Sequence
atgc intronic sequence ATGC exonic sequence...ttaaactgcacacactccagttttttttaactggaaaggatttgtgcccgttgtatcccaagagagcttatagttatacgattttttgtctgtcttgcagACAATTGTTCCCTTATCTGGGCACTTTGATTATTCATTTGCATCATCATGGCATCCTGATGGTGTGACCTTTGCCACTGGAAACCAGGACAAAACCTGCC
Basic information
species | Glycine max |
transcript | GLYMA04G12500.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G12500.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G56190.2 (Arabidopsis thaliana), 3'ss of exon 9
ttaaactgcacacactccagttttttttaactggaaaggatttgtgcccgttgtatcccaagagagcttatagttatacgattttttgtctgtcttgcagACAATTGTTCCCTTATCTGGGCACTTTGATTATTCATTTGCATCATCATGGCATCCTGATGGTGTGACCTTTGCCACTGGAAACCAGGACAAAACCTGCC
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-----------gtacttaacattcttcttcccggcacc-atctat-ttcactgcg----ggtaggtcttggagccttacggttttgagttt-tgtttcagACGATCGGGACGCTAAAAGGTCACTTAGATTATTCATTTGCATCAGCTTGGCATCCAAACGGTGTAACATTTGCCACAGGAAACCAAGACAAGACCTGTC
upper sequence: GLYMA04G12500.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv19s0015g01750.t01 (Vitis vinifera), 3'ss of exon 8
---ttaaactgcacacactcca--gttttttttaactggaaa-ggatttgtgc---ccgttgtatcccaagagagcttatagttatacgattttttgtctgt----cttgcagACAATTGTTCCCTTATCTGGGCACTTTGATTATTCATTTGCATCATCATGGCATCCTGATGGTGTGACCTTTGCCACTGGAAACCAGGACAAAACCTGCC
|| | |||| | || | | ||| || |||| ||| | || | | | || | | | |||||| ||| | |||||||||| | | || || | ||||||||| ||||||||||||||||| ||||| | ||||||||||| || ||||||||||| |||||||||||||||||||
gtattcatctgctctgtttctgtggcaatgacctactataatcaaatttatgcatctctctgaaggctgaaagtggaagcatgtgc-tgattttgaatctctgatccttgcagACAGTCATGCCATTGTGTGGGCACTTGGATTATTCATTTGCATCGGCATGGAACCCTGATGGTGTAACTTTTGCCACTGGGAACCAGGACAAAACCTGCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcccgttgtatcccaagagagcttatagttatacgattttttgtctgtcttgcagACAATTGTTCCCTTATCTGGGCACTTTGATTATTCATTTGCATCATCATGGCATCCTGATGGTGTGACCTTTGCCACTGGAAACCAGGACAAAACCTGCC
ttttttgtctgtctt CT-rich tract
ttatacgatttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttaaactgcacacactccagttttttttaactggaaaggatttgtgcccgttgtatcccaagagagcttatagttatacgattttttgtctgtcttgcagACAATTGTTCCCTTATCTGGGCACTTTGATTATTCATTTGCATCATCATGGCATCCTGATGGTGTGACCTTTGCCACTGGAAACCAGGACAAAACCTGCC
- - - - cacacac
- - - - - - - - - - - - - - - - - - - - tttgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - atcccaa