Sequence
atgc intronic sequence ATGC exonic sequencegtgtataatctgaaaatagcacatcatgttgttatttatagtttcttatgtgaaaaaagtattactaaaatttgagattacatagGTTTTTGAAGGCAAGAAAGTTTGATGTGGAGAAGGCAAAGCAAATGTGGGTTGATATGCTGCAGTGGAGAAAGGAATTCGCTGCAGATACCATTCTTGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g24430.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g24430.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G162461_T01 (Zea mays), 3'ss of exon 3
gtgtataatctgaaaatagcacatcatgttgttatttatagtttcttatgtgaaaaaagtattactaaaatttgagattacatagGTTTTTGAAGGCAAGAAAGTTTGATGTGGAGAAGGCAAAGCAAATGTGGGTTGATATGCTGCAGTGGAGAAAGGAATTCGCTGCAGATACCATTCTTGAG
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gtatgtgat------atagtaaaggattgtatgatt-gcattttcatgtgtggtagcattgctg--aaagtttgggatcatgaagATTTCTCAAGGCAAGAAAGTTTGATATCGAGAAGGCAAAGCAAATGTGGTCTGATATGCTGAAGTGGAGAAAGGAGTTCGGTGCAGATACCATTCTCGAG
upper sequence: LOC_Os02g24430.2 (Oryza sativa), 3'ss of exon 3
lower sequence: AT4G39180.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgtataatctgaaaatagcacatcatgttgttatttatagtttcttatgtgaaaaaagtattactaaaatttgagattacatagGTTTTTGAAGGCAAGAAAGTTTGATGTGGAGAAGGCAAAGCAAATGTGGGTTGATATGCTGCAGTGGAGAAAGGAATTCGCTGCAGATACCATTCTTGAG
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-------------gttaggtccttcctcttgatcttttgattttcttcttctccattgctctgatcaa---tcgaaatatatcagGTTCTTGAGGGCAAGAAAGTTTGATCTCGAAAAGGCTAAGCAAATGTGGTCTGATATGCTTAACTGGAGGAAAGAATATGGCGCAGACACGATCATGGAG
upper sequence: LOC_Os02g24430.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv04s0023g02400.t01 (Vitis vinifera), 3'ss of exon 1
-------------------gtgtataatctgaaaatagcacatcatgttgttatttatagtttcttatgtgaaaaaagtattactaaaatttgagattacatagGTTTTTGAAGGCAAGAAAGTTTGATGTGGAGAAGGCAAAGCAAATGTGGGTTGATATGCTGCAGTGGAGAAAGGAATTCGCTGCAGATACCATTCTTGAG
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ggcaattctaatttctactgttcctcacccaactgcgg-agaccattattttatgcttcatttctt---taactagccttccaacgtactctttcgtaatccagATTTTTGAAGGCGAGGAAATTTGATCTTGAGAAAACAAAACAAATGTGGATTGATATGCTTCAATGGAGGAAGGACTTCGGTGCTGACACAATTATGGAG
upper sequence: LOC_Os02g24430.2 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ28804 (Selaginella moellendorffii), 3'ss of exon 1
gtgtataatctgaaaatagcacatcatgttgttatttatagtttcttatgtgaaaaaagtattactaaaa-tttgagattacatagGTTTTTGAAGGCAAGAAAGTTTGATGTGGAGAAGGCAAAGCAAATGTGGGTTGATATGCTGCAGTGGAGAAAGGAATTCGCTGCAGATACCATTCTTGAG
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-----------------------------------gta-agccaagcatcgccggcaagtgctgttaaaaatctctccctgtgtagATTTTTGAAAGCCAGGAGGTTCGATCTGGAGAAGGCCAAGCAAATGTGGGCCGATATGCTGCAATGGCGCAGGGAAAACGGTGTCGATACGATTGAAGAG
upper sequence: LOC_Os02g24430.2 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ17479 (Selaginella moellendorffii), 3'ss of exon 1
gtgtataatctgaaaatagcacatcatgttgttatttatagtttcttatgtgaaaaaagtattactaaaa-tttgagattacatagGTTTTTGAAGGCAAGAAAGTTTGATGTGGAGAAGGCAAAGCAAATGTGGGTTGATATGCTGCAGTGGAGAAAGGAATTCGCTGCAGATACCATTCTTGAG
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-----------------------------------gta-agccaagcatcgccggcaagtgttgttaaaaatctctccctgtgtagATTTTTGAAAGCCAGGAAGTTCGATCTGGAGAAGGCCAAGCAAATGTGGGCCGATATGCTGCAATGGCGCAGGGAAAACGGTGTCGATACGATTGAAGAGMapped 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|88389044|gb|CI595278.1|CI595278EST: CTTGAAGAGTTGCTACCATCTCACCATGATGACTACCACATGATGCTAAG GTTTTTGAAGGCAAGAA
genomic: CTTGAAGAGTTGCTACCATCTCACCATGATGACTACCACATGATGCTAAGgtgtataatc ... gattacatagGTTTTTGAAGGCAAGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttatttatagtttcttatgtgaaaaaagtattactaaaatttgagattacatagGTTTTTGAAGGCAAGAAAGTTTGATGTGGAGAAGGCAAAGCAAATGTGGGTTGATATGCTGCAGTGGAGAAAGGAATTCGCTGCAGATACCATTCTTGAG
tactaaa putative branch site (score: 1)
ttatgtgaaaaaagta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtataatctgaaaatagcacatcatgttgttatttatagtttcttatgtgaaaaaagtattactaaaatttgagattacatagGTTTTTGAAGGCAAGAAAGTTTGATGTGGAGAAGGCAAAGCAAATGTGGGTTGATATGCTGCAGTGGAGAAAGGAATTCGCTGCAGATACCATTCTTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT