Sequence
atgc intronic sequence ATGC exonic sequence...ataatactatcttcttctgaccctggaagttgtagtatatgcctaataaacttccttaacaagtgtcaactgatgactatcttcattttttcatttgaagGAAGAGTATGACTGAATATGATCCACGTTTGGTAGCTCCAACATGCTTGTACCTGGCATCAAAAGCAGAAGAAAGCACAGTGCAGGCTCGGCTTCTTGTA
Basic information
species | Glycine max |
transcript | GLYMA18G33140.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G33140.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os09g32680.4 (Oryza sativa), 3'ss of exon 3
-ataatactatcttct-tctgaccctggaagttgtagtatatgcctaataaacttccttaacaag-tgtcaactgatgactatcttcattttttcatttgaagGAAGAGTATGACTGAATATGATCCACGTTTGGTAGCTCCAACATGCTTGTACCTGGCATCAAAAGCAGAAGAAAGCACAGTGCAGGCTCGGCTTCTTGTA
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cacagtgctttctaatatttcattccagaacatttaat---tctttgttgcagtggaacatcaagctattagaattttgttctgatgctggatatgtttacagAAAGAGCATGACTGAATATGATCCTCGTCTGGTAGCACCAACCTGTTTGTATTTGGCATCAAAGGTGGAAGAGAGCACAGTGCAAGCAAGACTTCTTGTC
upper sequence: GLYMA18G33140.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G48640.1 (Arabidopsis thaliana), 3'ss of exon 4
---------------------------------------------------------------------------------ataatactatcttcttctgaccctggaagttgtagtatatgcctaataaacttccttaacaag--tgtcaact--gatgacta---tcttcattttttcatttga-------agGAAGAGTATGACTGAATATGATCCACGTTTGGTAGCTCCAACATGCTTGTACCTGGCATCAAAAGCAGAAGAAAGCACAGTGCAGGCTCGGCTTCTTGTA
| || | | ||| | || | | | ||| | |||| ||| || | ||| | | || ||| ||||| |||| | | | | || ||||||||| || | ||| || || | || |||| || ||||||||||||||||| ||||| |||||||||| ||||||||| || ||||||
gtatgcaatgtatttttgatatgatcgtatacatcaatgtgcatctttgtgtatgtgaggaatgaaatgagttaaattcttgtcatgccagtgtctctctatgttgcatctc-tgctatcaaaaacgttaactgtgttacgaaagttttcagttttggtgtctaatatcttccttttgttactatactatctcagAAAGAGTATGGTAGAGTTTGAGCCTCGACTTGTTGCTCTTACGTGCTTGTACCTGGCATCTAAAGCTGAAGAAAGCATAGTGCAGGCCAGGAATCTTGTT
upper sequence: GLYMA18G33140.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv00s0360g00050.t01 (Vitis vinifera), 3'ss of exon 4
--ataatactatcttcttctgaccctggaagttgtagtatatgcctaataaacttccttaacaagtgtcaactgatgactatcttcattttttcatttgaagGAAGAGTATGACTGAATATGATCCACGTTTGGTAGCTCCAACATGCTTGTACCTGGCATCAAAAGCAGAAGAAAGCACAGTGCAGGCTCGGCTTCTTGTA
||| | | | | | | || || | ||||| | | || | || || |||| | | || || || |||||| ||||||||||||||| | || |||||||| |||||||| |||| ||||||||||||||||||| ||||||||| | |||||||||
agatagcattttgagcacttcttctcacaaattaattcaggcagactgtaaaccccggactggatctcttgctaagcttaatttttatttgtgctttc--agAAAAGCTATGACAGAATATGATCCACGTCTTGTGGCTCCAACTAGCTTGTACTTGGCTGCAAAAGCAGAAGAAAGCACTGTGCAGGCTAGACTTCTTGTA
upper sequence: GLYMA18G33140.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S18_263V6.1 (Physcomitrella patens), 3'ss of exon 2
ataatactatcttcttctgaccctgg----aagttgtagtatatgcctaataaacttccttaacaagtgtcaactgatgactatcttcattttttcatttgaagGAAGAGTATGACTGAATATGATCCACGTTTGGTAGCTCCAACATGCTTGTACCTGGCATCAAAAGCAGAAGAAAGCACAGTGCAGGCTCGGCTTCTTGTA
| || ||| || | || ||||| |||| ||| || ||| || || | | | | || | | | || | | | ||||| ||| | | |||| |||||| || || || || || ||||| |||||||||| || ||||||||||||||||||||||||||| | |||||||
-gcgtcctgccttgtttagtttcttattctaagttttagt-tattcc-aattaattttcgtggtgccattttgttaataatc-tgtatggcttcttgtgcgcagGAAAAGTTTCTCGGAATTTGATCCGCGGTTAGTTGCCCCGACATGTCTGTACCTGGCCTCCAAAGCAGAAGAAAGCACAGTGCAGGCTAAGATTCTTGTT
upper sequence: GLYMA18G33140.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S427_18V6.1 (Physcomitrella patens), 3'ss of exon 4
----ataatactatcttcttctgaccctggaagttgtagtatatgcctaataaacttccttaacaagtgtcaactgatgactatcttcattttttcatttgaagGAAGAGTATGACTGAATATGATCCACGTTTGGTAGCTCCAACATGCTTGTACCTGGCATCAAAAGCAGAAGAAAGCACAGTGCAGGCTCGGCTTCTTGTA
| ||||| || |||| | | | || || | | | || | | | | | | || | | | ||| ||| | | || || ||| | | |||| |||||||| | || ||||| ||||| |||| ||||| || |||||||||||||| |||||||||||| |||||||||
tgatttcctacta-ctacttcaaaacaattaggtcagtttagccaatttctcttttgccatggcta-tatttgccgacaaggagttggattcttttgt--gcagAAAAAGTTTCTCCGAATTCGATCCACGGCTAGTTGCTCCTACATGTCTGTATCTGGCCTCCAAAGCAGAAGAAAGTACAGTGCAGGCTAAGCTTCTTGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataaacttccttaacaagtgtcaactgatgactatcttcattttttcatttgaagGAAGAGTATGACTGAATATGATCCACGTTTGGTAGCTCCAACATGCTTGTACCTGGCATCAAAAGCAGAAGAAAGCACAGTGCAGGCTCGGCTTCTTGTA
aactgat putative branch site (score: 3)
tcttcattttttcatt putative PPT
ttcattttttcattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ataatactatcttcttctgaccctggaagttgtagtatatgcctaataaacttccttaacaagtgtcaactgatgactatcttcattttttcatttgaagGAAGAGTATGACTGAATATGATCCACGTTTGGTAGCTCCAACATGCTTGTACCTGGCATCAAAAGCAGAAGAAAGCACAGTGCAGGCTCGGCTTCTTGTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - ctgaccc
- - - - - - - - - - - - - - - - - - -tatgcct
- - - - - - - - - - - - - - - - - - - - - - - - - - -ccttaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actgatg