Sequence
atgc intronic sequence ATGC exonic sequence...ggattctctatttttatacatcttgtttgatagaatcatagtctggctggaaagtaattcattaagtgagagatataatttaactttttttaactgatagGTAGATTTAGACACCTCCCTGTTGTGGAAAATGGTGAAGTCATTGCCATGCTGGATATCACCAAATGTCTTTATGATGCCATATCTAGAATGGAGAGCGC
Basic information
species | Glycine max |
transcript | GLYMA06G16570.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G16570.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os12g07190.1 (Oryza sativa), 3'ss of exon 3
ggattctctatttt---tatacatcttgtttgatagaatcatagtctggctggaaagtaattcattaagtgagagatataatttaactttttttaactgatagGTAGATTTAGACACCTCCCTGTTGTGGAAAATGGTGAAGTCATTGCCATGCTGGATATCACCAAATGTCTTTATGATGCCATATCTAGAATGGAGAGCGC
||| || | || ||| | |||| ||| | ||||| | | || | | | || | | | || | | | |||||| ||||||||||||||| ||||||||||||||||| || ||||| |||||||| || | ||||| ||||| ||||| ||||| ||| |||| | ||
--tttcactttgttacacatagaccttggttggctagaaattagtccctttttcaca-aacatactgactgtagtttctttaaaatgttcatacatattttagGTAAATTTAGACACCTCCCAGTTGTGGAAAATGGTGAGGTTATTGCTATGCTGGACATTGCTAAATGCCTTTACGATGCAATATCAAGACTGGAAAAGGC
upper sequence: GLYMA06G16570.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os11g06930.1 (Oryza sativa), 3'ss of exon 3
--ggattctctatttttatacatct-tgtttgatagaatcatagtctggctggaaagtaattcattaagtgagagatataatttaactttttttaactgatagGTAGATTTAGACACCTCCCTGTTGTGGAAAATGGTGAAGTCATTGCCATGCTGGATATCACCAAATGTCTTTATGATGCCATATCTAGAATGGAGAGCGC
|| || ||| || | | | | | | || || | ||| | | |||| || || ||| | | | |||| | |||||| |||||||| || |||||||||||||| || ||||||||||| || || | ||||| || |||||||| ||||| ||| |||| | ||
atgggctcatcattccaattgttttatatactgtctctccgtattccaagtatgttcattttcctctccttagagctaatatgaaacactc---acgttttagGAAAATTTAGGCACCTCCCAGTGGTGGAAAATGGTGAGGTTATTGCCATGCTAGACATTGCAAAATGCCTCTATGATGCAATATCAAGACTGGAAAAGGC
upper sequence: GLYMA06G16570.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g73040.1 (Oryza sativa), 3'ss of exon 3
---------ggattctctatttttatacatcttgtttgatagaatcatagtctggctggaaagtaattcattaagtgagagatataatttaactttttttaactgatagGTAGATTTAGACACCTCCCTGTTGTGGAAAATGGTGAAGTCATTGCCATGCTGGATATCACCAAATGTCTTTATGATGCCATATCTAGAATGGAGAGCGC
|||||| | || | | | ||| | || | | | | | | | | || | || | | || ||||| ||| | || ||||| || ||||| |||||| | ||||| || |||||||||||||| || ||||| | ||||||||||| || || |||||||| | ||
aagttagatagattcttt-cttatgttcttctgagtgaattattttccttttctttttgggtctgaatgctctcttgtgg----caacatggcattcattaac----agGAAAGTTCAGACATCTTCCTGTAGTGGAACACGGTGAGGTAATTGCCATGCTGGACATTACCAAGTTCCTTTATGATGCAATTTCAAGAATGGAAAAGGC
upper sequence: GLYMA06G16570.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G131118_T01 (Zea mays), 3'ss of exon 1
--------ggattctctatttttatacatcttgtttgatagaatcatagtctggctggaaagtaattcattaagtgagagatataatttaactttttttaactgatagGTAGATTTAGACACCTCCCTGTTGTGGAAAATGGTGAAGTCATTGCCATGCTGGATATCACCAAATGTCTTTATGATGCCATATCTAGAATGGAGAGCGC
| | ||| || | || || |||| | || | || | || || | || |||| | | || | |||| | |||| ||| | ||||| | |||||||||||| || ||||| ||||||||||| || ||||| |||||||| || | |||||||| |||||||| ||||| ||| |||| | ||
tgcataggctaaacctcattatttca-atgttccttga-ataaacttactttga--ggtatgttattc-ctgtctctgaagt-taatatgttttttctta--ttatagGGAAATTTAGACACCTTCCGGTTGTTGAAAATGGTGAGGTTATTGCGATGCTGGACATTGCAAAATGTCTCTATGATGCAATATCAAGACTGGAAAAGGC
upper sequence: GLYMA06G16570.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G031609_T02 (Zea mays), 3'ss of exon 3
------ggattctctatttttatacatcttgtttgatagaatcatagtctggctggaaagtaattcattaagtgagagatataatttaactttttttaactgatagGTAGATTTAGACACCTCCCTGTTGTGGAAAATGGTGAAGTCATTGCCATGCTGGATATCACCAAATGTCTTTATGATGCCATATCTAGAATGGAGAGCGC
| | ||| || | || || |||| | || | || | || || | || |||| || || || || | |||||| | ||||| | |||||||||||| || ||||| ||||||||||| || ||||| |||||||| || | |||||||| |||||||| ||||| ||| |||| | ||
cataggctaaacctcattatttca-atgttccttga-ataaacttaatttga--ggtatgttattcctttctctgaagtta--atatggtttttttcttattatagGGAAATTTAGACACCTTCCAGTTGTTGAAAATGGTGAGGTTATTGCGATGCTGGACATTGCAAAATGTCTGTATGATGCAATATCAAGACTGGAAAAGGC
upper sequence: GLYMA06G16570.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G052277_T01 (Zea mays), 3'ss of exon 3
-----ggattctctatttttatacatcttgtttgatagaatcatagtctggctggaaagtaattcattaagtgagagatataatttaactttttttaactgatagGTAGATTTAGACACCTCCCTGTTGTGGAAAATGGTGAAGTCATTGCCATGCTGGATATCACCAAATGTCTTTATGATGCCATATCTAGAATGGAGAGCGC
|| | | | | | || || |||| | || | || | | | | |||||| | || || | ||||||| || |||||| |||||||||||| || ||||| ||||||||||| || ||||| ||| |||| || || ||||| || |||||||| ||||| ||| |||| | ||
gcataggctaaccctcatgtttttatgttacttga-ataaacttacttcgat--atatgctattcatctttctgaatttaatgttgtagatttttta--tgttagGTAAATTTAGACACCTTCCAGTTGTAGAAAATGGTGAGGTTATTGCGATGTTGGACATTACAAAATGCCTCTATGATGCAATATCAAGACTGGAAAAGGC
upper sequence: GLYMA06G16570.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G126656_T01 (Zea mays), 3'ss of exon 3
ggattctctatttttatacatcttgtttgata----gaatcatagtctggctggaaagtaattcattaagtgagagatataatttaactttttttaactgatagGTAGATTTAGACACCTCCCTGTTGTGGAAAATGGTGAAGTCATTGCCATGCTGGATATCACCAAATGTCTTTATGATGCCATATCTAGAATGGAGAGCGC
| | | || | || | || || | || ||| | | |||| | |||| ||| | || || || | | | | |||| | |||||||||||| || ||||| ||||||||||| || ||||| |||||||| || | ||||| |||||||| || ||| | ||| |||| | ||
--gctgtttgttctcatgtccttgcttagaaaccctgagtcaagtcttagttggatat--gttcactaacatcagcttttacaatatgttctctcatattttagGGAAATTTAGACACCTTCCCGTTGTAGAAAATGGTGAGGTTATTGCTATGCTGGACATTGCAAAATGCCTTTATGAAGCAATAGCAAGACTGGAAAAGGC
upper sequence: GLYMA06G16570.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv07s0031g02750.t01 (Vitis vinifera), 3'ss of exon 3
ggattctctatttttatacatcttgtttgatagaatcatagtctggctggaaagtaattcattaagtgagagatataatttaactttttttaactgatagGTAGATTTAGACACCTCCCTGTTGTGGAAAATGGTGAAGTCATTGCCATGCTGGATATCACCAAATGTCTTTATGATGCCATATCTAGAATGGAGAGCGC
|| | | ||| ||| || || | |||| | | | | || | || || || || | ||| | || | ||| | ||||| |||||||||||||| |||||||||||||| |||||||| ||||||| || || || || |||||||| |||||| ||||||||| ||
tatttatttcatttcatatatgcacttcatttgaatgaattctttattacttattagcctaatatttgttttatggcatcttgcttgtgttggtcaacagGCAAGTTTAGGCACCTCCCTGTTGTAGAAAATGGTGAAGTTATTGCCATATTGGATATTACAAAGTGCCTCTATGATGCTATATCTCGAATGGAGAAGGC
upper sequence: GLYMA06G16570.2 (Glycine max), 3'ss of exon 3
lower sequence: EFJ12244 (Selaginella moellendorffii), 3'ss of exon 3
ggattctctatttttatacatcttgtttgatagaatcatagtctggctggaaagtaattcattaagtgagagatataatttaactttttttaactgatagGTAGATTTAGACACCTCCCTGTTGTGGAAAATGGTGAAGTCATTGCCATGCTGGATATCACCAAATGTCTTTATGATGCCATATCTAGAATGGAGAGCGC
|| | | | || | |||||| || | || ||| ||| ||| | |||||||||||| || || ||||| ||||| ||||||||||| |||||||||| || ||||| | |||||||| || | |||||||||| ||
----------------------------------------gtattctacaactttgatagccttcgtgagattcccaa---acctccatttctctg-cagGGAAATTTAGACACCTTCCAGTCGTGGAGAATGGCGAAGTCATTGCACTGCTGGATATAACAAAATGCTTGTATGATGCGATTGCGAGAATGGAGAAAGC
upper sequence: GLYMA06G16570.2 (Glycine max), 3'ss of exon 3
lower sequence: EFJ25849 (Selaginella moellendorffii), 3'ss of exon 3
ggattctctatttttatacatcttgtttgatagaatcatagtctggctggaaagtaattcattaagtgagagatataatttaactttttttaactgatagGTAGATTTAGACACCTCCCTGTTGTGGAAAATGGTGAAGTCATTGCCATGCTGGATATCACCAAATGTCTTTATGATGCCATATCTAGAATGGAGAGCGC
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-----------------------------------gtattctacaactttgaaagccttc-----gtgagattcccaa---acctccatttctctg-cagGGAAATTTAGACACCTTCCAGTCGTGGAGAATGGCGAAGTCATTGCACTGCTGGATATAACAAAATGCTTGTATGATGCGATTGCGAGAATGGAGAAAGCMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|15337751|gb|BI498407.1|BI498407EST: TGTCACGTCGGATACGCTCGCCATTGATGCGCTTCAGAAAATGATTCAGG GTAGATTTAGACACCTCCCTGTTGTGGAAAATGGTGAAGTCATTGCCATGC
genomic: TGTCACGTCGGATACGCTCGCCATTGATGCGCTTCAGAAAATGATTCAGGgttagcttcg ... taactgatagGTAGATTTAGACACCTCCCTGTTGTGGAAAATGGTGAAGTCATTGCCATGC
EST:
gi|8826826|gb|BE210556.1|BE210556EST: TGTCACGTCGGATACGCTCGCCATCGATGCGCTTCAGAAAATGATTCATG GTAGATTTAGACACCCTCC-TGTTGTGGAAAATGG
genomic: TGTCACGTCGGATACGCTCGCCATTGATGCGCTTCAGAAAATGATTCAGGgttagcttcg ... taactgatagGTAGATTTAGACACC-TCCCTGTTGTGGAAAATGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctggaaagtaattcattaagtgagagatataatttaactttttttaactgatagGTAGATTTAGACACCTCCCTGTTGTGGAAAATGGTGAAGTCATTGCCATGCTGGATATCACCAAATGTCTTTATGATGCCATATCTAGAATGGAGAGCGC
ttttaac putative branch site (score: 2)
cttttttt CT-rich tract
agatataatttaactt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggattctctatttttatacatcttgtttgatagaatcatagtctggctggaaagtaattcattaagtgagagatataatttaactttttttaactgatagGTAGATTTAGACACCTCCCTGTTGTGGAAAATGGTGAAGTCATTGCCATGCTGGATATCACCAAATGTCTTTATGATGCCATATCTAGAATGGAGAGCGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - ttgtttg
- - - - - - - - - - - - - - - - - - - - - -tggctgg