Sequence
atgc intronic sequence ATGC exonic sequence...aaatattgaatacccagaattgtaacgtgttagagcaaagcactctaacttgctttcagtggggtgaatctgttgtgaactaacttgctttctctttcagCGAAAAGGATCAGGCTGAAAACTTGATGATTGTTGACCTTCTAAGGAATGACCTTGGCCGTGTCTGTGATCCTGGATCTGTTCATGTGCCACGTCTCATG
Basic information
species | Glycine max |
transcript | GLYMA20G31970.1 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G31970.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os06g48620.1 (Oryza sativa), 3'ss of exon 12
--aaatattgaatacccagaattgtaacgtgttagagcaaagcactctaacttgctttcagtggggtgaatctgttgtgaactaacttgctttctctttcagCGAAAAGGATCAGGCTGAAAACTTGATGATTGTTGACCTTCTAAGGAATGACCTTGGCCGTGTCTGTGATCCTGGATCTGTTCATGTGCCACGTCTCATG
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gcaagtatctgatagatacttttttcac-tgttcaaacattatgattttggtt-ttaccagtcctcacaat--actg-atattttcttatgtgtttcaacagTGAAAAAGATCAAGCTGAGAACTTGATGATTGTTGACCTCCTAAGAAACGATCTTGGTAAGGTTTGTGAACCTGGGAGTGTGCATGTTCCTCGCCTCATG
upper sequence: GLYMA20G31970.1 (Glycine max), 3'ss of exon 15
lower sequence: AT2G28880.1 (Arabidopsis thaliana), 3'ss of exon 13
aaatattgaatacccagaattgtaacgtgttagagcaaagcactctaacttgctttcagtggggtgaatctgttgtgaactaacttgctttctcttt---cagCGAAAAGGATCAGGCTGAAAACTTGATGATTGTTGACCTTCTAAGGAATGACCTTGGCCGTGTCTGTGATCCTGGATCTGTTCATGTGCCACGTCTCATG
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gtacaccaaacacgttg--ttctagaatcattgaatgt----ttcttaattgttcacatcaatgctactttaacgttgtttttttccccatgtcttataacagTGAGAAGAATCAAGCCGAGAATCTGATGATTGTTGACCTTCTAAGGAATGATCTCGGTCGTGTCTGTGAGCCTGGCTCAGTCCATGTACCTAACCTCATG
upper sequence: GLYMA20G31970.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv13s0019g04170.t01 (Vitis vinifera), 3'ss of exon 12
---aaatattgaatacccagaattgtaacgtgttagagcaaagcactctaacttgctttcagtggggtgaatctgttgtgaactaacttgctttctcttt-cagCGAAAAGGATCAGGCTGAAAACTTGATGATTGTTGACCTTCTAAGGAATGACCTTGGCCGTGTCTGTGATCCTGGATCTGTTCATGTGCCACGTCTCATG
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tacaaatatctaatgaagacaatgtttttgagtccaaaaataataattt--ttaaagcctaatatgttg--cctgccataaactaactctctcttcctcaacagTGAAAAAGATCAGGCTGAAAATCTGATGATTGTTGATCTTCTAAGAAATGACCTTGGTCGTGTCTGTGAACCTGGATCTATTCATGTTCCTTGTCTTATG
upper sequence: GLYMA20G31970.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv13s0019g04180.t01 (Vitis vinifera), 3'ss of exon 11
aaatattgaatacccaga-attgtaacgtgttagagcaaagcactctaact-tgctttcagtggggtgaatctgttgtgaactaacttgctttctcttt-----------cagCGAAAAGGATCAGGCTGAAAACTTGATGATTGTTGACCTTCTAAGGAATGACCTTGGCCGTGTCTGTGATCCTGGATCTGTTCATGTGCCACGTCTCATG
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----------aatctagctattttttggtgtacgtgcaatacaattttgttatgattt---ttgcatgcattgtttgtaaactaacacgtacgctctttaattatctgaacagTGAAAAGGATCAGGCTGAAAATTTGATGATTGTTGATCTGCTGAGGAATAATCTGGGTCGTGTCTGCGAGGTGGGTTCTGTGCATGTACCCCTTCTCATGMapped 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|15204341|gb|BI427109.1|BI427109EST: CTCAAATTAAAATTACAGTTCAG CGAAAAGGATCAGGCTGAAAACTTGATGATTGTTGACCTTCTAAGGAATGA
genomic: CTCAAATTAAAATTACAGTTCAGgtgacctata ... tctctttcagCGAAAAGGATCAGGCTGAAAACTTGATGATTGTTGACCTTCTAAGGAATGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taacttgctttcagtggggtgaatctgttgtgaactaacttgctttctctttcagCGAAAAGGATCAGGCTGAAAACTTGATGATTGTTGACCTTCTAAGGAATGACCTTGGCCGTGTCTGTGATCCTGGATCTGTTCATGTGCCACGTCTCATG
aactaac putative branch site (score: 1)
cttgctttctctttc CT-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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaatattgaatacccagaattgtaacgtgttagagcaaagcactctaacttgctttcagtggggtgaatctgttgtgaactaacttgctttctctttcagCGAAAAGGATCAGGCTGAAAACTTGATGATTGTTGACCTTCTAAGGAATGACCTTGGCCGTGTCTGTGATCCTGGATCTGTTCATGTGCCACGTCTCATG
- - - - - - cccagaa
- - - - - - - - - - - - - - - - - -caaagca
- - - - - - - - - - - - - - - - - - - - - - - - cttgctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctgttg