| | ||| |||| | | ||||| | | | || |||||||| |||| || || |||||| |||| || ||||| || ||||||||||||||||| || || || |||||||||||||||||||||||||||
cttgagata--tttaacgatgttgagattct---gtccatataatgatatgatatgttcataaataacatgcataaatctgggctatttccctctcttgatacagCATGGAGACCATTATCCTGGGCGACAAAAGAATAGGGATCAAAACAAGTGTTCTAGAGGAAAAGGCCACGGCTTGTAACATGCTTTGTTGCTATGCTGAT
upper sequence: GLYMA05G28950.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv06s0004g00500.t01 (Vitis vinifera), 3'ss of exon 7
ctaataatgatttcattcttatggagaataagaagcacacataaaaacattttttgtttaggcgggacaaa--tataattaagttttatttatccattgtagTATGGAGACTATTACTCTTGGGGACAAACGAATTGGAATCAAGACTAGTGTTCTAGAGGAAAAAGCTACAGCATGTAACATGCTTTGTTGCTATGCTGAT
|| || | || | ||| | | |||| | |||| || | ||| | | | | ||| ||| | ||||| ||||||||||| |||||||||||||| |||||||| || |||||||||||||| || ||||| ||||| || || || |||||||| ||||||||||| |||
-tactatctagagcaagggca-atagagtgttgtttagccataggatcattgttgctgaaggatatttgggattttgctgacagtttttttgttcattgcagTATGGAGACCATTACTCTTGGGGATAAACGAATAGGGATCAAGACTAGTGTCCTGGAGGAGAAAGCCACCGCTTGCAACATGCTATGTTGCTATGCCGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacattttttgtttaggcgggacaaatataattaagttttatttatccattgtagTATGGAGACTATTACTCTTGGGGACAAACGAATTGGAATCAAGACTAGTGTTCTAGAGGAAAAAGCTACAGCATGTAACATGCTTTGTTGCTATGCTGAT
tttatcc CT-rich tract
aaatataattaagttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctaataatgatttcattcttatggagaataagaagcacacataaaaacattttttgtttaggcgggacaaatataattaagttttatttatccattgtagTATGGAGACTATTACTCTTGGGGACAAACGAATTGGAATCAAGACTAGTGTTCTAGAGGAAAAAGCTACAGCATGTAACATGCTTTGTTGCTATGCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - -ttcattc
- - - - - - - - - - - - - aataagaa
- - - - - - - - - - - - - - - - - -cacacat
- - - - - - - - - - - - - - - - - - - - - aaaaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggcggga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaatataa