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'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaggctaactgtatatattatttttcagtatatgaaacttttagaccagtaaatagacaattttacataggcacatatctgacttgcatttctggagcagGCCGAGAACATCAAGTTTACCTTGGAGCAGCAGATGGTGTTCTTCGCTAGATTAGTGGGGCACTTCAAGGTGGCTGATGGCATCACTCCAATCAAGATCG

Basic information

species Oryza sativa
transcript LOC_Os06g11190.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g11190.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G000231_T01 (Zea mays), 3'ss of exon 14
aaggctaactgtatatattatttttcagtata-tgaaacttttagaccagtaaatagaca-attttacataggcacatatctgacttgcatttctg-gagcagGCCGAGAACATCAAGTTTACCTTGGAGCAGCAGATGGTGTTCTTCGCTAGATTAGTGGGGCACTTCAAGGTGGCTGATGGCATCACTCCAATCAAGATCG
 | | |||   | |  |||| | |     | | |  || ||  | |     || || | | |  | | |   | ||||  || || |||||| ||  || ||||| ||||||||||| ||||||||||||||| ||||||||||||| || |||||||||||  | ||||||||| |||||| ||| |||||||||||||| |
-aagttaagcattttaattaatataggacaaacttgaatttgcatagtgcaaactacagatagctaatacctg-acatg-ctcacatgcattcctttgaacagGCTGAGAACATCAAATTTACCTTGGAGCAGGAGATGGTGTTCTTGGCAAGATTAGTGGGAGAGTTCAAGGTGCCTGATGACATAACTCCAATCAAGATTG

upper sequence: LOC_Os06g11190.1 (Oryza sativa), 3'ss of exon 17
lower sequence: Vv18s0001g11140.t01 (Vitis vinifera), 3'ss of exon 17
aaggctaactgtatatattatttttcagtatatgaaacttttagaccagtaaatagacaattttacataggcacatatctgacttgcatttctggagcagGCCGAGAACATCAAGTTTACCTTGGAGCAGCAGATGGTGTTCTTCGCTAGATTAGTGGGGCACTTCAAGGTGGCTGATGGCATCACTCCAATCAAGATCG
       | | | ||| || | | | |  | ||  || |||||     | |  || | | ||  |  ||  || ||   ||  || |||         |||| || || || || || || |||||||| || ||||| ||||| ||| | |||||||| |||||||||||||| ||||  || ||||| ||||| ||||
-gtatgtattatctatgttttatctaatcacat--aatttttatttttg-aggtaaata-ttagaattaatcaaat---tgttttacat---------agGCTGAAAATATTAAATTCACATTGGAGCAACAAATGGTATTCTTTGCTCGTTTAGTGGGACACTTCAAGGTGGCAGATGAGATTACTCCCATCAAAATCG
















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|88263099|gb|CI366873.1|CI366873
EST:     TTCCTGTTGCTTTGGTCGAGTATGAAGGGGAACAACGTGTTTTCCGCAAG                         GCCGAGAACATCAAGTTTACCTTGGAGCAGCAGATGGTGTTCTTCGCTAGA
genomic: TTCCTGTTGCTTTGGTCGAGTATGAAGGGGAACAACATGGTTTCCGCAAGgtctgacgag ... tctggagcagGCCGAGAACATCAAGTTTACCTTGGAGCAGCAGATGGTGTTCTTCGCTAGA
EST: gi|88264886|gb|CI367537.1|CI367537
EST:     TTCCTGTTGCTTTGGTCGAGTATGAAGGGGAACAACATGGTTTCCGCAAG                         GCCGAGAACATCAAGTTTACCTTGGAGCAGCAGATGGTGTTCTTCGCTAGA
genomic: TTCCTGTTGCTTTGGTCGAGTATGAAGGGGAACAACATGGTTTCCGCAAGgtctgacgag ... tctggagcagGCCGAGAACATCAAGTTTACCTTGGAGCAGCAGATGGTGTTCTTCGCTAGA
EST: gi|88253789|gb|CI352415.1|CI352415
EST:     TTCCTGTTGCTTTGGTCGAGTATGAAGGGGAACAACATGGTTTCCGCAAG                         GCCGAGAACATCAAGTTTACCTTGGAGCAGCAGATGGTGTTCTTCGCTAGA
genomic: TTCCTGTTGCTTTGGTCGAGTATGAAGGGGAACAACATGGTTTCCGCAAGgtctgacgag ... tctggagcagGCCGAGAACATCAAGTTTACCTTGGAGCAGCAGATGGTGTTCTTCGCTAGA
EST: gi|87026895|gb|CI259548.1|CI259548
EST:     TTCCTGTTGCTTTGGTCGAGTATGAAGGGGAACAACATGGTTTCCGCAAG                         GCCGAGAACATCAAGTTTACCTTGGAGCAGCAGATGGTGTTCTTCGCTAGA
genomic: TTCCTGTTGCTTTGGTCGAGTATGAAGGGGAACAACATGGTTTCCGCAAGgtctgacgag ... tctggagcagGCCGAGAACATCAAGTTTACCTTGGAGCAGCAGATGGTGTTCTTCGCTAGA
EST: gi|29629333|gb|CB634344.1|CB634344
EST:     TTCCTGTTGCTTTGGTCGAGTATGAAGGGGAACAACATGGTTTCCGCAAG                         GCCGAGAACATCAAGTTTACCTTGGAGCAGCAGATGGTGTTCTTCGCTAGA
genomic: TTCCTGTTGCTTTGGTCGAGTATGAAGGGGAACAACATGGTTTCCGCAAGgtctgacgag ... tctggagcagGCCGAGAACATCAAGTTTACCTTGGAGCAGCAGATGGTGTTCTTCGCTAGA
EST: gi|29625693|gb|CB630704.1|CB630704
EST:     TTCCTGTTGCTTTGGTCGAGTATGAAGGGGAACAACATGGTTTCCGCAAG                         GCCGAGAACATCAAGTTTACCTTGGAGCAGCAGATGGTGTTCTTCGCTAGA
genomic: TTCCTGTTGCTTTGGTCGAGTATGAAGGGGAACAACATGGTTTCCGCAAGgtctgacgag ... tctggagcagGCCGAGAACATCAAGTTTACCTTGGAGCAGCAGATGGTGTTCTTCGCTAGA
EST: gi|88852504|gb|CI374272.1|CI374272
EST:     TCCTGTTGCTTTGGTCGAGTATGAAGGGGGAACAACATGGTTTCCGCAAG                         GCCGAGAACATCAAGTTTACCTTGGACCAGCAGATGGTGTTCTTCGCTAGA
genomic: TCCTGTTGCTTTGGTCGAGTATGAA-GGGGAACAACATGGTTTCCGCAAGgtctgacgag ... tctggagcagGCCGAGAACATCAAGTTTACCTTGGAGCAGCAGATGGTGTTCTTCGCTAGA
EST: gi|88250962|gb|CI349192.1|CI349192
EST:     TTCCTGTTGCTTTGGTCGAGTATGAAGGGGAACAACATGGTTTCCGCAAG                         GCCGAGAACATCAAGTTTACCTTGGAGCAGCAGATGGTGTTGTTCGCTAGA
genomic: TTCCTGTTGCTTTGGTCGAGTATGAAGGGGAACAACATGGTTTCCGCAAGgtctgacgag ... tctggagcagGCCGAGAACATCAAGTTTACCTTGGAGCAGCAGATGGTGTTCTTCGCTAGA
EST: gi|88297249|gb|CI545339.1|CI545339
EST:     TTCCTGTTGCTTTGGTCGAGTATGAAGGGGAACAACATGGTTTCCGCAAG                         GCCGAGAACATCAAGTTTACCTTGGAGCAGCAGATGGTGTTCTTCGCTAGA
genomic: TTCCTGTTGCTTTGGTCGAGTATGAAGGGGAACAACATGGTTTCCGCAAGgtctgacgag ... tctggagcagGCCGAGAACATCAAGTTTACCTTGGAGCAGCAGATGGTGTTCTTCGCTAGA
EST: gi|86865372|gb|CI330883.1|CI330883
EST:     TTCCTGTTGCTTTGGTCGAGTATGAAGGGGAACAACATGGTTTCCGCAAG                         GCCGAGAACATCAAGTTTACCTTGGAGCAGCAGATGNTGTTCTTCGCTAGA
genomic: TTCCTGTTGCTTTGGTCGAGTATGAAGGGGAACAACATGGTTTCCGCAAGgtctgacgag ... tctggagcagGCCGAGAACATCAAGTTTACCTTGGAGCAGCAGATGGTGTTCTTCGCTAGA
EST: gi|88272823|gb|CI386083.1|CI386083
EST:     TTCCTCTTGCTTTGGTCGAGTATGAAGGGGAACAACATGGTTTCCGCAAG                         GCCGAGAACATCAAG-TTACCTTGGAGCAGCAGATGGTGTTCTTCGCTAGA
genomic: TTCCTGTTGCTTTGGTCGAGTATGAAGGGGAACAACATGGTTTCCGCAAGgtctgacgag ... tctggagcagGCCGAGAACATCAAGTTTACCTTGGAGCAGCAGATGGTGTTCTTCGCTAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccagtaaatagacaattttacataggcacatatctgacttgcatttctggagcagGCCGAGAACATCAAGTTTACCTTGGAGCAGCAGATGGTGTTCTTCGCTAGATTAGTGGGGCACTTCAAGGTGGCTGATGGCATCACTCCAATCAAGATCG
                               atctgac  putative branch site (score: 3)
                                         catttct  putative PPT
     aaatagacaatttta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaggctaactgtatatattatttttcagtatatgaaacttttagaccagtaaatagacaattttacataggcacatatctgacttgcatttctggagcagGCCGAGAACATCAAGTTTACCTTGGAGCAGCAGATGGTGTTCTTCGCTAGATTAGTGGGGCACTTCAAGGTGGCTGATGGCATCACTCCAATCAAGATCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcacata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acttgca