Sequence
atgc intronic sequence ATGC exonic sequence...tttatagcatgtacagaccggttttaattgatctttacatgcaactgtttatgtttgcttatgtagtatttacagcagtatcttgcatttaacttcccagGTCAATGCCTTCAGGGAAAGGAGAGCACTTGCTTTGACATTGAATGACACCAAAACGGCAGTGAACAAACTTCATCGAATGCTCAATTTTATAGTTGCAA
Basic information
species | Glycine max |
transcript | GLYMA20G23910.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G23910.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G53470.1 (Arabidopsis thaliana), 3'ss of exon 2
tttatagcatgtacagaccggttttaattgatctttacatgcaactgtttatgtttgcttatgta--gtatttacagcagtatcttgcatttaacttcccagGTCAATGCCTTCAGGGAAAGGAGAGCACTTGCTTTGACATTGAATGACACCAAAACGGCAGTGAACAAACTTCATCGAATGCTCAATTTTATAGTTGCAA
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--------------------gtaagtgtttgttttcagttcaaatttcaaaaactttcttacgtatgacaatgatgctagattcttaaatct--ttttctagGTTAATGCCTTTAGAGAACGAAGAGCACTAGCTTTAACATTAAACGATACAAAAACAGCAGTGAACAGGCTTCATCGAATCGTTGATGTATTGGTCAGCA
upper sequence: GLYMA20G23910.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv03s0038g03030.t01 (Vitis vinifera), 3'ss of exon 5
------tttatagcatgtacagaccggttttaattgatctttacatgcaactgtttatgtttgcttatgtagtatttacagcagtatcttgcatttaacttcccagGTCAATGCCTTCAGGGAAAGGAGAGCACTTGCTTTGACATTGAATGACACCAAAACGGCAGTGAACAAACTTCATCGAATGCTCAATTTTATAGTTGCAA
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ccacaccccatgg-atgcatgaatatgaatttgcagattctaacacacagcacctatcttttactcgctgattgataatgtgtaagtcttggtt-----gtttcagGTTAATGCTTTCAGAGAAAGGAGAGCACTTGCCTTGACATTGAATGACACAAAAACAGCCGTTAACAAACTTCATCAAATGGTGAATGTTGTAGTTTTCA
upper sequence: GLYMA20G23910.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv03s0038g02980.t01 (Vitis vinifera), 3'ss of exon 3
------tttatagcatgtacagaccggttttaattgatctttacatgcaactgtttatgtttgcttatgtagtatttacagcagtatcttgcatttaact-tcccagGTCAATGCCTTCAGGGAAAGGAGAGCACTTGCTTTGACATTGAATGACACCAAAACGGCAGTGAACAAACTTCATCGAATGCTCAATTTTATAGTTGCAA
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ccacacctcatgg-atgcataaatatgaatttgcagattctaacacgcagcacctattttttactcgctgattg------ataatgtgtaagccttggctgtttcagGTTAATGCTTTCAGAGAAAGGCGAGCACTTGCTTTGACATTGAATGACACAAAAACAGCCGTTAACAAACTTCATCAAATGGTGAATGTTGTAGTTGTCAMapped 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|7146311|gb|AW508233.1|AW508233EST: GAGCGTCTGAAGCTGAGAGAATCAGCAAATCGGCCTTGAAGAACTGGGTG GTCAATGCCTTCATGGAAAGGAGAGCACTTGCTTTGACATTGAATGACACC
genomic: GAGCGTCTGAAGCTGAGAGAATCAGCAAATCGGCCTTGAAGAACTGGGTGgtgagaatta ... aacttcccagGTCAATGCCTTCAGGGAAAGGAGAGCACTTGCTTTGACATTGAATGACACC
EST:
gi|7146732|gb|AW508654.1|AW508654EST: GAGCGTCTGAAGCTGAGAGAATCAGCAAATCGGCCTTGAAGAACTGGGTG GTCAATGCCTTCAGGGAAAGGAGAGCACTTGCTTTGACATTGAATGACACC
genomic: GAGCGTCTGAAGCTGAGAGAATCAGCAAATCGGCCTTGAAGAACTGGGTGgtgagaatta ... aacttcccagGTCAATGCCTTCAGGGAAAGGAGAGCACTTGCTTTGACATTGAATGACACC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtttatgtttgcttatgtagtatttacagcagtatcttgcatttaacttcccagGTCAATGCCTTCAGGGAAAGGAGAGCACTTGCTTTGACATTGAATGACACCAAAACGGCAGTGAACAAACTTCATCGAATGCTCAATTTTATAGTTGCAA
atttaac putative branch site (score: 3)
cttccc CT-rich tract
ttatgtagtattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttatagcatgtacagaccggttttaattgatctttacatgcaactgtttatgtttgcttatgtagtatttacagcagtatcttgcatttaacttcccagGTCAATGCCTTCAGGGAAAGGAGAGCACTTGCTTTGACATTGAATGACACCAAAACGGCAGTGAACAAACTTCATCGAATGCTCAATTTTATAGTTGCAA
- - - gcatgta
- - - - - - - - - - - - - - - - - - acatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcattt