Sequence
atgc intronic sequence ATGC exonic sequence...tagtgcacgcatcagatcaactggcatatggattagactaaacttaatatggattatctaaaaatttactatttttgtgttctcttatgccactgaccagTGGTTCGAAGTTCTTGATGGGCTCTTGGGCCCGTACTGGAAGGCGGCCGGCCTCGCCTTCAACTGCACCTTCCTGCTCTTCGGCTCCGTCATCCAGCTGA
Basic information
species | Oryza sativa |
transcript | LOC_Os05g37470.3 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g37470.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G067022_T02 (Zea mays), 3'ss of exon 2
tagtgcacgcatcagatcaactggcatatggattagactaaacttaatatggatt---atctaaaaatttact-atttttgtgttctcttatgccactgaccagTGGTTCGAAGTTCTTGATGGGCTCTTGGGCCCGTACTGGAAGGCGGCCGGCCTCGCCTTCAACTGCACCTTCCTGCTCTTCGGCTCCGTCATCCAGCTGA
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ggatacggagagggagtctgctggagt-tggtctaagt--agtgcagcaggaattcaaatacccagctgaactgaacaatatgaattaac-tgccgttggccagTGGTTCGAAGTTCTGGACGGGCTCCTGGGCCCGTACTGGAAGGCGGCCGGGCTGGCGTTCAACTGCACGTTCCTGCTCTTCGGCACGGTCATCCAGCTGA
upper sequence: LOC_Os05g37470.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT5G01240.2 (Arabidopsis thaliana), 3'ss of exon 1
------tagtgcacgcatcagatcaactggcatat--ggattaga-ctaaacttaatatggattatctaaaaatttactatttttgtgttctcttatgccac-------------------tgaccagTGGTTCGAAGTTCTTGATGGGCTCTTGGGCCCGTACTGGAAGGCGGCCGGCCTCGCCTTCAACTGCACCTTCCTGCTCTTCGGCTCCGTCATCCAGCTGA
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gtaaattcttccttattttagtttag-tgacatattcgaatttgatctcacttttagatttactaaattgaattgcatgtttgttttgttttcttaacacaaaaaaaataaaataaaaaaatgggaagTGGTTTGAAGTGCTTGATGGGCTGCTGGGTCCGTACTGGAAAGCAGCGGGGCTCGCATTTAATTGCACCTTCTTGTTATTCGGATCAGTCATCCAGCTCA
upper sequence: LOC_Os05g37470.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ36050 (Selaginella moellendorffii), 3'ss of exon 2
-------------------------------------------------------------------------tagtgcacgcatcaga--tcaactggcatatggattagactaaacttaatatggattat---ctaaaaatttactatttttgt------gttctcttatgccactgaccagTGGTTCGAAGTTCTTGATGGGCTCTTGGGCCCGTACTGGAAGGCGGCCGGCCTCGCCTTCAACTGCACCTTCCTGCTCTTCGGCTCCGTCATCCAGCTGA
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gtagagttatgctaaagtttaaaacttttttctttcttttcttctcttctggctgtttgtgagaaggcttggagagtttagctgtagaactttgagagctccaagacttcttccaaagttcctgtagctagaacgtcgagagtttgttctcgctgctaaaagagtgatatttgttcttgac-agTGGTTCGAAGTTCTCGATGGTCTCTTGGGACCATACTGGAAGGCCGCTGGATTCACTTTTAACTGTACATTTCTTCTCTTTGGCTCGGTGATTCAGCTCA
upper sequence: LOC_Os05g37470.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ18760 (Selaginella moellendorffii), 3'ss of exon 2
----------------------------------------------------------------------------tagtgcacgcatcaga--tcaactggcatatggattagactaaacttaatatggatta---tctaaaaatttactatttttgt-----gttctcttatgccactgaccagTGGTTCGAAGTTCTTGATGGGCTCTTGGGCCCGTACTGGAAGGCGGCCGGCCTCGCCTTCAACTGCACCTTCCTGCTCTTCGGCTCCGTCATCCAGCTGA
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gtagagttatgctaaagtttaaaacttttttcttctttcttttcttctcttctggctgtttgtgagaaggcttggagagtttagctgtagaactttgagagctccaagacttcttccaaagttcctgtagctagaacttcgagagtttgttctcgctgctaaaagagtgatattttttcttgacagTGGTTCGAAGTTCTCGATGGTCTCTTGGGACCATACTGGAAGGCCGCTGGATTCACTTTTAACTGTACATTTCTTCTCTTTGGCTCGGTGATTCAGCTCAMapped 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|29638464|gb|CB643473.1|CB643473EST: GCGCCCGCAAGGAGAAGGAAGGCGTCAGCTTCAAGAACCACGTCATCCAG TGGTTCGAAGTTCTTGATGGGCTCTTGGGCCCGTACTGGAAGGCGGCCGGC
genomic: GCGCCCGCAAGGAGAAGGAAGGCGTCAGCTTCAAGAACCACGTCATCCAGgtcggcaggg ... cactgaccagTGGTTCGAAGTTCTTGATGGGCTCTTGGGCCCGTACTGGAAGGCGGCCGGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatatggattatctaaaaatttactatttttgtgttctcttatgccactgaccagTGGTTCGAAGTTCTTGATGGGCTCTTGGGCCCGTACTGGAAGGCGGCCGGCCTCGCCTTCAACTGCACCTTCCTGCTCTTCGGCTCCGTCATCCAGCTGA
atctaaa putative branch site (score: 3)
attatctaaaaattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tagtgcacgcatcagatcaactggcatatggattagactaaacttaatatggattatctaaaaatttactatttttgtgttctcttatgccactgaccagTGGTTCGAAGTTCTTGATGGGCTCTTGGGCCCGTACTGGAAGGCGGCCGGCCTCGCCTTCAACTGCACCTTCCTGCTCTTCGGCTCCGTCATCCAGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA