Sequence
atgc intronic sequence ATGC exonic sequence...ttccatatttacatttattttggaatttctttcttatgaagaatattatccatatgtatattttgtttcaagattataattcttatttattattatgaagGTGTCTGAAGCTTCTGTCAGCAGAAACCGTAGCACTATAATTGTTCCGGCTGGAAGCTCCAGGGATGAAGGATGGGCAGCATTCAGGAACATTTTGGCAG
Basic information
species | Glycine max |
transcript | GLYMA20G03020.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G03020.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g15600.1 (Oryza sativa), 3'ss of exon 2
---------ttccatatttacatttattttggaatttctttcttatgaagaatattatccatatgtatattttgtttcaagattataattcttatttattattatgaagGTGTCTGAAGCTTCTGTCAGCAGAAACCGTAGCACTATAATTGTTCCGGCTGGAAGCTCCAGGGATGAAGGATGGGCAGCATTCAGGAACATTTTGGCAG
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ctaggcgaatttta-attaagaataatttcagaaaactacacatactttgatcagtcttgacataactatttatatt-----ttatcatccaacttttttcttc---agGTATCAGAGGCATCTGTCAACAGAAACCGTAGTACAATCATTGTTCCGGCTGGTAGTTCTGGTGAAGAAGGTTGGGAAGCATTCAGGAATGTATTGTTGG
upper sequence: GLYMA20G03020.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G049429_T01 (Zea mays), 3'ss of exon 2
ttccatatttacatttattttggaatttctttcttatgaagaatattatccatatgtatattttgtttcaagattataattcttatttattattatgaagGTGTCTGAAGCTTCTGTCAGCAGAAACCGTAGCACTATAATTGTTCCGGCTGGAAGCTCCAGGGATGAAGGATGGGCAGCATTCAGGAACATTTTGGCAG
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taatcttatagccctcgtctcctccctcctctccacctcggcatatagtttacaaacagccctttattgtagttgctcttacacaacattttgtatgtagGTTTCTGAGGCCTCTGTCAACAGAAACCGGAGTACCATAATTGTTCCAGCTGGCAGCTCTGGTGAAGAGGGCTGGGAAGCATTCAGAAATGTACTGTTGG
upper sequence: GLYMA20G03020.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G32080.1 (Arabidopsis thaliana), 3'ss of exon 2
----------------------------------------------------------------------------ttccatatttacatttat-----tttggaatttctttcttatgaagaatattatccatatgtatattttgtttcaagattataattctta--tttattattatga-agGTGTCTGAAGCTTCTGTCAGCAGAAACCGTAGCACTATAATTGTTCCGGCTGGAAGCTCCAGGGATGAAGGATGGGCAGCATTCAGGAACATTTTGGCAG
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gtagaaatttttctgttttacttaatgaatctgaagttttttttctttggtatatgtgaattgaagatttagggagtactagacttatggttaggaatgttcttttcattttggttatgtgactaattatcctgaggtatcagaagttgtaggaatgttctgatgggttttggtgtggtgttagGTGTCAGAAGCATCGGTTAGTAGAAATCGAAGTACCATTATTGTTCCAGCTGGAAGCTCTCCTGATGAAGGATGGGCAGCTTTCAGGAATATATTGGCTG
upper sequence: GLYMA20G03020.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0004g00040.t01 (Vitis vinifera), 3'ss of exon 1
ttccatatttacatttattttggaatttctttcttatgaagaatat-tatccatatgtatat--tttgtttcaaga----ttataattcttatttatt--attatgaagGTGTCTGAAGCTTCTGTCAGCAGAAACCGTAGCACTATAATTGTTCCGGCTGGAAGCTCCAGGGATGAAGGATGGGCAGCATTCAGGAACATTTTGGCAG
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---------ttcatgacttccaaaattgtgatatgagaaggcaggtctagtggtttgaatataatctggttcttgaagcttttttggtctaatggagtgaagtctgcagGTATCTGAAGCTTCTGTTAGCAGAAATAGGAGTACCATTATTGTTCCTGCAGGAAGCACTCGAGATGAAGGGTGGGCAGCATTCAGGAACATCTTGGCAGMapped 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|14991853|gb|BI317526.1|BI317526EST: GTTTTCTATTTTGACATTGGCGAGAATCGGAGGGGCCGTTTTTTGAAG GTGTCTGAAGCTTCTGTCAGCAGAAACCGTAGCACTATAATTGTTCCGGCT
genomic: GTTTTCTATTTTGACATTGGCGAGAATCGGAGGGGCCGTTTTTTGAAGgtacttggct ... tattatgaagGTGTCTGAAGCTTCTGTCAGCAGAAACCGTAGCACTATAATTGTTCCGGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatccatatgtatattttgtttcaagattataattcttatttattattatgaagGTGTCTGAAGCTTCTGTCAGCAGAAACCGTAGCACTATAATTGTTCCGGCTGGAAGCTCCAGGGATGAAGGATGGGCAGCATTCAGGAACATTTTGGCAG
tatattttgtttcaag 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttccatatttacatttattttggaatttctttcttatgaagaatattatccatatgtatattttgtttcaagattataattcttatttattattatgaagGTGTCTGAAGCTTCTGTCAGCAGAAACCGTAGCACTATAATTGTTCCGGCTGGAAGCTCCAGGGATGAAGGATGGGCAGCATTCAGGAACATTTTGGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - tatgaag
- - - - - - - - - - - - - - - - - - - - - - - - -ccatatg