Sequence
atgc intronic sequence ATGC exonic sequencegtctgagcatgaaccttctagagttgttcgttcctgcttctatgcaaatgcaaatggaatcaccttgaatatttatattaaatctgctaatatcattattaaaaagaacaagattgagcagcgtgttgagctcactccctgttatttcgagacagCGAATTGCCTGAGTTCCTTGGTGGCACTTGCACCTGCGAAGGCGGCTGCATGCGCTCCGACAAAGGGCCATGGAAAGATCCTGAAATCATAAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g04030.3 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g04030.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G171349_T01 (Zea mays), 3'ss of exon 5
gtctgagcatgaaccttctagagttgttcgttcctgcttctatgcaaatgcaaatggaatcaccttgaatatttatattaaatctgctaatatcattattaaaaagaacaagattgagcagcgtgttgagctcactccctgttatttcgagacagCGAATTGCCTGAGTTCCTTGGTGGCACTTGCACCTGCGAAGGCGGCTGCATGCGCTCCGACAAAGGGCCATGGAAAGATCCTGAAATCATAAAG
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-----------------------------------------------------------------------------gtttatttgctgaacaaactggactgaactcactgctcaggtttctttcttgacctctttgtgatgacgtgtgtgcagCGAGCTGCCCGAGTTCTTCGGCGGCACTTGCAACTGCGAGGGCGGCTGCATGCGCTCCGACAAAGGGCCATGGAAGGACCCTGAGATCCTCAAG
upper sequence: LOC_Os02g04030.3 (Oryza sativa), 3'ss of exon 5
lower sequence: AT4G36490.1 (Arabidopsis thaliana), 3'ss of exon 6
gtctgagcatgaaccttctagagttgttcgttcctgcttctatgcaaatgcaaatggaatcaccttgaatatttatattaaatctgctaatatcattattaaaaagaacaagattgagcagcgtgttgagctcactccctgttatttcgagacagCGAATTGCCTGAGTTCCTTGGTGGCACTTGCACCTGCG------AAGGCGGCTGCATGCGCTCCGACAAAGGGCCATGGAAAGATCCTGAAATCATAAAG
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-------------------------------------------------------------------gtgagctatgc-aagacgattagcatacaaattaatctatgttatatattatataacatgaaactgattcttattaatttgtgaccagTGAACTTCCTGAGTTTCTTGGAGGTTCATGTACTTGTGCTGACAATGGTGGCTGCATGCGCTCTGACAAAGGCCCATGGAAAAATCCAGAGATCATGAAGMapped 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|66932181|gb|CX119029.1|CX119029EST: GTCCTAGGCAACAAGTACCAGAGCAAGCTGCTGGAAGTGATTGATCCCAG CGAATTGCCTGAGTTCCTTGGTGGCACTTGCACCTGCGAAGGCGGCTGCAT
genomic: GTCCTAGGCAACAAGTACCAGAGCAAGCTGCTGGAAGTGATTGATCCCAGgtctgagcat ... ttcgagacagCGAATTGCCTGAGTTCCTTGGTGGCACTTGCACCTGCGAAGGCGGCTGCAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaaagaacaagattgagcagcgtgttgagctcactccctgttatttcgagacagCGAATTGCCTGAGTTCCTTGGTGGCACTTGCACCTGCGAAGGCGGCTGCATGCGCTCCGACAAAGGGCCATGGAAAGATCCTGAAATCATAAAG
agctcac putative branch site (score: 3)
ctccctgttatttc CT-rich tract
tgttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctgagcatgaaccttctagagttgttcgttcctgcttctatgcaaatgcaaatggaatcaccttgaatatttatattaaatctgctaatatcattattaaaaagaacaagattgagcagcgtgttgagctcactccctgttatttcgagacagCGAATTGCCTGAGTTCCTTGGTGGCACTTGCACCTGCGAAGGCGGCTGCATGCGCTCCGACAAAGGGCCATGGAAAGATCCTGAAATCATAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA