Sequence
atgc intronic sequence ATGC exonic sequence...tttattagtgttgcctaaaactgttgcacaatctgcttaatgcttttcctgtgagtgaatggtgttgtattgtctgagtttttattttttaatatttcagCGGTGAAGGAATTCCCGATTTGTTATTACTATTGATTCAATGGACCCAAAAAACAATGGTTGAGAAACTTACATACAGTGAAGAAGTGCAG
Basic information
species | Glycine max |
transcript | GLYMA20G30590.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G30590.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G76720.1 (Arabidopsis thaliana), 3'ss of exon 8
--tttattagtgttgcctaaaactgt-tgcacaatctgcttaat---gcttttcctgtgagtgaatggtgttgtat-tgtctgagt--ttttattttttaatatttcagCGGTGAAGGAATTCCCGATTTGTTATTACTATTGATTCAATGGACCCAAAAAACAATGGTTGAGAAACTTACATACAGTGAAGAAGTGCAG
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gtatgattcatgccgtatgaatctctatttactgtttgtaatatacagcgtaacagacaagttattcatcctaaacgtaattgggtaacgttggttcttgatattacagTGGAGAAGGGGTCCCAGATCTCTTGCTGTGGTTGGTTCAATGGGCTCAGAAAACAATGGTTGAGAAACTTACATATGTTGACGAAGTGCAG
upper sequence: GLYMA20G30590.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G76810.1 (Arabidopsis thaliana), 3'ss of exon 5
tttattagtgttgcctaaaactgttgcacaatctgcttaatgcttttcctgtgagtgaatggtgttgtat-tgtctgagt--ttttattttttaatatttcagCGGTGAAGGAATTCCCGATTTGTTATTACTATTGATTCAATGGACCCAAAAAACAATGGTTGAGAAACTTACATACAGTGAAGAAGTGCAG
||| | | | | | ||||| ||| | | || | | ||| | | | | | | || || || || || ||||| ||| || ||||| | || ||| | || | ||| |||||||| | || |||||||||||||||||||||||||| ||| |||||||||
-gtatgaatctctattta--ctgtt-tgtaatataca----gcgtaacagacaagttattcatcctaaacgtaattgggtaacgttggttcttgatattacagTGGAGAAGGGGTCCCAGATCTCTTGCTGTGGTTGGTTCAATGGGCTCAGAAAACAATGGTTGAGAAACTTACATATGTTGACGAAGTGCAG
upper sequence: GLYMA20G30590.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G76820.1 (Arabidopsis thaliana), 3'ss of exon 5
tttattagtgttgcctaaaactgttgcacaatctgcttaatgcttttcctgtgagtgaatggtgttgtat-tgtctgagt--ttttattttttaatatttcagCGGTGAAGGAATTCCCGATTTGTTATTACTATTGATTCAATGGACCCAAAAAACAATGGTTGAGAAACTTACATACAGTGAAGAAGTGCAG
||| ||| | | | ||||| ||| | | || | | ||| | | | | | | || || || || || ||||| ||| || ||||| | || ||| | || | ||| |||||||| | || |||||||||||||||||||||||||| ||| |||||||||
-gtatgagtctctattta--ctgtt-tgtaatataca----gcgtaacagacaagttattcatcctaaacgtaattgggtaacgttggttcttgatattacagTGGAGAAGGGGTCCCAGATCTCTTGCTGTGGTTGGTTCAATGGGCTCAGAAAACAATGGTTGAGAAACTTACATATGTTGACGAAGTGCAG
upper sequence: GLYMA20G30590.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0076g00310.t01 (Vitis vinifera), 3'ss of exon 5
---------------tttat---tagtgttgcctaaaactgttgcacaatct---gcttaatgcttttcctg-tgagtgaatggtgttgtattgtc-tgagtttttattttttaatattt-cagCGGTGAAGGAATTCCCGATTTGTTATTACTATTGATTCAATGGACCCAAAAAACAATGGTTGAGAAACTTACATACAGTGAAGAAGTGCAG
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gtatttctcatagcctctatgtctacccttgttatatcttgttccaggctcttcaactgaaaactctacaaaacgatttatttacaagccaatgtcctgatattttggattggtggatgtacagTGGTGAAGGCATCCCAGACCTATTGCTATTATTGGTTCATTGGACTCAGAAAACAATGGTTGAGAAACTCACATACAGCAGTGAAGTGCAGMapped 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|208052232|gb|GD853041.1|GD853041EST: AACAAAGAAATGGGAGAAACGTTCAGCATTGTGCCTACAAGTGCAATAAG CGGTGAAGGAATTCCCGATTTGTTATTACTATTGATTCAATGGAC
genomic: AACAAAGAAATGGGAGAAACGTTCAGCATTGTGCCTACAAGTGCAATAAGgtaatcatag ... aatatttcagCGGTGAAGGAATTCCCGATTTGTTATTACTATTGATTCAATGGAC
EST:
gi|193511466|gb|FK471745.1|FK471745EST: AACAAAGAAATGGGAGAAACGTTCAGCATTGTGCCTACAAGTGCAATAAG CGGTGAAAGGAATT
genomic: AACAAAGAAATGGGAGAAACGTTCAGCATTGTGCCTACAAGTGCAATAAGgtaatcatag ... aatatttcagCGGTGAA-GGAATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcctgtgagtgaatggtgttgtattgtctgagtttttattttttaatatttcagCGGTGAAGGAATTCCCGATTTGTTATTACTATTGATTCAATGGACCCAAAAAACAATGGTTGAGAAACTTACATACAGTGAAGAAGTGCAG
ttttaat putative branch site (score: 3)
tttttta CT-rich tract
tattgtctgagttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttattagtgttgcctaaaactgttgcacaatctgcttaatgcttttcctgtgagtgaatggtgttgtattgtctgagtttttattttttaatatttcagCGGTGAAGGAATTCCCGATTTGTTATTACTATTGATTCAATGGACCCAAAAAACAATGGTTGAGAAACTTACATACAGTGAAGAAGTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - tgttgcc
- - - - - - - - - - - - tgcacaa
- - - - - - - - - - - - - - - -tctgctt
- - - - - - - - - - - - - - - - - - - aatgctt
- - - - - - - - - - - - - - - - - - - - - - - -cctgtga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgtctg