Sequence
atgc intronic sequence ATGC exonic sequence...cttgcaaagggttaaattggcagtgtgtaatgattttgtacttctagacttctagtaatttctgcactgtcatctctgatcttctttctttatgttaaagGTATGAGCCATATCTCTGGGAGAATGAGAGACAGTCTTACCTACGACATGCTGTTCTCTTTGGTTTCTTTGTACAACTCAACCGTATGTACACAGATACT
Basic information
species | Glycine max |
transcript | GLYMA20G32980.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G32980.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G16300.4 (Arabidopsis thaliana), 3'ss of exon 3
cttgcaaagggttaaattggcagtgtgtaatgattttgtacttctagacttctagtaattt--ctgcactgtcatct----------ctgatcttctttcttt--atgttaaa---gGTATGAGCCATATCTCTGGGAGAATGAGAGACAGTCTTACCTACGACATGCTGTTCTCTTTGGTTTCTTTGTACAACTCAACCGTATGTACACAGATACT
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---gtaagaaatcttatccctaatctttacctacgtcata--tattatcttttactattttggctgctctatcgtcttgttgtcactctgattctagtattttgaatatcaaaaaagGTACGAGCCTTATCTTTGGGAGAACGAAAAGCAGTCGTACCTACGCCATGCTGTACTCTTTGGTTTCTTTGTGCAACTAAACCGAAT-------------
upper sequence: GLYMA20G32980.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G16300.1 (Arabidopsis thaliana), 3'ss of exon 3
cttgcaaagggttaaattggcagtgtgtaatgattttgtacttctagacttctagtaattt--ctgcactgtcatct----------ctgatcttctttcttt--atgttaaa---gGTATGAGCCATATCTCTGGGAGAATGAGAGACAGTCTTACCTACGACATGCTGTTCTCTTTGGTTTCTTTGTACAACTCAACCGTATGTACACAGATACT
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---gtaagaaatcttatccctaatctttacctacgtcata--tattatcttttactattttggctgctctatcgtcttgttgtcactctgattctagtattttgaatatcaaaaaagGTACGAGCCTTATCTTTGGGAGAACGAAAAGCAGTCGTACCTACGCCATGCTGTACTCTTTGGTTTCTTTGTGCAACTAAACCGAATGTACACAGATACT
upper sequence: GLYMA20G32980.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv00s0340g00080.t01 (Vitis vinifera), 3'ss of exon 3
cttgcaaagggttaaattggcagtgtgtaatgattttgtacttctagacttctagtaatttctgcactgtcatctctgatcttctttctttatgttaaagGTATGAGCCATATCTCTGGGAGAATGAGAGACAGTCTTACCTACGACATGCTGTTCTCTTTGGTTTCTTTGTACAACTCAACCGTATGTACACAGATACT
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ttggtgtgtctgttttttttctttcttttctaaatcattcaaattaaatagtcattttttaatgtgatggtacatggtgatttatgttaataaatttcagGTATGAGCCTTACCTCTGGGAGAACGAGAGGCAAGCATACCTCCGGCATGCTGTACTTTTTGGATTCTTTGTGCAACTTAATCGGATGTATACCGATACTMapped 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|26045771|gb|CA783256.1|CA783256EST: CAATTGTTAAATCGTCTTTCTCAGAAACTGGATCCCATAGACTGGCTTAC GTATGAGCCATATCTCTGGGA
genomic: CAATTGTTAAATCGTCTTTCTCAGAAACTGGATCCCATAGACTGGCTTACgtaagtctca ... tatgttaaagGTATGAGCCATATCTCTGGGA
EST:
gi|14990829|gb|BI316502.1|BI316502EST: CAATTGTTAAATCGTCTTTCTCAGAAACTGGATCCCATAGACTGGCTTAC GTATGAGCCATATCTCTGGGAGAATGAGAGACAGTCTTACCTACGACATGC
genomic: CAATTGTTAAATCGTCTTTCTCAGAAACTGGATCCCATAGACTGGCTTACgtaagtctca ... tatgttaaagGTATGAGCCATATCTCTGGGAGAATGAGAGACAGTCTTACCTACGACATGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agacttctagtaatttctgcactgtcatctctgatcttctttctttatgttaaagGTATGAGCCATATCTCTGGGAGAATGAGAGACAGTCTTACCTACGACATGCTGTTCTCTTTGGTTTCTTTGTACAACTCAACCGTATGTACACAGATACT
ctctgat putative branch site (score: 4)
tcatctctgatcttct CT-rich tract
tttctttatgttaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttgcaaagggttaaattggcagtgtgtaatgattttgtacttctagacttctagtaatttctgcactgtcatctctgatcttctttctttatgttaaagGTATGAGCCATATCTCTGGGAGAATGAGAGACAGTCTTACCTACGACATGCTGTTCTCTTTGGTTTCTTTGTACAACTCAACCGTATGTACACAGATACT
cttgcaa
- - - - - - - - - - - gtgtgta
- - - - - - - - - - - - - - - - - - - - cttctag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcactg