Sequence
atgc intronic sequence ATGC exonic sequencegtacgtgcttcctaaactgttaccattatttagtttcccaaatttatattttactctatttattatgccaatagaaatagatacactatactcactgcaaagtgcaatgataggcttcttcatgcattcatctatcctaatttaaccttgttggttttatcgaatcattttgatatttcagATGGGGCTAATGAGGAAACATCCTTCTATAATACCTTTTATGATCTACATATCCGATGAGGGCAAGCACACCGAGAGGTTTGCCGTACGTGCAAAGTACA
Basic information
species | Oryza sativa |
transcript | LOC_Os09g39870.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g39870.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G048553_T02 (Zea mays), 3'ss of exon 4
gtacgtgcttcctaaactgttaccattatttagtttcccaaatttatattttactctatttattatgccaatagaaatagatacactatactcactgcaaagtgcaatgataggcttcttcatgcattcatctatcctaatttaaccttgttggttttatcgaatcattttgat-atttcagATGGGGCTAATGAGGAAACATCCTTCTATAATACCTTTTATGATCTACATATCCGATGAGGGCAAGCACACCGAGAGGTTTGCCGTACGTGCAAAGTACA
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------------------------------------------------------------------------------agagccactatattgcatttgttttgctaataaaggtggagttgtaactttcattgtttacat---gcccactttattcca-catttcgttttaattatttcagATGGGTCTAATGAGGAAACATCCTTCGATAATACCTTTCATGATCTACATATCTAATGAGAGTAAGCACACAGAGAGGTTTGCTGTACGTGCGAAGTACA
upper sequence: LOC_Os09g39870.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G017334_T01 (Zea mays), 3'ss of exon 4
gtacgtgcttcctaaactgttaccattatttagtttcccaaatttatattttactctatttattatgccaa-tagaaatagatacactatact----cactgcaaagtgcaatgataggcttcttcatgcattcatctatcctaatttaaccttgttggttttatcgaatcattttgatatttcagATGGGGCTAATGAGGAAACATCCTTCTATAATACCTTTTATGATCTACATATCCGATGAGGGCAAGCACACCGAGAGGTTTGCCGTACGTGCAAAGTACA
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gtatgtgcttccagaaa----actattcatttgcatttctttcctatcattccagctattgattcttttaggtcgtatcagacccactatattgcatttcttctgctaatagaagtggagttgttagttgtaacattcattgttaacttgcccaaattattctacatttccttttaattattccagATGGGTCTAATGAGGAAACATCCTTCGATCATACCTTTCATGATCTACATCTCTAATGAGGGTAAGCACACAGAGAGGTTTGCTGTACGTGCAAAGTACA
upper sequence: LOC_Os09g39870.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA11G20130.1 (Glycine max), 3'ss of exon 4
gtacgtgcttcctaaactgttaccattatttagtttcccaaatttatattttactctatttattatgccaatagaaatagatacactatactcactgcaaagtgcaatgataggcttcttcatgcattcatctatcctaatttaaccttgttggttttatcgaatcattttgatattt---cagATGGGGCTAATGAGGAAACATCCTTCTATAATACCTTTTATGATCTACATATCCGATGAGGGCAAGCACACCGAGAGGTTTGCCGTACGTGCAAAGTACA
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------------------------------------------------------------------------------gtatgtttgattttcattattgtgtccttcactatttcttttcttatggatatcaattt--attt--tctcattagatagcaataaaaacttgaatactcatgcagATGGGGCTCATGAAGAAACATCCTTCAATTATACCATTTATGATACACATTACAAATGAGGATAAACACTTGGAAAGATTTGCTGTACGTGCAAAGTATA
upper sequence: LOC_Os09g39870.2 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv08s0040g01610.t01 (Vitis vinifera), 3'ss of exon 4
gtacgtgcttcctaaactgttaccattatttagtttcccaaatttatattttactctatttattatgccaatagaaatagatacactatactcactgcaaagtgcaatgataggcttcttcatgcattcatctatcctaatttaaccttgttggttttatcgaatcattttgatatttcagATGGGGCTAATGAGGAAACATCCTTCTATAATACCTTTTATGATCTACATATCCGATGAGGGCAAGCACACCGAGAGGTTTGCCGTACGTGCAAAGTACA
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------------------------------------------------------------ccttttatttataagatcttctaaactatgcaca----aaaagagaatatt----tttcttgtaaattgcttagtgatactaaaa-------ggttct------ttgttttgatttatcagATGGGCCTAATGAGAAAACATCCTTCAATCATACCATTCATGATTTACATCTCAAATGAAGACAAACATTTGGAACGATTTGCAGTTCGTGCAAAATACAMapped 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|2312028|gb|C28183.1|C28183EST: GCAAGGAATCAGTTGTTGTTGAGGGTGTTCACCTAAGCCTTAATTTTGTG ATGGGGCTAATGAGGGAAACATCCTTCTATAATACCTTTTATGATCTACAT
genomic: GCAAGGAATCAGTTGTTGTTGAGGGTGTTCACCTAAGCCTTAATTTTGTGgtacgtgctt ... gatatttcagATGGGGCTAATGAGG-AAACATCCTTCTATAATACCTTTTATGATCTACAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcatctatcctaatttaaccttgttggttttatcgaatcattttgatatttcagATGGGGCTAATGAGGAAACATCCTTCTATAATACCTTTTATGATCTACATATCCGATGAGGGCAAGCACACCGAGAGGTTTGCCGTACGTGCAAAGTACA
aatcattttgatattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgtgcttcctaaactgttaccattatttagtttcccaaatttatattttactctatttattatgccaatagaaatagatacactatactcactgcaaagtgcaatgataggcttcttcatgcattcatctatcctaatttaaccttgttggttttatcgaatcattttgatatttcagATGGGGCTAATGAGGAAACATCCTTCTATAATACCTTTTATGATCTACATATCCGATGAGGGCAAGCACACCGAGAGGTTTGCCGTACGTGCAAAGTACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG