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

gtgaggatgcatttatctcattttctcatatttgccgaaagaaaaaaaatataaccattgatgcgggtattacttttccaagtggaaattttatttacatctgcaaattcaaattaattaaattagtgagaatgtgtacaatttacctgatattctgattcttttgtgaagGTATGGATTATTGGGTAAGAAAATAAAAGACACATTTGGTCACATAGGAGGACCGATATTAGGTGGGCTTGTGGGACTGAAGAAGCCGAACAACCATGGC

Basic information

species Oryza sativa
transcript LOC_Os12g26290.5
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g26290.5 (Oryza sativa), 3'ss of exon 7
lower sequence: AC205471.4_FGT004 (Zea mays), 3'ss of exon 4
gtgaggatgcatttatctcattttctcatatttgccgaaagaaaaaaaatataaccattgatgcgggtattacttttccaagtggaaattttatttacatctgcaaattcaaattaattaaattagtgagaatgtgtacaa-tttacctgatattctgattcttttgtgaagGTATGGATTATTGGGTAAGAAAATAAAAGACACATTTGGTCACATAGGAGGACCGATATTAGGTGGGCTTGTGGGACTGAAGAAGCCGAACAACCATGGC
||||||||  ||| ||||||||||||||||||||  ||||||||| ||         || | || |||||||||||||||||||||||||||||||||||||||| ||||||||||||||| ||||||||| ||||||||| |||||||   ||||| |||||||||||||||||||| ||||||||||||||||||||||| ||||||||||||||||||||||||| |||||||||||| |||||  |||||||||||| ||||||||||
gtgaggatatatt-atctcattttctcatatttgttgaaagaaaacaa---------ttaacgctggtattacttttccaagtggaaattttatttacatctgcatattcaaattaattaa-ttagtgagattgtgtacaaatttacct--cattctaattcttttgtgaagGTATGGTTTATTGGGTAAGAAAATAAAAGATACATTTGGTCACATAGGAGGACCGACATTAGGTGGGCTCGTGGGGTTGAAGAAGCCGATCAACCATGGC

upper sequence: LOC_Os12g26290.5 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM5G818450_T01 (Zea mays), 3'ss of exon 2
gtgaggatgcatttatctcattttctcatatttgccgaaagaaaaaaaatataaccattgatgcgggtattacttttccaagtggaaattttatttacatctgcaaattcaaattaattaaattagtgagaatgtgtacaa-tttacctgatattctgattcttttgtgaagGTATGGATTATTGGGTAAGAAAATAAAAGACACATTTGGTCACATAGGAGGACCGATATTAGGTGGGCTTGTGGGACTGAAGAAGCCGAACAACCATGGC
||||||||  ||| ||||||||||||||||||||  ||||||||| ||         || | || | ||||||||||||||||||||||||||||||||| | || ||||||||||||||| ||||||||| ||||||||| |||||||   ||||| |||||||||||||||||||  ||||||||||||||||||||||| ||||||||||||||||||||||||| ||||||||||||||||||| |||||||||||| ||||||||||
gtgaggatatatt-atctcattttctcatatttgttgaaagaaaacaa---------ttaacgctgatattacttttccaagtggaaattttatttacatgt-catattcaaattaattaa-ttagtgagattgtgtacaaatttacct--cattctaattcttttgtgaagGTATGATTTATTGGGTAAGAAAATAAAAGATACATTTGGTCACATAGGAGGACCGACATTAGGTGGGCTTGTGGGATTGAAGAAGCCGATCAACCATGGC

upper sequence: LOC_Os12g26290.5 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G100724_T01 (Zea mays), 3'ss of exon 4
gtgaggatgcatttatctcattttctcatatttgccgaaagaaaaaaaatataaccattgatgcgggtattacttttccaagtggaaattttatttacatctgcaaattcaaattaattaaattagtgagaatgtgtacaa-tttacctgatattctgattcttttgtgaagGTATGGATTATTGGGTAAGAAAATAAAA-GACACATTTGGTCACATAGGAGGACCGATATTAGGTGGGCTTGTGGGACTGAAGAAGCCGAACAACCATGGC
||||||||  ||| ||||| ||||||||||||||  ||||||||| ||         || |  | |||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||| ||||||||| |||||||    |||| |||||||||||||||||||| ||||||||||||||||||||| || |||||||||||||||||||||||||  |||||||||||||||||| |||||||||||| ||||||||| 
gtgaggatatatt-atctcgttttctcatatttgttgaaagaaaacaa---------ttaacactggtattacttttccaagtggaaattttatttacatctgcaaattcaaattaattaa-ttagtgagattgtgtacaaatttacct--cgttctaattcttttgtgaagGTATGGTTTATTGGGTAAGAAAATAAAAAGATACATTTGGTCACATAGGAGGACCGACGTTAGGTGGGCTTGTGGGATTGAAGAAGCCGATCAACCATGG-

upper sequence: LOC_Os12g26290.5 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G312997_T01 (Zea mays), 3'ss of exon 6
gtgaggatgcatttatctcattttctcatatttgccgaaagaaaaaaaatataaccattgatgcgggtattacttttccaagtggaaattttatttacatctgcaaattcaaattaattaaattagtgagaatgtgtacaa-tttacctgatattctgattcttttgtgaagGTATGGATTATTGGGTAAGAAAATAAAAGACACATTTGGTCACATAGGAGGACCGATATTAGGTGGGCTTGTGGGACTGAAGAAGCCGAACAACCATGGC
||||||||  ||| ||||||||||||||||||||  ||||||||| ||         || | || ||||||||||||||||||||||||||||||||||||||||||||||||| |||||| ||||||||| ||||||||| ||||||| ||||||| |||||||||||||||||||| ||||||||||||||||||||||| ||||||||||||||||||||||||  ||||||||||||||||||| |||||||||||| ||||||||||
gtgaggatatatt-atctcattttctcatatttgttgaaagaaaacaa---------ttaacgctggtattacttttccaagtggaaattttatttacatctgcaaattcaaataaattaa-ttagtgagattgtgtacaaatttacctcatattctaattcttttgtgaagGTATGGTTTATTGGGTAAGAAAATAAAAGATACATTTGGTCACATAGGAGGACCGGCATTAGGTGGGCTTGTGGGATTGAAGAAGCCGATCAACCATGGC

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|29615618|gb|CB620630.1|CB620630
EST:     GTCGAGCTTCTCAAGACAAAAACCATGAGAGCTGCAATGCGTGCAAATTG                         GTATGGATTATTGGGTAAGAAAATAAAAGACACATTTGGTCACATAGGAGG
genomic: GTCGAGCTTCTCAAGACAAAAACCATGAGAGCTGCAATGCGCGCAAATTGgtgaggatgc ... ttttgtgaagGTATGGATTATTGGGTAAGAAAATAAAAGACACATTTGGTCACATAGGAGG
EST: gi|29620985|gb|CB625996.1|CB625996
EST:     GTCGAGCTTCTCAAGACAAAAACCATGAGAGCTGCAATGCGTGCAAATTG                         GTATGGATTATTGGGTAAGAAAATAAAAGACACATTTGGTCACATAGGAGG
genomic: GTCGAGCTTCTCAAGACAAAAACCATGAGAGCTGCAATGCGCGCAAATTGgtgaggatgc ... ttttgtgaagGTATGGATTATTGGGTAAGAAAATAAAAGACACATTTGGTCACATAGGAGG
EST: gi|29613656|gb|CB618669.1|CB618669
EST:     GTCGAGCTTCTCAAGACAAAAACCATGAGAGCTGCAATGCGTGCAAATTG                         GTATGGATTATTGGGTAAGAAAATAAAAGACACATTTGGTCACATAGGAGG
genomic: GTCGAGCTTCTCAAGACAAAAACCATGAGAGCTGCAATGCGCGCAAATTGgtgaggatgc ... ttttgtgaagGTATGGATTATTGGGTAAGAAAATAAAAGACACATTTGGTCACATAGGAGG
EST: gi|29613620|gb|CB618633.1|CB618633
EST:     GTCGAGCTTCTCAAGACAAAAACCATGAGAGCTGCAATGCGTGCAAATTG                         GTATGGATTATTGGGTAAGAAAATAAAAGACACATTTGGTCACATAGGAGG
genomic: GTCGAGCTTCTCAAGACAAAAACCATGAGAGCTGCAATGCGCGCAAATTGgtgaggatgc ... ttttgtgaagGTATGGATTATTGGGTAAGAAAATAAAAGACACATTTGGTCACATAGGAGG
EST: gi|58585656|gb|CF983964.1|CF983964
EST:     GTCGAGCTTCTCAAGACAAAAACCATGAGAGCTGCAATGCGCGCAAATTG                         GTATGGATTATTGGGTAAGAAAATAAAAGACACATTTGGTCACATAGGAGG
genomic: GTCGAGCTTCTCAAGACAAAAACCATGAGAGCTGCAATGCGCGCAAATTGgtgaggatgc ... ttttgtgaagGTATGGATTATTGGGTAAGAAAATAAAAGACACATTTGGTCACATAGGAGG
EST: gi|29620729|gb|CB625740.1|CB625740
EST:     GTCGAGCTTCTCAAGACAAAAACCATGAGAGCTGCAATGCGTGCAAATTG                         GTATGGATTATTGGGTAAGAAAATAAAAGACACATTTGGTCACATAGGAGG
genomic: GTCGAGCTTCTCAAGACAAAAACCATGAGAGCTGCAATGCGCGCAAATTGgtgaggatgc ... ttttgtgaagGTATGGATTATTGGGTAAGAAAATAAAAGACACATTTGGTCACATAGGAGG
EST: gi|66924965|gb|CX111813.1|CX111813
EST:     GTCGAGCTTCTCAAGACAAAAACCATGAGAGCTGCAATGCGCGCAAATTG                         GTATGGATTATTGGGTAAGAAAATAAAAGACACATTTGGTCACATAGGAGG
genomic: GTCGAGCTTCTCAAGACAAAAACCATGAGAGCTGCAATGCGCGCAAATTGgtgaggatgc ... ttttgtgaagGTATGGATTATTGGGTAAGAAAATAAAAGACACATTTGGTCACATAGGAGG
EST: gi|29613584|gb|CB618597.1|CB618597
EST:     GTCGAGCTTCTCAAGACAAAAACCATGAGAGCTGCAATGCGTGCAAATTG                         GTATGGATTATTGGGTAAGAAAATAAAAGACACATTTGGTCACATAGGAGG
genomic: GTCGAGCTTCTCAAGACAAAAACCATGAGAGCTGCAATGCGCGCAAATTGgtgaggatgc ... ttttgtgaagGTATGGATTATTGGGTAAGAAAATAAAAGACACATTTGGTCACATAGGAGG
EST: gi|29677261|gb|CB673536.1|CB673536
EST:     GTCGAGCTTCTCAAGACAAAAACCATGAGAGCTGCAATGCGCGCAAATTG                         GTATGGATTATTGGGTAAGAAAATAAA-GACACATTTGGTCACA
genomic: GTCGAGCTTCTCAAGACAAAAACCATGAGAGCTGCAATGCGCGCAAATTGgtgaggatgc ... ttttgtgaagGTATGGATTATTGGGTAAGAAAATAAAAGACACATTTGGTCACA
EST: gi|29612897|gb|CB617910.1|CB617910
EST:     GTCGAGCTTCTCAAGACAAAAACCATGAGAGCTGCAATGCGTGCAAATTG                         GTATGGATTATTGGGTAAGAAAATAAAAGACACATTTGGTCACATAGGAGG
genomic: GTCGAGCTTCTCAAGACAAAAACCATGAGAGCTGCAATGCGCGCAAATTGgtgaggatgc ... ttttgtgaagGTATGGATTATTGGGTAAGAAAATAAAAGACACATTTGGTCACATAGGAGG
EST: gi|29629207|gb|CB634218.1|CB634218
EST:     TCGAGCTTCTCAAGACAAAAACCATGAGAGCTGNCA-TGCGCGCAAATTG                         GTATGGATTATTGGGT
genomic: TCGAGCTTCTCAAGACAAAAACCATGAGAGCTG-CAATGCGCGCAAATTGgtgaggatgc ... ttttgtgaagGTATGGATTATTGGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attaaattagtgagaatgtgtacaatttacctgatattctgattcttttgtgaagGTATGGATTATTGGGTAAGAAAATAAAAGACACATTTGGTCACATAGGAGGACCGATATTAGGTGGGCTTGTGGGACTGAAGAAGCCGAACAACCATGGC
                                    ttctgat  putative branch site (score: 3)
                                          ttcttttgt  CT-rich tract
                    tacaattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaggatgcatttatctcattttctcatatttgccgaaagaaaaaaaatataaccattgatgcgggtattacttttccaagtggaaattttatttacatctgcaaattcaaattaattaaattagtgagaatgtgtacaatttacctgatattctgattcttttgtgaagGTATGGATTATTGGGTAAGAAAATAAAAGACACATTTGGTCACATAGGAGGACCGATATTAGGTGGGCTTGTGGGACTGAAGAAGCCGAACAACCATGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC