Sequence
atgc intronic sequence ATGC exonic sequencegtgaacctcaacctccctgcctcccccagcattttcagatttcagctttccttcctttgattaggtgttttttgtttttgttttttctgtgtaggagCCCACGGAGCCACCGGAGTGGAAGGAGGTGTTCGAGGATCCCCTGCTGCCACTCATGGTCGACATTGGCTGCG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g35170.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g35170.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G054378_T02 (Zea mays), 3'ss of exon 1
-------------------------------------gtgaacctcaacctccctgcc---tcccccagcattttcagatttcagctttccttcctttgattaggtgttttttgtttttgttttttctgtgtaggagCCCACGGAGCCACCGGAGTGGAAGGAGGTGTTCGAGGATCCCCTGCTGCCACTCATGGTCGACATTGGCTGCG
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gtagcacgtgaacccgctcagctcatccttctcggtaaagcactcctaattcctcacccattttttcaagattaccaagcgagcacagtcactcgtattttccgttaatttgtgctctgttttgcggtgcgtagGAGCCCACGGGGCCGCCAGAGTGGAAGGAGGTGTTCGACGACCCCTTGCTTCCCCTCATGGTCGACATCGGCTGCG
upper sequence: LOC_Os01g35170.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G054378_T03 (Zea mays), 3'ss of exon 2
---gtgaacctcaacctccctgcc---tcccccagcattttcagatttcagctttccttcctttgattaggtgttttttgtttttgttttttctgtgtaggagCCCACGGAGCCACCGGAGTGGAAGGAGGTGTTCGAGGATCCCCTGCTGCCACTCATGGTCGACATTGGCTGCG
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gtaaagcactcctaattcctcacccattttttcaagattaccaagcgagcacagtcactcgtattttccgttaatttgtgctctgttttgcggtgcgtagGAGCCCACGGGGCCGCCAGAGTGGAAGGAGGTGTTCGACGACCCCTTGCTTCCCCTCATGGTCGACATCGGCTGCG
upper sequence: LOC_Os01g35170.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G154087_T02 (Zea mays), 3'ss of exon 2
---gtgaacctcaacctccctgcc---tcccccagcattttcagatttcagctttccttcctttgattaggtgttttttgtttttgttttttctgtgtaggagCCCACGGAGCCACCGGAGTGGAAGGAGGTGTTCGAGGATCCCCTGCTGCCACTCATGGTCGACATTGGCTGCG
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gtaaagcactcctaactcctcacccatttttttaatattgccaagcgagcacaggcactcgtattttcagttaatttgtgctctgttttgcggtgcgtagGAGCCCACGGGGCCGCCAGAGTGGAAGGAGGTGTTCGACGACCCCTTGCTTCCCCTCATGGTCGACATCGGCTGCGMapped 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|58693195|gb|CK081882.1|CK081882EST: ATCACCTGCGCATCCGGCAGCACGTCAACCCGCTCAGCTCCTCTTTCTCGGAG
genomic: ATCACCTGCGCATCCGGCAGCACGTCAACCCGCTCAGCTCCTCTTTCTC---Ggtgaacctca ... tgtgtagg
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagctttccttcctttgattaggtgttttttgtttttgttttttctgtgtaggagCCCACGGAGCCACCGGAGTGGAAGGAGGTGTTCGAGGATCCCCTGCTGCCACTCATGGTCGACATTGGCTGCG
ctttgat putative branch site (score: 5)
tgttttttgtttttgt putative PPT
tgttttttgtttttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaacctcaacctccctgcctcccccagcattttcagatttcagctttccttcctttgattaggtgttttttgtttttgttttttctgtgtaggagCCCACGGAGCCACCGGAGTGGAAGGAGGTGTTCGAGGATCCCCTGCTGCCACTCATGGTCGACATTGGCTGCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC