Sequence
atgc intronic sequence ATGC exonic sequencegtgtgtaaacttgcctgaactcgtaattgtcttgtcagtactactatgaatgcagtattctaacttttgagttacaacaaaactttaaagATTGCAGGATCAGATGAAGAAAACTATCCACTGACCAGACAAGTGCAGAGAGATGTATGGATTCATCAACATCCTCCAAACTGCAGTGATCCAAGCTTGA
Basic information
species | Oryza sativa |
transcript | LOC_Os02g56500.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g56500.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA20G36630.2 (Glycine max), 3'ss of exon 4
gtgtgtaaacttgcct-gaactcgtaattg-tcttgtcagtact----actatgaa------tgcagtattctaacttttgagttacaacaaaactttaa-agATTGCAGGATCAGATGAAGAAAACTATCCACTGACCAGACAAGTGCAGAGAGATGTATGGATTCATCAACATCCTCCAAACTGCAGTGATCCAAGCTTGA
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--ttgtgaacttctttagaacataaaaatgatatttacaatgttcatgattaaaaaagaagctggaatgttgcaaggttt-attgatatagaagcttttgcagATTGCAGGGTCCGATGAAGAAAACTATCCCTTGACTAGAAAAGTTCAGCGTGACATATGGATGCATCAGCATCCTTTGAACTGCAGCAGCCCGGATGTCA
upper sequence: LOC_Os02g56500.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA20G36630.1 (Glycine max), 3'ss of exon 3
--------gtgtgtaaacttgcctgaactcgtaattgtcttgtcagtactactatgaatgcagtattctaacttttgagttacaacaaaactttaa-agATTGCAGGATCAGATGAAGAAAACTATCCACTGACCAGACAAGTGCAGAGAGATGTATGGATTCATCAACATCCTCCAAACTGCAGTGATCCAAGCTTGA-------
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cttctttagaacataaaaatg---atatttacaatgttcatg--attaaaaaagaagctggaatgttgcaaggttt-attgatatagaagcttttgcagattgcagGGTCCGATGAAGAAAACTATCCCTTGACTAGAAAAGTTCAGCGTGACATATGGATGCATCAGCATCCTTTGAACTGCAGCAGCCCGGATGTCAAGTTCCT
upper sequence: LOC_Os02g56500.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA10G30840.1 (Glycine max), 3'ss of exon 3
gtgtgtaaacttgcct-gaactcgtaattgtcttgt-cagtact----acta------tgaatgcagtattctaacttttgagttacaacaaaac-tttaaagATTGCAGGATCAGATGAAGAAAACTATCCACTGACCAGACAAGTGCAGAGAGATGTATGGATTCATCAACATCCTCCAAACTGCAGTGATCCAAGCTTGA
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--ttgtgaacttctttagaacataaaaatgacatttacaatgttcatgattaaagaattagatggaatgttgtgaagttt-attcacatagaagcatttgcagATTGCAGGGTCCGATGAAGAAAACTATCCCTTGACTAGAAAAGTGCAGCGTGACATATGGATCCATCAGCATCCTTTAAACTGTAGTAGCCCGGATGTCAMapped 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|25806441|gb|CA762402.1|CA762402EST: TGTTTTTCAGGTCAAATGCTAAATCTGACAGGGCGCCATATCCACCTTGG ATTGCAGGATCAGATGAAGAAAACTATCCACTGACCAGACAAGTGCAGAGA
genomic: TGTTTTTCAGGTCAAATGCTAAATCTGACAGGGCGCCATATCCACCTTGGgtgtgtaaac ... aactttaaagATTGCAGGATCAGATGAAGAAAACTATCCACTGACCAGACAAGTGCAGAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagtactactatgaatgcagtattctaacttttgagttacaacaaaactttaaagATTGCAGGATCAGATGAAGAAAACTATCCACTGACCAGACAAGTGCAGAGAGATGTATGGATTCATCAACATCCTCCAAACTGCAGTGATCCAAGCTTGA
ttctaac putative branch site (score: 1)
aacaaaactttaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgtaaacttgcctgaactcgtaattgtcttgtcagtactactatgaatgcagtattctaacttttgagttacaacaaaactttaaagATTGCAGGATCAGATGAAGAAAACTATCCACTGACCAGACAAGTGCAGAGAGATGTATGGATTCATCAACATCCTCCAAACTGCAGTGATCCAAGCTTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT