Sequence
atgc intronic sequence ATGC exonic sequencegtatggaataccttgatatgataaattaatttattgtcataatttttattattatatttattctttggaatatattgcagGAAGACAGGCAAAGGGCTTTGTTGCAGTTGCAGTTGAAAGTGATGAGTGACAAGCCCAAAGAGGACCAAGAAGTGAATTCAAAACAG
Basic information
species | Glycine max |
transcript | GLYMA20G35130.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G35130.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G22275.1 (Arabidopsis thaliana), 3'ss of exon 12
gtatggaataccttgatatgataaattaatttattgtcataatttttattattatatttattctttggaatatattgcagGAAGACAGGCAAAGGGCTTTGTTGCAGTTGCAGTTGAAAGTGATGAGTGACAAGCCCAAAGAGGACCAAGAAGTGAATTCAAAACAG
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----gtaagtgctttttaagatccatta------taagatgaatct--ttatgagtttaacttatgggctaaccttgcagGAAGAGAGGCAAAGAGCTTTGGTGCAGTTACAGTGGAAGGTGATGAGTGACAATCCACCTGAGGAGCAAGAAGTAAACTCAAACAAG
upper sequence: GLYMA20G35130.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G22260.1 (Arabidopsis thaliana), 3'ss of exon 12
gtatggaataccttgatatgataaattaatttattgtcataatttttattattatatttattctttggaatatattgcagGAAGACAGGCAAAGGGCTTTGTTGCAGTTGCAGTTGAAAGTGATGAGTGACAAGCCCAAAGAGGACCAAGAAGTGAATTCAAAACAG
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---gtaagtgctttcttaagat---ccaatataagatga--atctttatgggtttaactaatg---ggctaaccttgcagGAAGAGAGGCAACGAGCTTTGGTGCAGTTACAGTGGAAGGTGATGAGTGACAATCCACCTGAAGAGCAAGAAGTAAACTCAAACAAG
upper sequence: GLYMA20G35130.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv18s0001g05600.t01 (Vitis vinifera), 3'ss of exon 12
gtatggaataccttgatatgataaattaatttattgtcataatttttattattatatttattctttggaatatattgcagGAAGACAGGCAAAGGGCTTTGTTGCAGTTGCAGTTGAAAGTGATGAGTGACAAGCCCAAAGAGGACCAAGAAGTGAATTCAAAACAG
||||| | | || | | || | | ||| ||||| | | || ||| || |||||| |||||| ||||||||||| || || ||||| ||||| ||||||| |||||| ||||||||||| | ||||||| | |||||||||||||||| ||
gtatgtagttcccttaagtgcaataagaat-----gtcattttatgtaac-ttaaccttgatctttg---tatattacagGAAGACAGACAGAGAGCTTTATTGCAATTGCAGTGGAAAGTAATGAGTGACAAAACACAAGAGGATCCAGAAGTGAATTCAAAAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaatttattgtcataatttttattattatatttattctttggaatatattgcagGAAGACAGGCAAAGGGCTTTGTTGCAGTTGCAGTTGAAAGTGATGAGTGACAAGCCCAAAGAGGACCAAGAAGTGAATTCAAAACAG
aattaat putative branch site (score: 3)
ataatttttattatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatggaataccttgatatgataaattaatttattgtcataatttttattattatatttattctttggaatatattgcagGAAGACAGGCAAAGGGCTTTGTTGCAGTTGCAGTTGAAAGTGATGAGTGACAAGCCCAAAGAGGACCAAGAAGTGAATTCAAAACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT