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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaatttttatctgatgactttttttggttatattttttgcaactttcctccatatttatcatctgccttcttttggacagGGGTACAATAAGATATGCTAGTGTCCATGCCCATTTAGGCCGTACTGGTAGCAGAAGGGATGATCTGGAATCATTAGCATATACATTAATATTTCTTCTC

Basic information

species Oryza sativa
transcript LOC_Os01g56580.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56580.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G116086_T01 (Zea mays), 3'ss of exon 9
gttaatttttatctgatgactttttttggttatattttttgcaactttcctccatatttatcatctgccttcttttggacagGGGTACAATAAGATATGCTAGTGTCCATGCCCATTTAGGCCGTACTGGTAGCAGAAGGGATGATCTGGAATCATTAGCATATACATTAATATTTCTTCTC
|||  |||||  |  ||    | ||||  | || ||  || |||   | | |     |||   | |||| | |  | ||||| |||||||||||||| |||||||||||||| |||||||| ||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||| 
gtttctttttgccaaatagtgtgtttt--tcat-ttcctttcaa---tacactggccttac--tttgccctttccttgacagAGGTACAATAAGATACGCTAGTGTCCATGCACATTTAGGACGTACTGGTAGCAGAAGGGATGATCTGGAATCATTAGCATATACATTGATATTTCTTCTT

upper sequence: LOC_Os01g56580.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 9
gttaatttttatctgatgactttttttggttatattttttgcaactttcctccatatttatcatctgccttcttttggacagGGGTACAATAAGATATGCTAGTGTCCATGCCCATTTAGGCCGTACTGGTAGCAGAAGGGATGATCTGGAATCATTAGCATATACATTAATATTTCTTCTC
|||  | | ||| | ||||||| |||    |   | | ||     ||| |    |  | || || ||||||  ||||  |||||| |||||||| ||||||||||| ||||| ||||||||  | ||||| ||  |||||||||| || || ||| | ||||| ||| || |||||||  | 
gtt--tgtatattttatgacttgtttgtcatggctatattttgcttttacatattgatgataatatgcctt--tttgtgcagGGGAACAATAAGGTATGCTAGTGTACATGCACATTTAGGTAGGACTGGAAGTCGAAGGGATGACCTTGAGTCACTGGCATACACACTAGTATTTCTCATA

upper sequence: LOC_Os01g56580.2 (Oryza sativa), 3'ss of exon 9
lower sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 9
----gttaatttttatctgatgactttttttggttatattttttgcaactttcctccatatttatcatctgccttcttttggacagGGGTACAATAAGATATGCTAGTGTCCATGCCCATTTAGGCCGTACTGGTAGCAGAAGGGATGATCTGGAATCATTAGCATATACATTAATATTTCTTCTC
     || |||  | | || |  ||||  |    |   |  | |  |  |||    || || | |  |  || |  | |    ||| || |||||||| ||||| |||  |||||| ||| | || ||||| || ||  | |||||||||||||| ||||| || |||||||||||||||||  | 
gtattttgattggtgtatgttatctttcctactattgttggtatatatattttgctcacatctttgttacgcttcatat---gcagAGGAACAATAAGGTATGCAAGTTGCCATGCACATCTTGGTCGTACAGGAAGTCGGAGGGATGATCTGGAGTCATTGGCTTATACATTAATATTTCTGATG

upper sequence: LOC_Os01g56580.2 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 9
----gttaatttttatctgatgactttttttggttatattttttgcaactttcctccatatttatcatctgccttcttttggacagGGGTACAATAAGATATGCTAGTGTCCATGCCCATTTAGGCCGTACTGGTAGCAGAAGGGATGATCTGGAATCATTAGCATATACATTAATATTTCTTCTC
    ||  |||| |   || | |            | | |  ||  | ||||     ||||| |||      | |||||||| |||||| |||||| | ||||| ||||| ||||| |||||||| || || || || |||||||||||||| || ||| |||| || ||||||||||||||  | 
gtttgtggatttctggatgttcataaaaaaaaaaaaaaatgctttgacctttataatatattaatc-----tcctcttttgg-cagGGGAACAATACGGTATGCAAGTGTGCATGCACATTTAGGACGGACAGGAAGTAGAAGGGATGATCTCGAGTCACTAGCTTACACATTAATATTTCTCATT

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|29629024|gb|CB634035.1|CB634035
EST:     ACGCCAAATGGACAGCATGTTGATTATGATCAAAGGCCAGACATATTTAG                         GGGTACAATAAGATATGCT
genomic: ACGCCAAATGGACAGCATGTTGATTATGATCAAAGGCCAGACATATTTAGgttaattttt ... ttttggacagGGGTACAATAAGATATGCT
EST: gi|29623307|gb|CB628318.1|CB628318
EST:     ACGCCAAATGGACAGCATGTTGATTATGATCAAAGGCCAGACATATTTAG                         GGGTACAATAAGATATGCTAGTGTCCATGCCCATTTAGGCCGTACTGGTAG
genomic: ACGCCAAATGGACAGCATGTTGATTATGATCAAAGGCCAGACATATTTAGgttaattttt ... ttttggacagGGGTACAATAAGATATGCTAGTGTCCATGCCCATTTAGGCCGTACTGGTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttatattttttgcaactttcctccatatttatcatctgccttcttttggacagGGGTACAATAAGATATGCTAGTGTCCATGCCCATTTAGGCCGTACTGGTAGCAGAAGGGATGATCTGGAATCATTAGCATATACATTAATATTTCTTCTC
                                 tcatctgccttctttt  CT-rich tract
                          atatttatcat  TA-rich tract