Sequence
atgc intronic sequence ATGC exonic sequenceTGAAGCACACATGATAAAATCTCCCAAAAGTTTAATATCCCTCGCTGCTGCTGCTCTTACGGCTGATCGGCGTTGGTGTCTTACTGGTACACCTATTCAGgtgaatacaggagtagatttgactgtccatataattgaaccaatcctatttaaccctagttttcataagaatgttgcagcagataaatagaatgtgcactcctagttttcctgcatctatcagcctcttaggtgcttatgcattcaatgttttttacgagttttactctgatggcag
Basic information
species | Oryza sativa |
transcript | LOC_Os02g32570.2 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g32570.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G015190_T01 (Zea mays), 5'ss of exon 10
TGAAGCACACATGATAAAATCTCCCAAAAGTTTAATATCCCTCGCTGCTGCTGCTCTTACGGCTGATCGGCGTTGGTGTCTTACTGGTACACCTATTCAGgtgaatacaggagtagatttgactgtccatataa-------ttgaaccaatcctatttaaccctagttttcataagaatgttgcagcagataaatagaatgtgcactcctagttttcctgcatctatcagcctcttaggtgcttatgcattcaatgttttttacgagttttactctgatggcag
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CGAAGCACACATGATAAAATCTTCTAAAAGTTTGATATCCCTAGCTGCGGCTGCTCTGACTGCAGATCGGCGCTGGTGTCTCACTGGTACACCAATTCAGgtgagaatatgtgtagatctatcggtctttgttagaattccctgaacatatcatgtttatccctaatgc-----aggattatggagccgacattt--------tactcttatttttcacgcatgtatttgcgtactaggtgcttatgcattcaaa----tttatgaagtttactttactcacag
upper sequence: LOC_Os02g32570.2 (Oryza sativa), 5'ss of exon 3
lower sequence: AT5G22750.1 (Arabidopsis thaliana), 5'ss of exon 10
TGAAGCACACATGATAAAATCTCCCAAAAGTTTAATATCCCTCGCTGCTGCTGCTCTTACGGCTGATCGGCGTTGGTGTCTTACTGGTACACCTATTCAGgtgaatacaggagtagatttgactgtccatataattgaaccaatcctatttaaccctagttttcataagaatgttgcagcagataaatagaatgtgcactcctagttttcctgcatctatcagcctcttaggtgcttatgcattcaatgttttttacgagttttactctgatggcag
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CGAGGCACATACCATCAAAAACTCAAAAAGCCAAATTTCCTTGGCTGCTGCAGCTCTGGTTGCTGATAGGCGTTGGTGTCTTACGGGTACTCCTATTCAGgtgatt---------ggtctttttgtctagggtttagaaagaa--------aatctttgttct--tgaccgtcctatagaccaaactttattaggacactgccattctatctatggaag----------------------------------------------------------
upper sequence: LOC_Os02g32570.2 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv06s0061g01190.t01 (Vitis vinifera), 5'ss of exon 10
TGAAGCACACATGATAAAATCTCCCAAAAGTTTAATATCCCTCGCTGCTGCTGCTCTTACGGCTGATCGGCGTTGGTGTCTTACTGGTACACCTATTCAGgtgaatacaggagtagatttgactgtccatataattgaaccaatcctatt-taaccctagttttcataagaatgt-tgcagcagataaatagaatgtgcactcctagttttcctgcatctatcagcctcttaggtgcttatgcattcaatgttttttacgagttttactctgatggcag
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TGAGGCGCATACTATAAAATCCTCTAAAAGCCAAATTTCTATGGCGGCGGCTGCACTAATTGCTGATCGCCGATGGTGTCTTACTGGTACTCCTATCCAGgtgagtttagtggaaaatttttgtgatgccatccttacgtttaaatgattgtcccttttgttttcttctggacaaattttttaggtaagtt--ttttggatt-----------------------------------------------------------------------------
upper sequence: LOC_Os02g32570.2 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S41_174V6.1 (Physcomitrella patens), 5'ss of exon 10
TGAAGCACACATGATAAAA---TCTCCCAAAAGTTTAATATCCCTCGCTGCTGCTGCTCTTACGGCTGATCGGCGTTGGTGTCTTACTGGTACACCTATTCAGgtgaatacaggagtagatttgactgtccatataattgaaccaatcctatttaaccctagttttcataagaatgttgcagcagataaatagaatgtgcactcctagttttcctgcatctatcagcctcttaggtgcttatgcattcaatgttttttacgagttttactctgatggcag
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TGAGGCTCACACCATCAAAGCATTTCGCACAAGT---ACATCTAAAGCAGTTTTTATGCTGACTGCCGACCGACGGTGGTGTCTTACTGGAACACCTATTCAGgtgaattcgg-------cctctttgt---tgtatgtaaaacatcttggtttcatgtcgat--------agatgtttctg----tgttcgaagcgttgttcccatgtactcttgtctttattt-------------------------------------------------------Mapped 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|66917088|gb|CX103936.1|CX103936EST: TTGCTCTTACGGCTGATCGGCGTTGGTGTCTTACTGGTACACCTATTCAG AACAACTTGGAGGATATATACAGCCTTTTCCGGTTTTTGAGGGTTGAACCG
genomic: CTGCTCTTACGGCTGATCGGCGTTGGTGTCTTACTGGTACACCTATTCAGgtgaatacag ... ctgatggcagAACAACTTGGAGGATATATACAGCCTTTTCCGGTTTTTGAGGGTTGAACCG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGAAGCACACATGATAAAATCTCCCAAAAGTTTAATATCCCTCGCTGCTGCTGCTCTTACGGCTGATCGGCGTTGGTGTCTTACTGGTACACCTATTCAGgtgaatacaggagtagatttgactgtccatataattgaaccaatcctatttaaccctagttttcataagaatgttgcagcagataaatagaatgtgcactcctagttttcctgcatctatcagcctcttaggtgcttatgcattcaatgttttttacgagttttactctgatggcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT