Sequence
atgc intronic sequence ATGC exonic sequencegtaagtgttccttgtctttctttacgaatctgtgtgcaagccttttcttaatctgatgaaaaacaccagaagttgattatattgtgtggttaaaaccccctttttctgcagAAGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGCCTAAAGAATGTCCAGTGTGCTCACAGTATTTTAAG
Basic information
species | Glycine max |
transcript | GLYMA15G01360.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G01360.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g05080.1 (Oryza sativa), 3'ss of exon 4
-----------------gtaagtgttccttgtcttt----ctttacgaatct----gtgtgcaagccttttcttaatctg----atgaa------------aaacacca--gaagttga-ttatattgtgtggttaaaaccccctttttctgcagAAGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGCCTAAAGAATGTCCAGTGTGCTCACAGTATTTTAAG
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gtatagtacctgtgcatgctaat-ttccttgtttttgacctataaagaagcttctaggatgaaatcttctcctgcatcttctctataaatattcatcgactaaccaccaatggaattaacttaaactgca-aattgcaatgattgatattttcagAGGACGAGCATGATGTCGTGTGGTTTTGGTTGGAGAAAGGCAAGCCACATGAATGCCCTGTCTGCACTCAGTATTTCTCG
upper sequence: GLYMA15G01360.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv09s0002g06000.t01 (Vitis vinifera), 3'ss of exon 4
--------------------gtaagtgttccttgtctttc-tttacgaatctgtgtgcaagccttt--tcttaatctgatgaaaaacaccagaagtt-gattatattgtg--tggttaaaaccccctttttctgcagAAGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGCCTAAAGAATGTCCAGTGTGCTCACAGTATTTTAAG
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gtaagcctctgtcacttactctctttaattattattttccatttatttatttct-tacaattaattaatttgcatcccattaaattctttctaattttggttgctctgttatttatttatttgtttttcgtctgcagAGGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGTCACATGAATGCCCTGTGTGCTCACAGTATTTCACGMapped 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|6071202|gb|AW100589.1|AW100589EST: CAGAAGGATAGTTGGATGCCCAGGAGATGAAGGCG AAGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGCCTAAAG
genomic: CAGAAGGATAGTTGGATGCCCAGGAGATGAAGGCGgtaagtgttc ... ttttctgcagAAGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGCCTAAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaaaaacaccagaagttgattatattgtgtggttaaaaccccctttttctgcagAAGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGCCTAAAGAATGTCCAGTGTGCTCACAGTATTTTAAG
agttgat putative branch site (score: 5)
ccccctttttctgc putative PPT
aagttgattatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtgttccttgtctttctttacgaatctgtgtgcaagccttttcttaatctgatgaaaaacaccagaagttgattatattgtgtggttaaaaccccctttttctgcagAAGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGCCTAAAGAATGTCCAGTGTGCTCACAGTATTTTAAG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA