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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatacagtacagattagcagtttatgttttgctacagataagttcagtttctgaaacttgacagtgacactccattcctttctgtgcagTGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCCCTCCGCGGAAA

Basic information

species Oryza sativa
transcript LOC_Os05g36270.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g36270.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G322953_T05 (Zea mays), 3'ss of exon 2
gtaatacagtac---agattagcagtttatgttttgctacagat---aagttcagtttctgaaacttgacagtgacactccattcctttctg--tgcagTGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCCCTCCGCGGAAA--------------------------------------
||||  |  |     | | ||       ||       ||||  |   | ||||      |     |||||  || |||||    | ||  ||  |||||||||| || ||||||||||||||||||||||||||  |||||||| |  |||||||||| ||                                      
gtaacgcgctctcctacactacatacacatacacccgtacacgtcccaggttctcggcttaggcattgactttggcactctgcgctttcttgcgtgcagTGTGTCCTCGTGTCTGAAGAGAACGAGGAGGCCATCTTCGTCGACCCGGCCCTCCGCGGGAAGTTCGTCAATCCTTTGCTCCTCCATCCCGACCTCGTAA

upper sequence: LOC_Os05g36270.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G322953_T04 (Zea mays), 3'ss of exon 2
gtaatacagtac---agattagcagtttatgttttgctacagat---aagttcagtttctgaaacttgacagtgacactccattcctttctg--tgcagTGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCCCTCCGCGGAAA
||||  |  |     | | ||       ||       ||||  |   | ||||      |     |||||  || |||||    | ||  ||  |||||||||| || ||||||||||||||||||||||||||  |||||||| |  |||||||||| ||
gtaacgcgctctcctacactacatacacatacacccgtacacgtcccaggttctcggcttaggcattgactttggcactctgcgctttcttgcgtgcagTGTGTCCTCGTGTCTGAAGAGAACGAGGAGGCCATCTTCGTCGACCCGGCCCTCCGCGGGAA
















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|33688486|gb|CF316725.1|CF316725
EST:     TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACG                         TGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
genomic: TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACGgtaatacagt ... ttctgtgcagTGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
EST: gi|88354625|gb|CI678668.1|CI678668
EST:     TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACG                         TGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
genomic: TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACGgtaatacagt ... ttctgtgcagTGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
EST: gi|88309089|gb|CI654708.1|CI654708
EST:     TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACG                         TGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTC
genomic: TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACGgtaatacagt ... ttctgtgcagTGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTC
EST: gi|29670800|gb|CB667075.1|CB667075
EST:     TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACG                         TGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
genomic: TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACGgtaatacagt ... ttctgtgcagTGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
EST: gi|33683625|gb|CF311864.1|CF311864
EST:     TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACG                         TGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
genomic: TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACGgtaatacagt ... ttctgtgcagTGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
EST: gi|88332374|gb|CI656243.1|CI656243
EST:     TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACG                         TGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
genomic: TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACGgtaatacagt ... ttctgtgcagTGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
EST: gi|33679306|gb|CF307545.1|CF307545
EST:     TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACG                         TGTGTTCTTGTGTCTGAAG
genomic: TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACGgtaatacagt ... ttctgtgcagTGTGTTCTTGTGTCTGAAG
EST: gi|33686898|gb|CF315137.1|CF315137
EST:     TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACG                         TGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
genomic: TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACGgtaatacagt ... ttctgtgcagTGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
EST: gi|33693501|gb|CF321740.1|CF321740
EST:     TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACG                         TGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
genomic: TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACGgtaatacagt ... ttctgtgcagTGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
EST: gi|33684972|gb|CF313211.1|CF313211
EST:     TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACG                         TGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
genomic: TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACGgtaatacagt ... ttctgtgcagTGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
EST: gi|29656833|gb|CB653108.1|CB653108
EST:     TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACG                         TGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
genomic: TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACGgtaatacagt ... ttctgtgcagTGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
EST: gi|88329945|gb|CI652332.1|CI652332
EST:     TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACG                         TGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
genomic: TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACGgtaatacagt ... ttctgtgcagTGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
EST: gi|29644325|gb|CB649332.1|CB649332
EST:     TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACG                         TGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
genomic: TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACGgtaatacagt ... ttctgtgcagTGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
EST: gi|33688998|gb|CF317237.1|CF317237
EST:     TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACG                         TGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
genomic: TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACGgtaatacagt ... ttctgtgcagTGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
EST: gi|29663073|gb|CB659348.1|CB659348
EST:     TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACG                         TGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC
genomic: TGCTCTCCAACGAAGTCTTCGTCAAGGCGCTCGTCAGCAGCGGCCGCACGgtaatacagt ... ttctgtgcagTGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagataagttcagtttctgaaacttgacagtgacactccattcctttctgtgcagTGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCCCTCCGCGGAAA
                     acttgac  putative branch site (score: 4)
                                 cactccattcctttct  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatacagtacagattagcagtttatgttttgctacagataagttcagtttctgaaacttgacagtgacactccattcctttctgtgcagTGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCCCTCCGCGGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG