Sequence
atgc intronic sequence ATGC exonic sequencegtgagtattttccattttttcttataacaattctttggtgatgcagtggcagtgcatgggtcagtttgttgtccttccttttacttaagctatgactacttgccctgtgcagAGGACAAGCTGAGAGAGAATTCAGAGTGGAAGTTGAAGCAATTGGTCATGTCCGACACAAGAATTTGGTTCGCCTTTTGGGGTACTGTGTTGAAGGCACT
Basic information
species | Oryza sativa |
transcript | LOC_Os12g01740.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g01740.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G162702_T01 (Zea mays), 3'ss of exon 1
gtgagtattttccattttttcttataacaattctttggtgatgcagtggcagtgcatgggtcagtttgttgtccttccttttacttaagctatgactacttgccctgtgcagAGGACAAGCTGAGAGAGAATTCAGAGTGGAAGTTGAAGCAATTGGTCATGTCCGACACAAGAATTTGGTTCGCCTTTTGGGGTACTGTGTTGAAGGCACT
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----------gtgagctttttctgtagcaattttttattgaagcagtggcagtacatgcctttgccc-ttctgctttcttt--cttacagtggaattgtctgtcatgtgcagAGGACAGGCTGAGAGAGAATTCAGAGTGGAAGTCGAGGCAATTGGCCATGTTCGTCACAAGAATTTGGTCCGCCTTTTGGGTTACTGTGTTGAGGGTACT
upper sequence: LOC_Os12g01740.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT5G18500.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgagtattttccattttttcttataacaattctttggtgatgcagtggcagtgcatgggtcagtttgttgtccttccttttacttaagctatgac-tacttgccctgtgcagAGGACAAGCTGAGAGAGAATTCAGAGTGGAAGTTGAAGCAATTGGTCATGTCCGACACAAGAATTTGGTTCGCCTTTTGGGGTACTGTGTTGAAGGCACT
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---------gtaagttttttttcacaaa-------tggtgaatcaa----gattcaagatttcatttcttgaatccttttttcttttaatggtgatgtttttgtatttcttagAGGACAAGCTGATAAAGACTTCAGAGTTGAAGTTGAAGCTATAGGTCACGTTCGACATAAAAACTTGGTCCGCCTTCTCGGATATTGTATGGAAGGAACGMapped 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|58605888|gb|CK033921.1|CK033921EST: AGATTATCAAATGGCACCCCAGTGGCTGTCNNNNNNNTCCTTAACAATCT AGGACAAGCTGAGAGAGAATTCAGAGTGGAAGTTGAAGCAATTGGTCATGT
genomic: AGATTATCAAATGGCACCCCAGTGGCTGTCAAAAAAATCCTTAACAATCTgtgagtattt ... ccctgtgcagAGGACAAGCTGAGAGAGAATTCAGAGTGGAAGTTGAAGCAATTGGTCATGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gggtcagtttgttgtccttccttttacttaagctatgactacttgccctgtgcagAGGACAAGCTGAGAGAGAATTCAGAGTGGAAGTTGAAGCAATTGGTCATGTCCGACACAAGAATTTGGTTCGCCTTTTGGGGTACTGTGTTGAAGGCACT
cttgccct CT-rich tract
ttttacttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtattttccattttttcttataacaattctttggtgatgcagtggcagtgcatgggtcagtttgttgtccttccttttacttaagctatgactacttgccctgtgcagAGGACAAGCTGAGAGAGAATTCAGAGTGGAAGTTGAAGCAATTGGTCATGTCCGACACAAGAATTTGGTTCGCCTTTTGGGGTACTGTGTTGAAGGCACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG