Sequence
atgc intronic sequence ATGC exonic sequence...aatttatgtatagttgcttaggttatttacacggtcttgttgcttttggcaatgcttaatttagtaggaactgaattttctttttactttttccctttagTGGTCAGACAAGCTCCAGAAACTTCATTTCCAAGAATTGGTAATGTTCCTTCAACACCTTCCAACAGAGAACTGGACTCACCGGGAGCTTGAGATGGTGC
Basic information
species | Glycine max |
transcript | GLYMA11G13330.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G13330.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os09g34040.1 (Oryza sativa), 3'ss of exon 9
-------------------------------------------------------------aatttatgtatagt---tgcttaggttatttacacggtcttgttgcttt---tggcaatgcttaatttagtaggaactgaattttctttttactttttccctttagTGGTCAGACAAGCTCCAGAAACTTCATTTCCAAGAATTGGTAATGTTCCTTCAACACCTTCCAACAGAGAACTGGACTCACCGGGAGCTTGAGATGGTGC
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gtaagttgaagtaccccttgactgttcataattatttttttcaacttcagtgtatgcaagtgttgcatgcctggtgcaggcaaatgcagttttcacaatgtttctggtgtaaatactaatgtccaagtccattgtaattaagttctctctttatttctacc--tcagTGGTCAGACAAGCTGAAGAAACTTGATTTTCAAGAGATGGTCATGTTCCTTCAGCACCTTCCGACGAGGAACTGGGCTCACCATGAGCTTGAGATGGTGC
upper sequence: GLYMA11G13330.1 (Glycine max), 3'ss of exon 9
lower sequence: AT2G30710.1 (Arabidopsis thaliana), 3'ss of exon 9
aatttatgtatagttgcttaggttatttacacggtcttgttgcttttggcaatgcttaatttagtag-------gaactgaattttctttttactttttccc--tttagTGGTCAGACAAGCTCCAGAAACTTCATTTCCAAGAATTGGTAATGTTCCTTCAACACCTTCCAACAGAGAACTGGACTCACCGGGAGCTTGAGATGGTGC
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-----gtaagcaaacactgaatcgaatataac--ttgcgttggtcttgaaaatgttttcttctataaaccacgagaatcaaatacaagttgtttctgtaaacaatgcagTGGTCTGATGAGCTGAAGAAGCTAGATTTTCAAGAAATGGTAATGTTCCTGCAACACCTTCCGACACATAACTGGTCAGACCAAGAGCTCGAAATGGTTT
upper sequence: GLYMA11G13330.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv05s0094g00070.t01 (Vitis vinifera), 3'ss of exon 9
aatttatgtatagttgcttagg---ttatttacacggtcttgttgcttttggcaatgcttaatttagtaggaactgaattttctttttactttttccctttagTGGTCAGACAAGCTCCAGAAACTTCATTTCCAAGAATTGGTAATGTTCCTTCAACACCTTCCAACAGAGAACTGGACTCACCGGGAGCTTGAGATGGTGC
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tgtttgtgttttttttccttgagatttctttgcacaat-tagaagct--agattaagcatgaaacacttaaccatgtgtacactgttttttgtttgttttcagTGGTCGGATACGCTTCAGAAGCTTGATTTCCAAGAGCTGGTAATGTTCCTTCAACACCTTCCAACTCATAACTGGACTCACCAAGAGCTCGAGATGGTGCMapped 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|192328709|gb|FK022523.1|FK022523EST: CTGCCTTACCAGACTTCCTAGTATATATATTTGCCAGCTTCCTTCTAGCG TGGTCAGACAAGCTCCAGAAACTTCATTTCCAAGAATTGGTAATGT
genomic: ATGCCTTACCAGACTTCCTAGTATATATATTTGCCAGCTTCCTTCTAACGgtgagctaac ... ttccctttagTGGTCAGACAAGCTCCAGAAACTTCATTTCCAAGAATTGGTAATGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttggcaatgcttaatttagtaggaactgaattttctttttactttttccctttagTGGTCAGACAAGCTCCAGAAACTTCATTTCCAAGAATTGGTAATGTTCCTTCAACACCTTCCAACAGAGAACTGGACTCACCGGGAGCTTGAGATGGTGC
gcttaat putative branch site (score: 4)
ctgaattttcttttta putative PPT
tgaattttctttttac 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatttatgtatagttgcttaggttatttacacggtcttgttgcttttggcaatgcttaatttagtaggaactgaattttctttttactttttccctttagTGGTCAGACAAGCTCCAGAAACTTCATTTCCAAGAATTGGTAATGTTCCTTCAACACCTTCCAACAGAGAACTGGACTCACCGGGAGCTTGAGATGGTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - gttgctt
- - - - - - - - - - - - - ttacacg
- - - - - - - - - - - - - - - - - - -tgttgct
- - - - - - - - - - - - - - - - - - - - - - - - -caatgct