Sequence
atgc intronic sequence ATGC exonic sequence...gaatttttaattcagtttaattttgttggcatgtttatagtttatactaactaaatgattttttttccatccccttcactgtctctatcatgttttgtagCTGGAGTCCCCATTGAGAACATCCTTTACCTTGGAGGTCCTAACATTGCCTCAGAAATTTACAACAAGGAATATGCAAACGCTAGGATATGTGGGGCAGA
Basic information
species | Glycine max |
transcript | GLYMA12G01380.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G01380.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g58740.1 (Oryza sativa), 3'ss of exon 2
---------gaattttta-attcagtttaattttgttggcatgtttatagtttatactaactaaatgattttttttccatccccttcactgtctctatcatgttttgtagCTGGAGTCCCCATTGAGAACATCCTTTACCTTGGAGGTCCTAACATTGCCTCAGAAATTTACAACAAGGAATATGCAAACGCTAGGATATGTGGGGCAGA
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ttaacggccgagtgttcatgcttggttttacttc-ttaac-tgttt-tgaattatatccttccaat--ttatttctgcaa----ttta-tatttgttttgttttctgcagCGGGGGTTCCATTGGAAAACATTCTTTATCTTGGAGGCCCTAACATTGCTTCAGAAATTTACAATAAAGAATATGCAAATGCTCGTATATGTGGAGCTGA
upper sequence: GLYMA12G01380.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g71280.1 (Oryza sativa), 3'ss of exon 2
---gaatttttaattcagtttaa-ttttgttggcatgtttatagtttatactaactaaatgattttttttccatccccttcactgtctctatcatgttttgtagCTGGAGTCCCCATTGAGAACATCCTTTACCTTGGAGGTCCTAACATTGCCTCAGAAATTTACAACAAGGAATATGCAAACGCTAGGATATGTGGGGCAGA
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gacatgcatttatgtgatattaactttcgttgacccaacc-tattccttccc--ttgttttattcaaattacaactaattcagcattt-taaaataaattgcagCTGGAGTTCCAACTGAGAATATACTATATCTTGGAGGCCCAAACATTGCCTCAGAGATTTATAACAAAGAATATGCAAATGCTCGAATCTGTGGGTCCAA
upper sequence: GLYMA12G01380.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os05g41590.1 (Oryza sativa), 3'ss of exon 1
----gaatttttaattcagtttaat-tttgttggcatgtttatagtttatactaactaaatgattttttttccatccccttcactgtctctatcatgttttgtagCTGGAGTCCCCATTGAGAACATCCTTTACCTTGGAGGTCCTAACATTGCCTCAGAAATTTACAACAAGGAATATGCAAACGCTAGGATATGTGGGGCAGA
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gtttcactgtataattgattttaccatccactgg--tcttcatctttcctaccatgttg-tagcctttaatgttttttgtttcttatgatgggcctatt--gcagCTGGAGTTCCATTGGAGAATATTCTATATCTTGGAGGTCCTAACATTGCATCTGAGATATATAACAAAGAATATGCAAATGCTCGCATATGTGGAGCTGA
upper sequence: GLYMA12G01380.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G155348_T01 (Zea mays), 3'ss of exon 2
gaattt--ttaattcagtttaattttgttggcatgtttatagtttatactaactaaatgattttttttccatccccttcactgtctctatcatgttttgtagCTGGAGTCCCCATTGAGAACATCCTTTACCTTGGAGGTCCTAACATTGCCTCAGAAATTTACAACAAGGAATATGCAAACGCTAGGATATGTGGGGCAGA
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gcatctggttgaaacgtataaacagtttttttctgcttaatgcttggcctgcttatttgagatcagcagtacagact--gatttttaaggaatgcattgcagCTGGAGTTCCAACTGAAAATATACTCTATCTTGGAGGACCAAACATCGCCTCGGAAATTTATAACAAAGAATATGCAAACGCTCGAATCTGTGGATCCAA
upper sequence: GLYMA12G01380.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G090747_T02 (Zea mays), 3'ss of exon 2
gaatttttaattcagtttaattttgttggcatgtttatagtttatactaactaaatgattttttttccatccccttcactgtctctatcatgttttgtagCTGGAGTCCCCATTGAGAACATCCTTTACCTTGGAGGTCCTAACATTGCCTCAGAAATTTACAACAAGGAATATGCAAACGCTAGGATATGTGGGGCAGA
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agatacatatatatgctcaatgcttcctcctaatctccaagtatttgttgtcccctctttgattttgtatgatttattatggactattggtataatgcagCTGGAGTTCCATCAGAGAATATTCTTTATCTTGGCGGACCTAATATTGCTTCTGAAATTTACAACAAAGAATATGCAAATGCACGTATTTGTGGAGCTGA
upper sequence: GLYMA12G01380.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv13s0158g00340.t01 (Vitis vinifera), 3'ss of exon 1
gaatttttaattcagtttaattttgttggcatgt-ttatagtttatactaactaaatgattttttttccatccccttcactgtctc-------tatcatgttttgtagCTGGAGTCCCCATTGAGAACATCCTTTACCTTGGAGGTCCTAACATTGCCTCAGAAATTTACAACAAGGAATATGCAAACGCTAGGATATGTGGGGCAGA
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-------tcaccacattctctgtagtttttatttgtcctaattgatgccaccttttttattttactttc-tccacttctttgcctcattattatattgtgctttgcagCTGGAGTTCCCATGGAGAATATTCTCTATCTTGGTGGACCGAATATTGCCTCAGAAATTTACAACAAGGAATACGCTAATGCTCGCATATGTGGAGCTGA
upper sequence: GLYMA12G01380.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S114_190V6.1 (Physcomitrella patens), 3'ss of exon 3
-----------gaatttttaattcagtttaattttgttggcatgtttatagtttatactaactaaatgattttttttccatccccttcactgtctctatcatgttttgtagCTGGAGTCCCCATTGAGAACATCCTTTACCTTGGAGGTCCTAACATTGCCTCAGAAATTTACAACAAGGAATATGCAAACGCTAGGATATGTGGGGCAGA
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tgtgtgtgtgtaaatgtgtcctccagctggctcttgtcaggttgaa-atggtatgaattaatatgagggttgggactgaat-------attgtgta-attgtgatt--cagCCGGCGTGCCTTCTGAAAATGTTTTGTACCTGGGAGGTCCGAACATTGCTTCTGAAGTTTACAACAAGGAGTATGCTAATGCACGGATCTGCGGGTCTGAMapped 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|58014578|gb|CX701320.1|CX701320EST: CACGGATAATAACTCCCACGCTAATGATC-ATCAAAGCAA CTGGAGTCCCCATTGAGAACATCCTTTACCTTGGAGGTCCTAACATTGCT
genomic: CACGGATAATAACTCCCACGCTAATGATCAATC-AAGCAAgtgagataca ... tgttttgtagCTGGAGTCCCCATTGAGAACATCCTTTACCTTGGAGGTCCTAACATTGCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actaactaaatgattttttttccatccccttcactgtctctatcatgttttgtagCTGGAGTCCCCATTGAGAACATCCTTTACCTTGGAGGTCCTAACATTGCCTCAGAAATTTACAACAAGGAATATGCAAACGCTAGGATATGTGGGGCAGA
taaatgatttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaatttttaattcagtttaattttgttggcatgtttatagtttatactaactaaatgattttttttccatccccttcactgtctctatcatgttttgtagCTGGAGTCCCCATTGAGAACATCCTTTACCTTGGAGGTCCTAACATTGCCTCAGAAATTTACAACAAGGAATATGCAAACGCTAGGATATGTGGGGCAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - gcatgtt