Sequence
atgc intronic sequence ATGC exonic sequencegtattacttgtttaatcaaagaacactatgattcttttattctcaaatatccaaattctaaattaaagcaactgcacagGACAATTGATCGCCGTAAAAGAGTTATATTAGCCATGGATGCTGCATTTGGCATGGAATATTTGCATGGGAAGAATATAGTTCATTTTGATCTAAAGTGT
Basic information
species | Oryza sativa |
transcript | LOC_Os02g54510.3 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g54510.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G052658_T01 (Zea mays), 3'ss of exon 4
gtattacttgtttaatcaaagaac----actat--gattcttttattctcaaatatccaaattctaaattaaagcaactgcacagGACAATTGATCGCCGTAAAAGAGTTATATTAGCCATGGATGCTGCATTTGGCATGGAATATTTGCATGGGAAGAATATAGTTCATTTTGATCTAAAGTGT
||| || | || |||| ||||| | ||| ||| ||| ||||| |||| || ||||||||||||| || |||||||||||||||||| || ||||| |||||||||||||||||||||||||||||||| ||||||||||||||||||||||| |||||||| || || |||
gtactatatattgaatccaagaaataagaatatttgatcttttatttctcctgtatc-gaactctaaattaaagcgcttgtgcagGACAATTGATCGCCGGAAGAGAGTAATATTAGCCATGGATGCTGCATTTGGCATGGAGTATTTGCATGGGAAGAATATAGTCCATTTTGACCTGAAATGT
upper sequence: LOC_Os02g54510.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G039106_T03 (Zea mays), 3'ss of exon 3
gtattacttgtttaatcaaagaacactatgattcttttattctcaaatatccaaattct-aaattaaagcaactgcacagGACAATTGATCGCCGTAAAAGAGTTATATTAGCCATGGATGCTGCATTTGGCATGGAATATTTGCATGGGAAGAATATAGTTCATTTTGATCTAAAGTGT
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gcactacattttctaaagcaagaaataagaatatatttggtcttctatttctcctttatcaaaataaagcacttgtgcagGACAATAGATCGCCGGAAGAGAGTAATATTAGCCATGGATGCTGCATTTGGCATGGAATATTTGCACGGGAAGAATATAGTCCATTTTGACCTGAAGTGT
upper sequence: LOC_Os02g54510.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA13G01190.1 (Glycine max), 3'ss of exon 7
------------------------------------------------------------gtattacttgtttaatcaaagaacactatgattcttttattctcaaatatccaaattctaaatta-aagcaactgcacagGACAATTGATCGCCGTAAAAGAGTTATATTAGCCATGGATGCTGCATTTGGCATGGAATATTTGCATGGGAAGAATATAGTTCATTTTGATCTAAAGTGT
|| | | | ||| || | || | | | | ||| | | | ||| ||||| | |||| ||||| ||||| ||||| || | || |||||||||||||||||||||| ||||| ||||||||||| || || || |||||||||||| | || |||
gtaacttgatgcatgcatgggcttatatttcatcaatatttaatatgttttaaggcactcaaatgtgcagccttccatatgaaaaccctcatggactggtgatgtattatttatgctgtttattctgagcaatttaacagAACAATAGATCGTCGTAAGAGGCTCATTATAGCCATGGATGCTGCATTTGGGATGGAGTATTTGCATGGAAAAAACATTGTTCATTTTGATTTGAAATGT
upper sequence: LOC_Os02g54510.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA17G07320.1 (Glycine max), 3'ss of exon 10
-----------------------------------------------------------------gtattacttgtttaatcaaagaacactatgattcttttattctcaaatatccaaattctaaatta-aagcaactgcacagGACAATTGATCGCCGTAAAAGAGTTATATTAGCCATGGATGCTGCATTTGGCATGGAATATTTGCATGGGAAGAATATAGTTCATTTTGATCTAAAGTGT
| | || ||| | | | || || || | | | ||| | | | ||| ||||| | |||| ||||| ||||| ||||| || | || |||||||||||||||||||||| ||||| ||||||||||| || || || || ||||||||| | || |||
gtaatttgatgcatgcatgggcttatatttcatcaatatttaatagtatgctttaaggcactgaaatgtgcagccttccatctgaaagccctcatggactgttgatgt-atttatttatgctgtttattctgagcaatttaacagAACAATAGATCGTCGTAAGAGGCTCATTATAGCCATGGATGCTGCATTTGGGATGGAGTATTTGCATGGAAAAAACATTGTGCATTTTGATTTGAAATGT
upper sequence: LOC_Os02g54510.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT5G57610.1 (Arabidopsis thaliana), 3'ss of exon 5
--------gtattacttgtttaatcaaagaacactatgattcttttattctcaaatatccaaattctaaattaaagcaactgcacagGACAATTGATCGCCGTAAAAGAGTTATATTAGCCATGGATGCTGCATTTGGCATGGAATATTTGCATGGGAAGAATATAGTTCATTTTGATCTAAAGTGT
|| | || | || | || | ||||| | || | ||| |||| | || | ||| | ||| || |||||||| || |||||| | || ||||||||||| |||||||||| ||||| |||||||| || ||||| || |||||||| ||| | ||||||
gtaaaaaagtttcacctattcatgcattatatactattttcctagagtatccaattatctgacatc-acattggttgactcctccagAACTATTGATCGTCGCAAAAGACTCATCATAGCCATGGATACTGCATTTGGGATGGAGTATTTGCACGGAAAGAACATTGTTCATTTCGATTTGAAGTGTMapped 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|66924155|gb|CX111003.1|CX111003EST: GAGTTTATGATCAATGGATCTCTCAAACAGTTTTTGAGNNNNNNNGACAG GACAATTGATCGCCGTAAAAGAGTTATATTAGCCATGGATGCTGCATTTGG
genomic: GAGTTTATGATCAATGGATCTCTCAAACAGTTTTTGAGAAAAAAAGACAGgtattacttg ... aactgcacagGACAATTGATCGCCGTAAAAGAGTTATATTAGCCATGGATGCTGCATTTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actatgattcttttattctcaaatatccaaattctaaattaaagcaactgcacagGACAATTGATCGCCGTAAAAGAGTTATATTAGCCATGGATGCTGCATTTGGCATGGAATATTTGCATGGGAAGAATATAGTTCATTTTGATCTAAAGTGT
ttctaaa putative branch site (score: 2)
aaatatccaaattcta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattacttgtttaatcaaagaacactatgattcttttattctcaaatatccaaattctaaattaaagcaactgcacagGACAATTGATCGCCGTAAAAGAGTTATATTAGCCATGGATGCTGCATTTGGCATGGAATATTTGCATGGGAAGAATATAGTTCATTTTGATCTAAAGTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA