Sequence
atgc intronic sequence ATGC exonic sequencegtattaaggatgacaaccttgagcactcaaacaaatgtgtgaattatacaataaatgaactttccttctgttacaatattcagAGATCTGTCCAAACTCTGAGTGGTGGTCAGAAGCAGAGGGTTGCCATTGCTGGTGCTCTTGCTGAAGCTTGTAAAGTTCTGTTGTTGGATGAGCTCACAA
Basic information
species | Glycine max |
transcript | GLYMA06G15900.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G15900.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g56400.1 (Oryza sativa), 3'ss of exon 3
----gtattaaggatgacaaccttgagcactcaaacaaatgtgtgaattatacaataaatgaactttccttctgttacaatattcagAGATCTGTCCAAACTCTGAGTGGTGGTCAGAAGCAGAGGGTTGCCATTGCTGGTGCTCTTGCTGAAGCTTGTAAAGTTCTGTTGTTGGATGAGCTCACAA
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gtaggcagctgacatgctccttttggattat-aatctattgtctg---cacaaggttcacaaacatccttcatccaaca-----cagAGGCCAATCCAAACTCTGAGTGGCGGGCAGAAGCAGAGAGTTGCAATTGCCGGTGCTTTAGCTGAAGCATCCAAAGTACTACTACTGGATGAGCTGACCA
upper sequence: GLYMA06G15900.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G111511_T05 (Zea mays), 3'ss of exon 1
gtattaaggatgacaaccttgagcactcaaacaaatgtgtgaattatacaataaatgaactttccttctgttacaatattcagAGATCTGTCCAAACTCTGAGTGGTGGTCAGAAGCAGAGGGTTGCCATTGCTGGTGCTCTTGCTGAAGCTTGTAAAGTTCTGTTGTTGGATGAGCTCACAA
||| | || | ||| | | | | | || | | || | | || ||||| | | | ||||| | ||||||||||||||||||| ||||| ||||| ||||| ||||||||||| | |||||||| | ||||| | || |||| || || || |
----gtaggcttctaaattccagcttttggatcataatctaaagtcttcacaatgttaataacccttcattcaaa-----cagAGGCCAATCCAAACTCTGAGTGGTGGGCAGAAACAGAGAGTTGCAATTGCTGGTGCGTTAGCTGAAGCATCCAAAGTATTACTGCTGGACGAACTGACCA
upper sequence: GLYMA06G15900.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G33460.1 (Arabidopsis thaliana), 3'ss of exon 3
gtattaaggatgacaaccttgagcactcaaacaaatgtgtgaattatacaata------aatgaactttcc-ttctgttacaatattcagAGATCTGTCCAAACTCTGAGTGGTGGTCAGAAGCAGAGGGTTGCCATTGCTGGTGCTCTTGCTGAAGCTTGTAAAGTTCTGTTGTTGGATGAGCTCACAA
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---gtcagtttatgtacattgaacaa-caataagttgtttatatcttctagttccttttactaaagtatagattttggtgttgtttccagAGACCGATTCAAACTCTCAGTGGTGGTCAGAAACAAAGAATTGCCATTGCTGGTGCTTTAGCTGAAGCGTGCAAAGTGCTATTGTTGGATGAGCTCACAA
upper sequence: GLYMA06G15900.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0044g01320.t01 (Vitis vinifera), 3'ss of exon 4
gtattaaggatgacaaccttgagcactcaa--acaaatgtgtgaattatacaataaatgaactttccttctgttacaatattcagAGATCTGTCCAAACTCTGAGTGGTGGTCAGAAGCAGAGGGTTGCCATTGCTGGTGCTCTTGCTGAAGCTTGTAAAGTTCTGTTGTTGGATGAGCTCACAA
||| || | || || ||||| | | | | | ||||||| || ||||| |||||||| | | ||||| || |||| || || || |||||||||||||| || ||||||||||||||||||||| | || ||||| |||||||| || ||| | |||||||||||||
----gtaggttgt--atattatgctctcaattatagaagcataaattatattttatgattacttttcttctgttgaacttttcagCGACCTGTTCAGACACTAAGTGGTGGTCAGAAACAAAGGGTTGCCATTGCTGGTGCTTTGGCAGAAGCGTGTAAAGTACTATTGCTAGATGAGCTCACAAMapped 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|58021712|gb|CX708453.1|CX708453EST: CTAGGGTGTCAAGAGCTTTGCATGCTGTAGGCCTGTCTGACTACATGAAG AGATCTGTCCAAACTCTGAGTGGTGGTCAGAAGCAGAGGGTTGCCATTGCT
genomic: CTAGGGTGTCAAGAGCTTTGCATGCTGTAGGCCTGTCTGACTACATGAAGgtattaagga ... caatattcagAGATCTGTCCAAACTCTGAGTGGTGGTCAGAAGCAGAGGGTTGCCATTGCT
EST:
gi|298172759|gb|HO020313.1|HO020313EST: CTAGGGTGTCAAGAGCTTTGCATGCTGTAGGCCTGTCTGACTACATGAAG AGATCTGTCCAAACTCTGAGTGGTGGTCAGAAGCAGAGGGTTGCCATTGCT
genomic: CTAGGGTGTCAAGAGCTTTGCATGCTGTAGGCCTGTCTGACTACATGAAGgtattaagga ... caatattcagAGATCTGTCCAAACTCTGAGTGGTGGTCAGAAGCAGAGGGTTGCCATTGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaacaaatgtgtgaattatacaataaatgaactttccttctgttacaatattcagAGATCTGTCCAAACTCTGAGTGGTGGTCAGAAGCAGAGGGTTGCCATTGCTGGTGCTCTTGCTGAAGCTTGTAAAGTTCTGTTGTTGGATGAGCTCACAA
ctttccttctgttac CT-rich tract
aattatacaataaatg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattaaggatgacaaccttgagcactcaaacaaatgtgtgaattatacaataaatgaactttccttctgttacaatattcagAGATCTGTCCAAACTCTGAGTGGTGGTCAGAAGCAGAGGGTTGCCATTGCTGGTGCTCTTGCTGAAGCTTGTAAAGTTCTGTTGTTGGATGAGCTCACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA