Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAACATACTAGGTCAACTAGCAGCCGCTATGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGGgtatgtttgctttatatgctattttggattttctaatgaaagacaattcgctgcttctgaaattttcacacctcagtttccaaatgttgacacttatgtc...

Basic information

species Oryza sativa
transcript LOC_Os06g15360.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g15360.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G035417_T03 (Zea mays), 5'ss of exon 2
AAACATACTAGGTCAACTAGCAGCCGCTATGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGGgtatgtttgctttatatgctattttggattttctaatgaaagacaattcgctgcttctgaaattttcacacctcagtttccaaatgttgacacttatgtc-----
 ||||||||||||||||| ||||| ||| |||||||  | || |||||||| ||||||||||||||||| || |||||||||  | |  ||||||   |||| ||   |||  | |  |    || |   | ||| ||   | || ||   |  ||||||| ||  |    || ||||      
GAACATACTAGGTCAACTGGCAGCTGCTGTGCCACAAACGCTGACAGTTACCCCAGAGGAACGGGAGGCTATCCAGCGGgtacatctcttttataacttattgtgttatttgcagttcatcttaaat-attccttttg---tcttgacctatgtgtttccagataatt-tgctcatgtttgcat
















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|88847927|gb|CI006113.1|CI006113
EST:     TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGG                         CTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
genomic: TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGGgtatgtttgc ... ttcttgacagCTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
EST: gi|88834598|gb|CI077881.1|CI077881
EST:     TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGG                         CTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
genomic: TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGGgtatgtttgc ... ttcttgacagCTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
EST: gi|29643187|gb|CB648194.1|CB648194
EST:     TGCCACAGGCACTTCCAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGG                         CTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
genomic: TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGGgtatgtttgc ... ttcttgacagCTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
EST: gi|29657665|gb|CB653940.1|CB653940
EST:     TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGG                         CTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
genomic: TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGGgtatgtttgc ... ttcttgacagCTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
EST: gi|29669285|gb|CB665560.1|CB665560
EST:     TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGG                         CTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
genomic: TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGGgtatgtttgc ... ttcttgacagCTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
EST: gi|29643233|gb|CB648240.1|CB648240
EST:     TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGG                         CTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
genomic: TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGGgtatgtttgc ... ttcttgacagCTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
EST: gi|33654536|gb|CF277150.1|CF277150
EST:     TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGG                         CTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
genomic: TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGGgtatgtttgc ... ttcttgacagCTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
EST: gi|29662304|gb|CB658579.1|CB658579
EST:     TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGG                         CTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
genomic: TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGGgtatgtttgc ... ttcttgacagCTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
EST: gi|29660321|gb|CB656596.1|CB656596
EST:     TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGG                         CTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
genomic: TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGGgtatgtttgc ... ttcttgacagCTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
EST: gi|87015278|gb|CI275468.1|CI275468
EST:     TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGG                         CTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
genomic: TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGGgtatgtttgc ... ttcttgacagCTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
EST: gi|86494540|gb|CI137173.1|CI137173
EST:     TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGG                         CTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
genomic: TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGGgtatgtttgc ... ttcttgacagCTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
EST: gi|86489922|gb|CI132555.1|CI132555
EST:     TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGG                         CTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
genomic: TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGGgtatgtttgc ... ttcttgacagCTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
EST: gi|29673855|gb|CB670130.1|CB670130
EST:     TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGG                         CTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
genomic: TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGGgtatgtttgc ... ttcttgacagCTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
EST: gi|29670072|gb|CB666347.1|CB666347
EST:     TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGG                         CTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
genomic: TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGGgtatgtttgc ... ttcttgacagCTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
EST: gi|88830186|gb|CI076442.1|CI076442
EST:     TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGG                         CTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
genomic: TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGGgtatgtttgc ... ttcttgacagCTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
EST: gi|29630613|gb|CB635622.1|CB635622
EST:     TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGG                         CTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
genomic: TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGGgtatgtttgc ... ttcttgacagCTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
EST: gi|2431315|gb|C73735.1|C73735
EST:     TGCCACAGGCACTTACAGTTACTNCAGAGGAACGGGAGGCCATTCAGCGG                         CTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGGTCTTCTTCGG
genomic: TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGGgtatgtttgc ... ttcttgacagCTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGG-TCTTCTTCGC
EST: gi|88220271|gb|CI219831.1|CI219831
EST:     TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGG                         CTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
genomic: TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGGgtatgtttgc ... ttcttgacagCTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
EST: gi|87028194|gb|CI111888.1|CI111888
EST:     TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGG                         CTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
genomic: TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGGgtatgtttgc ... ttcttgacagCTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
EST: gi|89197384|gb|CI010004.1|CI010004
EST:     TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGG                         CTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
genomic: TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGGgtatgtttgc ... ttcttgacagCTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
EST: gi|14980837|gb|BI305515.1|BI305515
EST:     TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGG                         CTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
genomic: TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGGgtatgtttgc ... ttcttgacagCTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
EST: gi|23514955|gb|BU673867.1|BU673867
EST:     TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGG                         CTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
genomic: TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGGgtatgtttgc ... ttcttgacagCTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
EST: gi|89186903|gb|CI053306.1|CI053306
EST:     TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGG                         CTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
genomic: TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGGgtatgtttgc ... ttcttgacagCTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
EST: gi|8859709|gb|AU097027.1|AU097027
EST:     TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGG                         CTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
genomic: TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGGgtatgtttgc ... ttcttgacagCTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
EST: gi|218488797|gb|FG951622.1|FG951622
EST:     TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGG                         CTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTCTCCG
genomic: TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGGgtatgtttgc ... ttcttgacagCTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCT-TC-G
EST: gi|88245156|gb|CI245005.1|CI245005
EST:     TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGG                         CTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
genomic: TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGGgtatgtttgc ... ttcttgacagCTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
EST: gi|33687246|gb|CF315485.1|CF315485
EST:     TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGG                         CTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
genomic: TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGGgtatgtttgc ... ttcttgacagCTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
EST: gi|29631165|gb|CB636174.1|CB636174
EST:     TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGG                         CTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
genomic: TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGGgtatgtttgc ... ttcttgacagCTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
EST: gi|87036144|gb|CI189591.1|CI189591
EST:     TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGG                         CTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
genomic: TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGGgtatgtttgc ... ttcttgacagCTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
EST: gi|32947880|gb|BP184452.1|BP184452
EST:     TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAACGG                         CTGGAGGCAATGGGGTTCAACCCGTGAGCTCGTTTTGGAGGTCTTCTTCGC
genomic: TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGGgtatgtttgc ... ttcttgacagCTGGAGGCAATGGGGTTCAACC-GTGAGCTCGTTTTGGAGGTCTTCTTCGC
EST: gi|8527786|gb|AU092601.1|AU092601
EST:     TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGG                         CTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA
genomic: TGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGGgtatgtttgc ... ttcttgacagCTGGAGGCAATGGGGTTCAACCGTGAGCTCGTTTTGGAGGTCTTCTTCGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAACATACTAGGTCAACTAGCAGCCGCTATGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGGgtatgtttgctttatatgctattttggattttctaatgaaagacaattcgctgcttctgaaattttcacacctcagtttccaaatgttgacacttatgtc

- - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA