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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCGgtatgcttttaccaatgcgctatttttgcatgatgctctaagttatttttcccttttagcaatcacatgattagtctgcccttccagcacaatctgggtg...

Basic information

species Oryza sativa
transcript LOC_Os01g60660.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g60660.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G166345_T01 (Zea mays), 5'ss of exon 10
GTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCGgtatgctt---ttaccaatgcgctat--ttttgcatgatgctc-taagttatttttcccttttagcaatcacatgattagtctgccct----tccagcacaatctgggtg-----------------------------------------------------------------------------------
||||||||||||||| ||||||||||| ||||| ||||| || ||||| |||||||| || ||||||  |||   |  ||  |  | |||  | |  ||| ||  || |    | || ||  ||   |  |   ||   ||||      |||    |  | ||| || |  ||                                                                                    
GTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGACAAGATTACCCCGgtacacttcagtggcctgtttgatatgatgtaacatcattgtcatggaatgttcttggctaacataacatactcaattatcagatcctgaattgaaacaccatgtttgtttttatttgatgaatgatgtcgcttattgctatactgtgcaaagtttaccactatggcgctaaccgcgttgtttatgcatccag

upper sequence: LOC_Os01g60660.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA06G14760.1 (Glycine max), 5'ss of exon 11
GTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCGgtatgcttttaccaatgcgctatttttgcatgatgctctaagttatttt-tcccttttagcaatcacatgattagtctgcccttccagcacaatctgggtg-
| ||||||| |||||||||||||| || || || || ||||||||||| || ||||| ||||||||||  | ||  || | || ||  |||||||  |  |  || | ||  | |   |  ||| |   |     ||     || | |    |    ||   |   
GATTGATGGAAAGCCAGAAGATGTACTAAACCCAAAAAAGAAACAGCTGGATAAGATTACACCGgtattttctttgcact-cgttaactttgcat--ttttaaaattcataatgtttatactagaagagatgatgttcacaagctcatgatactttttccatgcag

upper sequence: LOC_Os01g60660.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA04G40090.1 (Glycine max), 5'ss of exon 11
GTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCGgtatgcttttaccaatgcgctatttttgcatgatgctctaagttatttt-tcccttttagcaatcacatgattagtctgcccttccagcacaatctgggtg-
| ||||||| |||||||||||||| || || || || ||||||||||| || ||||| ||||||||||  | ||  || | || ||  |||||||  |  |  |  | ||  | | | |  ||| | | |     ||     || | |    |    ||   |   
GATTGATGGAAAGCCAGAAGATGTACTAAACCCAAAAAAGAAACAGCTGGAGAAGATTACACCGgtattttctttgcact-cgttaactttgcat--ttttaaacttcataatgttcatactagaagtgatgatgttcacaagctcatgatactttttccatgcag

Mapped 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|89189180|gb|CI048719.1|CI048719
EST:     CAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCG                         GATCTTCACACTGATGGAAATGGAATTGCAACATACCGAGGGGTACCCTTC
genomic: CAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCGgtatgctttt ... atgcacccagGATCTTCACACTGATGGAAATGGAATTGCAACATACCGAGGGGTACCCTTC
EST: gi|86594926|gb|CI258180.1|CI258180
EST:     CAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCG                         GATCTTCACACTGATGGAAATGGAATTGCAACATAACGAGGGGTACCCTTC
genomic: CAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCGgtatgctttt ... atgcacccagGATCTTCACACTGATGGAAATGGAATTGCAACATACCGAGGGGTACCCTTC
EST: gi|58688789|gb|CK077476.1|CK077476
EST:     CAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCG                         GATCTTCACACTGATGGAAATGGAATTGCAACATACCGAGGGGTACCCTTC
genomic: CAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCGgtatgctttt ... atgcacccagGATCTTCACACTGATGGAAATGGAATTGCAACATACCGAGGGGTACCCTTC
EST: gi|88272357|gb|CI386212.1|CI386212
EST:     CAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCG                         GATCTTCACACTGATGGAAATGGAATTGCAACATACCGAGGGGTACCCTTC
genomic: CAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCGgtatgctttt ... atgcacccagGATCTTCACACTGATGGAAATGGAATTGCAACATACCGAGGGGTACCCTTC
EST: gi|86418870|gb|CI053671.1|CI053671
EST:     CAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCG                         GATCTTCACACTGATGGAAATGGAATTGCAACATACCGAGGGGTACCCTTC
genomic: CAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCGgtatgctttt ... atgcacccagGATCTTCACACTGATGGAAATGGAATTGCAACATACCGAGGGGTACCCTTC
EST: gi|86492758|gb|CI135391.1|CI135391
EST:     CAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCG                         GATCTTCACACTGATGGAAATGGAATTGCAACATACCGAGGGGTACCCTTC
genomic: CAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCGgtatgctttt ... atgcacccagGATCTTCACACTGATGGAAATGGAATTGCAACATACCGAGGGGTACCCTTC
EST: gi|86429228|gb|CI075909.1|CI075909
EST:     CAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCG                         GATCTTCACACTGATGGAAATGGAATTGCAACATACCGAGGGGTACCCTTC
genomic: CAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCGgtatgctttt ... atgcacccagGATCTTCACACTGATGGAAATGGAATTGCAACATACCGAGGGGTACCCTTC
EST: gi|88206615|gb|CI206464.1|CI206464
EST:     CAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCG                         GATCTTCACACTGATGGAAATGGAATTGCAACATACCGAGGGGTACCCTTC
genomic: CAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCGgtatgctttt ... atgcacccagGATCTTCACACTGATGGAAATGGAATTGCAACATACCGAGGGGTACCCTTC
EST: gi|86834522|gb|CI344453.1|CI344453
EST:     CAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCG                         GATCTTCACACTGATGGAAATGGAAGTTGCAACATACCGAGGGGTACCCTT
genomic: CAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCGgtatgctttt ... atgcacccagGATCTTCACACTGATGGAAATGGAA-TTGCAACATACCGAGGGGTACCCTT
EST: gi|88408821|gb|CI554143.1|CI554143
EST:     CAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCG                         GATCTTCACACTGATGGAAATGGAATTGCAACATACCGAGGGGTACCCTTC
genomic: CAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCGgtatgctttt ... atgcacccagGATCTTCACACTGATGGAAATGGAATTGCAACATACCGAGGGGTACCCTTC
EST: gi|86434980|gb|CI106213.1|CI106213
EST:     CAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCG                         GATCTTCACACTGATGGAAATGGAATTGCAACATACCGAGGGGTACCCTTC
genomic: CAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCGgtatgctttt ... atgcacccagGATCTTCACACTGATGGAAATGGAATTGCAACATACCGAGGGGTACCCTTC
EST: gi|29672822|gb|CB669097.1|CB669097
EST:     CAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCG                         GATCTTCACACTGATGGAAATGGAATTGCAACATACCGAGGGGTACCCTTC
genomic: CAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCGgtatgctttt ... atgcacccagGATCTTCACACTGATGGAAATGGAATTGCAACATACCGAGGGGTACCCTTC
EST: gi|88959962|gb|CI381840.1|CI381840
EST:     CAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCG                         GATCTTCACACTGATGGAAATGGAATTGCAACATACCGAGGGGTACCCTTC
genomic: CAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCGgtatgctttt ... atgcacccagGATCTTCACACTGATGGAAATGGAATTGCAACATACCGAGGGGTACCCTTC
EST: gi|86823873|gb|CI258854.1|CI258854
EST:     CAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCG                         GATCTTCACACTGATGGAAATGGAATTGCAACATACCGAGGGGTACCCTTC
genomic: CAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCGgtatgctttt ... atgcacccagGATCTTCACACTGATGGAAATGGAATTGCAACATACCGAGGGGTACCCTTC
EST: gi|89198563|gb|CI016648.1|CI016648
EST:     CAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCG                         GATCTTCACACTGATGGAAATGGAATTGCAACATACCGAGGGGTACCCTTC
genomic: CAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCGgtatgctttt ... atgcacccagGATCTTCACACTGATGGAAATGGAATTGCAACATACCGAGGGGTACCCTTC
EST: gi|88448867|gb|CI557939.1|CI557939
EST:     CAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCG                         GATCTTCACACTGATGGAAATGGAATTGCAACATACCGAGGGGTACCCTTC
genomic: CAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCGgtatgctttt ... atgcacccagGATCTTCACACTGATGGAAATGGAATTGCAACATACCGAGGGGTACCCTTC
EST: gi|29642064|gb|CB647071.1|CB647071
EST:     CAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCG                         GATCTTCACACTGATGGAAATGGAATTGCAACATACCGAGGGGTACCCTTC
genomic: CAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCGgtatgctttt ... atgcacccagGATCTTCACACTGATGGAAATGGAATTGCAACATACCGAGGGGTACCCTTC
EST: gi|88831359|gb|CI083753.1|CI083753
EST:     CAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCG                         GATCTTCACACTGATGGAAATGGAATTGCAACATACCGAGGGGTACCCTTC
genomic: CAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCGgtatgctttt ... atgcacccagGATCTTCACACTGATGGAAATGGAATTGCAACATACCGAGGGGTACCCTTC
EST: gi|29642108|gb|CB647115.1|CB647115
EST:     CAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCG                         GATCTTCACACTGATGGAAATGGAATTGCAACATACCGAGGGGTACCCTTC
genomic: CAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCGgtatgctttt ... atgcacccagGATCTTCACACTGATGGAAATGGAATTGCAACATACCGAGGGGTACCCTTC
EST: gi|58694983|gb|CK083670.1|CK083670
EST:     CAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCG                         GATCTTCACACTGATGGAAATGGAATTGCAACATACCGAGGGGTACCCTTC
genomic: CAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCGgtatgctttt ... atgcacccagGATCTTCACACTGATGGAAATGGAATTGCAACATACCGAGGGGTACCCTTC
EST: gi|15852252|gb|BI805048.1|BI805048
EST:     CAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCG                         GATCTTCACACTGATGGAAATGGAATTGCAACATACCGAGGGGTACCCTTC
genomic: CAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCGgtatgctttt ... atgcacccagGATCTTCACACTGATGGAAATGGAATTGCAACATACCGAGGGGTACCCTTC
EST: gi|88380986|gb|CI523557.1|CI523557
EST:     CAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCG                         GATCTTCACACTGATGGAAATGGAATTGCAACATACCGAGGGGTACCCTTC
genomic: CAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCGgtatgctttt ... atgcacccagGATCTTCACACTGATGGAAATGGAATTGCAACATACCGAGGGGTACCCTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCGgtatgcttttaccaatgcgctatttttgcatgatgctctaagttatttttcccttttagcaatcacatgattagtctgcccttccagcacaatctgggtg

- - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccttcc