Sequence
atgc intronic sequence ATGC exonic sequence...tacaatttaaaaccttgggtgtgcctaatgactacctcattatatgttaatatgctctctatctcaagttcttgagttacctttgttaatttgctttcagAGTGTACCTGTGCAAGCTGGGCAAACGCCACCGTTATTGCAATACTTTGGAACTCTGTTAACCATGGGAAAACTCAATGCTTTTGAGTCACTGGAACTGT
Basic information
species | Glycine max |
transcript | GLYMA11G06720.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 11
--tacaatttaaaaccttgggtgtgcctaatgactacctcattatatgttaatatgctctctatctcaagttc-ttgagttacctttgttaatttgctttcagAGTGTACCTGTGCAAGCTGGGCAAACGCCACCGTTATTGCAATACTTTGGAACTCTGTTAACCATGGGAAAACTCAATGCTTTTGAGTCACTGGAACTGT
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attttcatttactttcctgtgttgggactgt-acaactaatcttaatgct--tatgctcttctgcttgacttagctttttcgtttctgtgctttaaaatgcagAGTGTTCCTGTTCAAGCTGGGCAAACGCCTCCACTCTTGCAGTACTTTGGCACATTGCTAACTCGGGGGAAGCTCAATGCTTACGAGTCTCTTGAGCTAT
upper sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 11
--tacaatttaaaaccttgggtgtgcctaatgactacctcattatatgttaatatgctctctatctcaagttc-ttgagttacctttgttaatttgctttcagAGTGTACCTGTGCAAGCTGGGCAAACGCCACCGTTATTGCAATACTTTGGAACTCTGTTAACCATGGGAAAACTCAATGCTTTTGAGTCACTGGAACTGT
| ||||| | || || | | || || | ||| | |||||||| || | || | | | ||| ||| | |||||||| ||||| ||||||||||||||||| || | ||||| |||||||| || || |||| ||| || |||||||||| ||||| || || || |
attttcatttactttcctgtgttgggactgt-acaactaatcttaatgct--tatgctcttctgcttgacttagctttttcgtttctgtgcttttaaatgcagAGTGTTCCTGTTCAAGCTGGGCAAACGCCTCCACTCTTGCAGTACTTTGGCACATTGCTAACTCGGGGGAAGCTCAATGCTTACGAGTCTCTTGAGCTAT
upper sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 9
tacaatttaaaaccttgggtgtgcctaatgactacctcattatatgttaatatgctctctatctcaa--gttcttgagttacctttgttaatttgctttcagAGTGTACCTGTGCAAGCTGGGCAAACGCCACCGTTATTGCAATACTTTGGAACTCTGTTAACCATGGGAAAACTCAATGCTTTTGAGTCACTGGAACTGT
| | | | || |||| | | |||| | ||| | ||| | || || ||||| ||| | ||| || |||||||| |||||||||||||||||||| || || | ||||| |||||||| || || |||| || || |||||||| |||||||| || || || |
cctgctatcaggattcatgtacatttaatcaat-tctcagtgtataa-gttcctttctttgacttaataattcttatgtttattactttatcaaaattgcagAGTGTTCCTGTGCAAGCTGGGCAAACACCCCCACTCTTGCAGTACTTTGGCACATTGCTAACTCGAGGGAAGCTCAATGCCTTTGAGTCTCTTGAGCTAT
upper sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 11
tacaatttaaaaccttgggtgtgcctaatgactacctcattatatgttaatatgctctctat-ctcaagttcttgagttacctttgttaatttgctttcagAGTGTACCTGTGCAAGCTGGGCAAACGCCACCGTTATTGCAATACTTTGGAACTCTGTTAACCATGGGAAAACTCAATGCTTTTGAGTCACTGGAACTGT
| |||| | | | | | | | | | | | | ||||| | | | |||| | | | | |||||| |||| || |||||||| ||||||||| |||| || || ||||| | ||||| |||||||| ||||||||||||| ||||||||||||||||| || ||||||||| |||
gatgctttatgagaattgaagagtttgctatcatttttacttatttataataaattgggaaaacacaagattgtcatctgtttttgttcattt-tttgcagAGTGTCCCTGTGCAATCTGGACAGACACCACCTCTGTTGCAGTACTTTGGTACTCTGTTAACCAGAGGAAAACTCAATGCTTTCGAATCACTGGAATTGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttaatatgctctctatctcaagttcttgagttacctttgttaatttgctttcagAGTGTACCTGTGCAAGCTGGGCAAACGCCACCGTTATTGCAATACTTTGGAACTCTGTTAACCATGGGAAAACTCAATGCTTTTGAGTCACTGGAACTGT
tgttaat putative branch site (score: 3)
tttgctttc CT-rich tract
tttgttaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tacaatttaaaaccttgggtgtgcctaatgactacctcattatatgttaatatgctctctatctcaagttcttgagttacctttgttaatttgctttcagAGTGTACCTGTGCAAGCTGGGCAAACGCCACCGTTATTGCAATACTTTGGAACTCTGTTAACCATGGGAAAACTCAATGCTTTTGAGTCACTGGAACTGT
- - - - - - - - gggtgtg
- - - - - - - - - - - - - - - -ctacctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acctttg