Sequence
atgc intronic sequence ATGC exonic sequenceCGTCGCGGCCGAGACCGCCGCGGCGCTCGCCGCCGCCTCGCTCGTCTTCCGCAAGTCCGACCCGGCCTACGCCAGCCGCCTCGTCGCCAGGGCCAAGAGGgtccgtgctcttctcgaccactcaatgctgctctcttgctgtgtcaccaatactctgttctccttctcccctgcttctttggttgctctgtttttgacatcctctgtttcgggattgtgtag
Basic information
species | Oryza sativa |
transcript | LOC_Os01g21070.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g21070.1 (Oryza sativa), 5'ss of exon 3
lower sequence: EFJ23913 (Selaginella moellendorffii), 5'ss of exon 2
------CGTCGCGGCCGAGACCGCCGCGGCGCTCGCCGCCGCCTCGCTCGTCTTCCGCAAGTCCGACCCGGCCTACGCCAGC-CGCCTCGTCGCCAGGGCCAAGAGGgtccgtgctcttctcgaccactcaatgctgctctcttgctgtgtcaccaatactctgttctccttctcccctgcttctttggtt--gctctgtttttgacatcctctgtttcgggattgtgtag-
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GGACATGGACACGCCCCGGAACGCCTACAAGATCGATCAATCCGCGCCCGGAT-CCGACGTCGCGGCGGAGACAGCCGCAGCGCTCGCCGCCGCCTCGATCgtcttccagtacgcgaagccggagtactcg-cgccaattgctcaacgcgtc-caaacaggcaagaaccctaaaaagcagagcccctgctttcgcgctaagtttaaaattttaaaattcggggcccttttag
upper sequence: LOC_Os01g21070.1 (Oryza sativa), 5'ss of exon 3
lower sequence: EFJ16113 (Selaginella moellendorffii), 5'ss of exon 2
CGTCGCGGCCGAGACCGCCGCGGCGCTCGCCGCCGCCTCGCTCGTCTTCCGCAAGTCCGACCCGGCCTACGCCAGCCGCCTCGTCGCCAGGGCCAAGAGGgtccgtgctcttctcgaccactcaatgctgctctcttgctgtgtcaccaatactctgttctccttctcccctgcttctttggttgctctgtttttgacatcctctgtttcgggattgtgtag
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CGTCGCGGGAGAGACCGCCGCCGCCCTCGCCGCCGCCTCCATCGTCTTCGCCGCCACCGATTCTTCCTACTCCCAGAGGCTCCTCGCCACTTCCAAGCAAgtaagtgatcga-tcgagcacccag----actttcatcgtttgg-ataggtggactttgctctaacttggct-tctctttgatcgtgatatag-----------------------------
upper sequence: LOC_Os01g21070.1 (Oryza sativa), 5'ss of exon 3
lower sequence: EFJ21535 (Selaginella moellendorffii), 5'ss of exon 2
------CGTCGCGGCCGAGACCGCCGCGGCGCTCGCCGCCGCCTCGCTCGTCTTCCGCAAGTCCGACCCGGCCTACGCCAGC-CGCCTCGTCGCCAGGGCCAAGAGGgtccgtgctcttctcgaccactcaatgctgctctcttgctgtgtcaccaatactctgttctccttctcccctgcttctttggtt--gctctgtttttgacatcctctgtttcgggattgtgtag-
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GGACATGGACACGCCCCGGAACGCCTACAAGATCGATCAATCCGCGCCCGGAT-CCGACGTCGCGGCGGAGACAGCCGCAGCGCTCGCCGCCGCCTCGATCgtcttccagtacgcgaagccggagtactcg-cgccaattgctcaacgcgtc-caaacaggcaagaaccctaaaaagcagagcccctgctttcgcgctaagtttaaaattttaaaattcgggacccttttagMapped 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|58654811|gb|CK043491.1|CK043491EST: GCAAGTCCGACCCGGCCTACGCCAGCCGCCTCGTCGCCAGGGCCAAGAGG GTGTGGGAGTTCGCGGACAAGCACAGGGGCACGTACAGCACCCGTCTCTCG
genomic: GCAAGTCCGACCCGGCCTACGCCAGCCGCCTCGTCGCCAGGGCCAAGAGGgtccgtgctc ... gattgtgtagGTGTTTGAGTTCGCGGACAAGCACAGGGGCACGTACAGCACCCGTCTCTCG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CGTCGCGGCCGAGACCGCCGCGGCGCTCGCCGCCGCCTCGCTCGTCTTCCGCAAGTCCGACCCGGCCTACGCCAGCCGCCTCGTCGCCAGGGCCAAGAGGgtccgtgctcttctcgaccactcaatgctgctctcttgctgtgtcaccaatactctgttctccttctcccctgcttctttggttgctctgtttttgacatcctctgtttcgggattgtgtag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG