Sequence
atgc intronic sequence ATGC exonic sequencegtttgttctcttgaaatgtcttcaatgtgtttttgaataatccaacctattgatgagctgttggctgttgtgctttccagTTTCCTGCACTATATCAACAAGGACCCAAGAATTTGTTCTTTGACTGGTATAGAATATTGGGGTGGATGGGCAATGGTCTCTATGCCTCCCTCATCATCT
Basic information
species | Glycine max |
transcript | GLYMA08G20330.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G20330.1 (Glycine max), 3'ss of exon 10
lower sequence: AT1G17500.1 (Arabidopsis thaliana), 3'ss of exon 9
gtttgttctcttgaaatgtcttcaatgtgtttttgaataatccaacctattgatgagctgttggctgttgtgctttccagTTTCCTGCACTATATCAACAAGGACCCAAGAATTTGTTCTTTGACTGGTATAGAATATTGGGGTGGATGGGCAATGGTCTCTATGCCTCCCTCATCATCT
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------------gtaaggtttactaagctgctgtgagtttctcacacg--caacaaactaactcgttctttgttctgcagTTTCCAGCGTTGTACCAACAAGGGAAGAAAAATCTCTTCTTTGACTGGTATAGAATACTTGGGTGGATGGGAAATGGTGTGTACTCCTCCCTTGTAATAT
upper sequence: GLYMA08G20330.1 (Glycine max), 3'ss of exon 10
lower sequence: AT1G54280.1 (Arabidopsis thaliana), 3'ss of exon 10
-----gtttgttctcttgaaatgtcttcaatgtgtttttgaataatccaaccta-----ttgatg-agctgttggc-tgttgtgctt-tccagTTTCCTGCACTATATCAACAAGGACCCAAGAATTTGTTCTTTGACTGGTATAGAATATTGGGGTGGATGGGCAATGGTCTCTATGCCTCCCTCATCATCT
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gttatataaagtcctctccatcatctttcacatatataacaaaaccttctttttggatcttgattcatttcttggcctgttttctttatctagTTCCCTGCATTGTATCAACAAGGCCCCAAGAACCTGTTCTTCGACTGGTACAGAATCCTTGGATGGATGGGGAATGGAGTTTATGCATCCATAGTCATCT
upper sequence: GLYMA08G20330.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv09s0002g01730.t01 (Vitis vinifera), 3'ss of exon 9
--gtttgttctcttgaaatgtcttcaatgtgtttttgaa-----taatccaacctat-tgatgagct----gttggctgttgtgctttccagTTTCCTGCACTATATCAACAAGGACCCAAGAATTTGTTCTTTGACTGGTATAGAATATTGGGGTGGATGGGCAATGGTCTCTATGCCTCCCTCATCATCT
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gtgagagtccaccattgatgccttcacttggaatttcatcctcttacatcaacctttgtcacaattttcacacttgcaattcctttttgcagTTTCCAGCACTGTATCAACAAGGACCCAGAAACTTGTTCTTCGACTGGTATAGGATATTTGGGTGGATGGGAAATGGTCTCTACACCTCCCTCATCATTTMapped 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|9204314|gb|BE330538.1|BE330538EST: TTTCACTCGGTGTTTTTGAACAAGATGTTCCGTCAGAAGTTTGTTTACAG TTTCCTGCACTATATCAACAAGGACCCAAGAATTTGTTCTTTGACTGGTAT
genomic: TTTCACTCGGTGTTTTTGAACAAGATGTTCCGTCAGAAGTTTGTTTACAGgtttgttctc ... tgctttccagTTTCCTGCACTATATCAACAAGGACCCAAGAATTTGTTCTTTGACTGGTAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtgtttttgaataatccaacctattgatgagctgttggctgttgtgctttccagTTTCCTGCACTATATCAACAAGGACCCAAGAATTTGTTCTTTGACTGGTATAGAATATTGGGGTGGATGGGCAATGGTCTCTATGCCTCCCTCATCATCT
tattgat putative branch site (score: 3)
tgctttcc putative PPT
ttttgaataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgttctcttgaaatgtcttcaatgtgtttttgaataatccaacctattgatgagctgttggctgttgtgctttccagTTTCCTGCACTATATCAACAAGGACCCAAGAATTTGTTCTTTGACTGGTATAGAATATTGGGGTGGATGGGCAATGGTCTCTATGCCTCCCTCATCATCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA