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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggttttctgaacagaatatgatatttccagttgtggtgcttattttataagctaaacaatttcttctcaagattgaacagaggtagtatgcgtgattattaatgtgtccattcagtaaaaaaggggctgtctaatgttattaatgtcgatttcttgtgttgatgtgctattcttatgttccctgaagTTTATCTTCTCAACCTCCCTCGACGGGAAAATTAAGGCATGGCTTTATGATCATATGGGATCCAGGGTAGATTATGATGCTCCAGGAAAATGGTGTACTA

Basic information

species Oryza sativa
transcript LOC_Os01g15020.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g15020.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G416836_T01 (Zea mays), 3'ss of exon 11
gtgggttttctgaacagaatatgatatttccagttgtggtgcttattttataagctaaacaatttcttctcaagattgaacagaggtagtatgcgtgattattaatgtgtccattcagtaaaaaaggg-gctgtctaatgttattaatgtcgatttcttgtgttgatgtgctattcttatgttccctgaagTTTATCTTCTCAACCTCCCTCGACGGGAAAATTAAGGCATGGCTTTATGATCATATGGGATCCAGGGTAGATTATGATGCTCCAGGAAAATGGTGTACTA
                                                                                      |    |   || |    |  |  |   | ||  |           ||| ||   | | |  | || | ||| || ||||||     |||||||||||   || |||| ||||||||||| ||||| || || ||||||||||| |||||||||||  || ||||||| ||||| || ||||| ||||| || || ||||||||||
-------------------------------------------------------------------------------------atctcttttttgttcgcaatagcatttgtccaagagctgtccccattgtttatcatcaattttatcaaattcctg-gttgat-----attcttatgtttgatgcagTTCATCTTCTCAACTTCCCTTGATGGAAAAATTAAGGCCTGGCTTTATGACAATGTGGGATCTAGGGTGGACTATGAAGCTCCTGGCAAGTGGTGTACTA

upper sequence: LOC_Os01g15020.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 13
gtgggttttctgaacagaatatgatatttccagttgtggtgcttattttataagctaaacaatttcttctcaagattgaacagaggtagtatgcgtgattattaatgtgtccattcagtaaaaaaggggctgtctaatgttattaatgtcgatttcttgtgttgatgtgctattcttatgttccctgaagTTTATCTTCTCAACCTCCCTCGACGGGAAAATTAAGGCATGGCTTTATGATCATATGGGATCCAGGGTAGATTATGATGCTCCAGGAAAATGGTGTACTA
                                                                                      |  |   |     |  || | |||   || |  |      |  ||    |   | |  ||  || | |          |  ||   || ||| |||   || |||| ||||||||||| ||||| || || ||||||||||| |||||||||||  |||||||||| ||||| || || |||||||| || || ||||||||||
------------------------------------------------------------------------------------acttattcacacagct-ctattttgttattttacaatttccagtactcagcagaatgagcaaaatcaagtctaa-----aacatgactttattacgtttgatgcagTTCATCTTCTCAACTTCCCTTGATGGAAAAATTAAGGCCTGGCTTTATGACAATATGGGATCTAGGGTGGACTACGATGCTCCTGGCAAGTGGTGTACTA

upper sequence: LOC_Os01g15020.2 (Oryza sativa), 3'ss of exon 13
lower sequence: AT5G27030.2 (Arabidopsis thaliana), 3'ss of exon 12
gtgggttttctgaacagaatatgatatttccagttgtggtgcttattttataagctaaacaatttcttctcaagattgaacagaggtagtatgcgtgattattaatgtgtccattcagtaaaaaaggggctgtctaatgttattaatgtcgatttcttgtgttgatgtgct--attcttatgttccctgaagTTTATCTTCTCAACCTCCCTCGACGGGAAAATTAAGGCATGGCTTTATGATCATATGGGATCCAGGGTAGATTATGATGCTCCAGGAAAATGGTGTACTA
                        |    | ||   ||    | |   ||||   || |  | || || |   | || | ||      || ||    |  || ||   | | |  || |  | |  |   | |||     ||| ||| ||  ||  ||      ||        ||||||| |    |  |||| || || |||||| || | || |||||||| || || |||||||||||| || |||| ||||| || || ||||||||||| || ||||||||||| |
-----------------------gtgcggcaaggattgaa--tcaaactatattttacatcaattattatactgttttaccaa--tccgtttgaagaacaataaagtagacgacacatttcatatagtattatcttgc-ctatgaatttctgttctttaccaaaatacatctcgttcttatttggatttcagTTCATATTTTCAACCGCCATAGATGGGAAAATAAAAGCCTGGCTTTATGATAATCTGGGTTCCAGAGTTGACTATGATGCTCCCGGTAAATGGTGTACGA

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|29628360|gb|CB633371.1|CB633371
EST:     ATGAGGCACCAGTGTATTCCATCTGCCCTCACCACAAAGAGAGTATTCAG                         TTTATCTTCTCAACCTCCCTCGACGGGAAAATTAAGGCATGGCTTTATGAT
genomic: ATGAGGCACCAGTGTATTCCATCTGCCCTCACCACAAAGAGAGTATTCAGgtgggttttc ... ttccctgaagTTTATCTTCTCAACCTCCCTCGACGGGAAAATTAAGGCATGGCTTTATGAT
EST: gi|29630452|gb|CB635461.1|CB635461
EST:     ATGAGGCACCAGTGTATTCCATCTGCCCTCACCACAAAGAGAGTATTCAG                         TTTATCTTCTCAACCTCCCTCGACGGGAAAATTAAGGCATGGCTTTATGAT
genomic: ATGAGGCACCAGTGTATTCCATCTGCCCTCACCACAAAGAGAGTATTCAGgtgggttttc ... ttccctgaagTTTATCTTCTCAACCTCCCTCGACGGGAAAATTAAGGCATGGCTTTATGAT
EST: gi|29628115|gb|CB633126.1|CB633126
EST:     ATGAGGCACCAGTGTATTCCATCTGCCCTCACCACAAAGAGAGTATTCAG                         TTTATCTTCTCAACCTCCCTCGACGGGAAAATTAAGGCATGGCTTTATGAT
genomic: ATGAGGCACCAGTGTATTCCATCTGCCCTCACCACAAAGAGAGTATTCAGgtgggttttc ... ttccctgaagTTTATCTTCTCAACCTCCCTCGACGGGAAAATTAAGGCATGGCTTTATGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgttattaatgtcgatttcttgtgttgatgtgctattcttatgttccctgaagTTTATCTTCTCAACCTCCCTCGACGGGAAAATTAAGGCATGGCTTTATGATCATATGGGATCCAGGGTAGATTATGATGCTCCAGGAAAATGGTGTACTA
                                     ttcttatgttccct  CT-rich tract
     tattaatgt  TA-rich tract