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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attcaagcacacatacatattttgttttggtggggggggggggggttggttaaaggctacttatccttcaaataatgtgcctcatatcacgctgttgcagGTTGCTGGAGATCTCCTGAAGCAATACCAGGAAAAATTTAAGGGAGGGACACTCTCAGCCACCTGGAACTACTTGAGGGACTCCATGGGCACCTACCTGT

Basic information

species Oryza sativa
transcript LOC_Os11g39220.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g39220.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G820287_T02 (Zea mays), 3'ss of exon 4
-----------------------------------------------------------attcaagcacacat------acatattttgttttggtggggggggggggggttggtt-----aaaggctacttatcc-------ttcaaataatgtgcctcatatcacgctgttgcagGTTGCTGGAGATCTCCTGAAGCAATACCAGGAAAAATTTAAGGGAGGGACACTCTCAGCCACCTGGAACTACTTGAGGGACTCCATGGGCACCTACCTGT
                                                            || | | |||  |      | |||   ||  ||   | ||   |  ||| |  |||     ||| ||||   || |        | |||||| |||| || | ||| ||| ||| |||| |||||||||||||| |||||||||||||| || ||||||||||||||||| |||| ||||||||| |||||  ||||||||||| | ||||||||||
gtacttatcagcacccttcggaaaagccagctgatggcttgtttttcagactgacgatatttgagggacatgttttctgaaataaactgagttca-gaggaaagttgggatcagtttctaaaaatgctatgaattcacttctccttaaataacgtgcatcttttcatgctcttgtagGTCGCTGGAGATCTCCTTAAGCAATACCAGGAGAATTTTAAGGGAGGGACACTTTCAGTCACCTGGAATTACTTACGGGACTCCATGAGTACCTACCTGT

upper sequence: LOC_Os11g39220.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G099666_T01 (Zea mays), 3'ss of exon 3
-attcaagcacacatacatattttgttttggtggggggggggggggttggttaaaggctacttatccttcaaataatgtgcctcatatcacgctgttgcagGTTGCTGGAGATCTCCTGAAGCAATACCAGGAAAAATTTAAGGGAGGGACACTCTCAGCCACCTGGAACTACTTGAGGGACTCCATGGGCACCTACCTGT
 ||| |  |||  | |   | |    |   | |     |      ||    || |  | |   | |    |||||| |||| || | ||| ||| ||| |||| |||||||||||||||||||| |||||||| || ||||||||||||||||| |||| ||||||||| ||||| |||||||||||||| ||||||||||
aatttatacactaaaaaggaataaaataaagggactatgacattagtcc-ctagaaaccaaacaccaactaaataacgtgcatcttttcatgctcttgtagGTCGCTGGAGATCTCCTGAAGCAGTACCAGGAGAAGTTTAAGGGAGGGACACTTTCAGTCACCTGGAATTACTTAAGGGACTCCATGGGTACCTACCTGT

upper sequence: LOC_Os11g39220.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G445791_T01 (Zea mays), 3'ss of exon 4
-----------------------------------------------------------------attcaagcacacatacatattttgttttggtggggggggggggggttggtt-----aaaggctacttatcc-------ttcaaataatgtgcctcatatcacgctgttgcagGTTGCTGGAGATCTCCTGAAGCAATACCAGGAAAAATTTAAGGGAGGGACACTCTCAGCCACCTGGAACTACTTGAGGGACTCCATGGGCACCTACCTGT
                                                                   ||| |    |  | |||   ||  ||   | ||   |  ||| |  |||     ||| ||||   || |        | |||||| |||| || | ||| ||| ||| |||| |||||||||||||| |||||||||||||| || ||||||||||||||||| |||| ||||||||| |||||  ||||||||||| | ||||||||||
gtacttatcagcacccttcggaaaagccagctgatggcttgtttttcagactgacgatatttgagggtcatgttttctgaaataaactgagttca-gaggaaagttgggatcagtttctaaaaatgctatgaattcacttctccttaaataacgtgcatcttttcatgctcttgtagGTCGCTGGAGATCTCCTTAAGCAATACCAGGAGAATTTTAAGGGAGGGACACTTTCAGTCACCTGGAATTACTTACGGGACTCCATGAGTACCTACCTGT

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|29666946|gb|CB663221.1|CB663221
EST:     ATGATATATTTCAGACATTTGAAGGAGATAATACAGTTCTTCTTCAGCAG                         GTTGCTGGAGATCTCCTGAAGCAATACCAGGAAAAATTTAAGGGAGGGACA
genomic: ATGATATATTTCAGACATTTGAAGGAGATAATACAGTTCTTCTTCAGCAGgtaccaatca ... gctgttgcagGTTGCTGGAGATCTCCTGAAGCAATACCAGGAAAAATTTAAGGGAGGGACA
EST: gi|33800672|gb|CF326206.1|CF326206
EST:     ATGATATATTTCAGACATTTGAAGGAGATAATACAGTTCTTCTTCAGCAG                         GTTGCTGGAGATCTCCTGAAGCAATACCAGGAAAAATTTAAGGGAGGGACA
genomic: ATGATATATTTCAGACATTTGAAGGAGATAATACAGTTCTTCTTCAGCAGgtaccaatca ... gctgttgcagGTTGCTGGAGATCTCCTGAAGCAATACCAGGAAAAATTTAAGGGAGGGACA
EST: gi|29684385|gb|CB680660.1|CB680660
EST:     ATGATATATTTCAGACATTTGAAGGAGATAATACAGTTCTTCTTCAGCAG                         GTTGCTGGAGATCTCCTGAAGCAATACCAGGAAAAATTTAAGGGAGGGACA
genomic: ATGATATATTTCAGACATTTGAAGGAGATAATACAGTTCTTCTTCAGCAGgtaccaatca ... gctgttgcagGTTGCTGGAGATCTCCTGAAGCAATACCAGGAAAAATTTAAGGGAGGGACA
EST: gi|29642868|gb|CB647875.1|CB647875
EST:     GGAGATAATACAGTTCTTTTTCAGCAG                         GTTGCTGGAGATCTCCTGAAGCAATACCAGGAAAAATTTAAGGGAGGGACA
genomic: GGAGATAATACAGTTCTTCTTCAGCAGgtaccaatca ... gctgttgcagGTTGCTGGAGATCTCCTGAAGCAATACCAGGAAAAATTTAAGGGAGGGACA
EST: gi|29669185|gb|CB665460.1|CB665460
EST:     ATGATATATTTCAGACATTTGAAGGAGATAATACAGTTCTTCTTCAGCAG                         GTTGCTGGAGATCTCCTGAAGCAATACCAGGAAAAATTTAAGGGAGGGACA
genomic: ATGATATATTTCAGACATTTGAAGGAGATAATACAGTTCTTCTTCAGCAGgtaccaatca ... gctgttgcagGTTGCTGGAGATCTCCTGAAGCAATACCAGGAAAAATTTAAGGGAGGGACA
EST: gi|29638689|gb|CB643698.1|CB643698
EST:     ATGATATATTTCAGACATTTGAAGGAGATAATACAGTTCTTCTTCAGCAG                         GTTGCTGGAGATCTCCTGAAGCAATACCAGGAAAAATTTAAGGGAGGGACA
genomic: ATGATATATTTCAGACATTTGAAGGAGATAATACAGTTCTTCTTCAGCAGgtaccaatca ... gctgttgcagGTTGCTGGAGATCTCCTGAAGCAATACCAGGAAAAATTTAAGGGAGGGACA
EST: gi|29636951|gb|CB641960.1|CB641960
EST:     ATGATATATTTCAGACATTTGAAGGAGATAATACAGTTCTTCTTCAGCAG                         GTTGCTGGAGATCTCCTGAAGCAATACCAGGAAAAATTTAAGGGAGGGACA
genomic: ATGATATATTTCAGACATTTGAAGGAGATAATACAGTTCTTCTTCAGCAGgtaccaatca ... gctgttgcagGTTGCTGGAGATCTCCTGAAGCAATACCAGGAAAAATTTAAGGGAGGGACA
EST: gi|29624634|gb|CB629645.1|CB629645
EST:     ATGATATATTTCAGACATTTGAAGGAGATAATACAGTTCTTCTTCAGCAG                         GTTGCTGGAGATCTCCTGAAGCAATACCAGGAAAAATTTAAGGGAGGGACA
genomic: ATGATATATTTCAGACATTTGAAGGAGATAATACAGTTCTTCTTCAGCAGgtaccaatca ... gctgttgcagGTTGCTGGAGATCTCCTGAAGCAATACCAGGAAAAATTTAAGGGAGGGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggttaaaggctacttatccttcaaataatgtgcctcatatcacgctgttgcagGTTGCTGGAGATCTCCTGAAGCAATACCAGGAAAAATTTAAGGGAGGGACACTCTCAGCCACCTGGAACTACTTGAGGGACTCCATGGGCACCTACCTGT
                     ttcaaataat  TA-rich tract