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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggctccccatggcttctctcccctctcaatcgcggccaaaattccactgggttttctgctacttttgagccataaatccccgagaaaccctaactaacaagtgattttccatcgcagGATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCCAACCTCGTCGTCATCAACCCAG

Basic information

species Oryza sativa
transcript LOC_Os04g09860.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g09860.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G101250_T02 (Zea mays), 3'ss of exon 1
gtaggctccccatggcttctctcccctctcaatcgcggccaaaattccactgggttt--tctgctacttttgagccataaatccccgagaaaccctaac----------taacaagtgattttccatc--gcagGATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCCAACCTCGTCGTCATCAACCCAG
||| || ||      | ||   ||   || |  | |  ||    | |||| |    |  | || | ||  ||  ||||||| ||| ||||||||||| |          | |||  ||||| |   ||  |||||| ||||||| |||||||||||| ||||| ||  |||| ||||||||| |||| || ||||||||||||||||
gtaagcgccatcgtccctcctcccttccttatcctcttccg---tcccaccgcacctggtttgttcctcctgc-ccataaaccccggagaaaccctagcgagcggcgattgacatttgattgtgtgtcccgcagGACTACCTCAGGACGGTGGTTCCGTCACAACTCTTGGCAGAGCGCGGCTCCAATCTTGTCGTCATCAACCCAG
















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|88332583|gb|CI651743.1|CI651743
EST:     CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATG                         GATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
genomic: CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATGgtaggctccc ... tccatcgcagGATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
EST: gi|88335917|gb|CI645518.1|CI645518
EST:     CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATG                         GATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
genomic: CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATGgtaggctccc ... tccatcgcagGATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
EST: gi|88308695|gb|CI653582.1|CI653582
EST:     CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATG                         GATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
genomic: CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATGgtaggctccc ... tccatcgcagGATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
EST: gi|88338766|gb|CI660537.1|CI660537
EST:     CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATG                         GATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
genomic: CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATGgtaggctccc ... tccatcgcagGATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
EST: gi|88341777|gb|CI642921.1|CI642921
EST:     CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATG                         GATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
genomic: CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATGgtaggctccc ... tccatcgcagGATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
EST: gi|88361061|gb|CI646085.1|CI646085
EST:     CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATG                         GATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
genomic: CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATGgtaggctccc ... tccatcgcagGATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
EST: gi|88377794|gb|CI637928.1|CI637928
EST:     CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATG                         GATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
genomic: CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATGgtaggctccc ... tccatcgcagGATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
EST: gi|58601435|gb|CK011963.1|CK011963
EST:     CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATG                         GATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
genomic: CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATGgtaggctccc ... tccatcgcagGATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
EST: gi|88346448|gb|CI637294.1|CI637294
EST:     CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATG                         GATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
genomic: CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATGgtaggctccc ... tccatcgcagGATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
EST: gi|88573821|gb|CI665590.1|CI665590
EST:     CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATG                         GATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
genomic: CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATGgtaggctccc ... tccatcgcagGATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
EST: gi|88664834|gb|CI701384.1|CI701384
EST:     CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATG                         GATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
genomic: CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATGgtaggctccc ... tccatcgcagGATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
EST: gi|29634037|gb|CB639046.1|CB639046
EST:     CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATG                         GATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
genomic: CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATGgtaggctccc ... tccatcgcagGATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
EST: gi|88726267|gb|CI749922.1|CI749922
EST:     CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATG                         GATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
genomic: CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATGgtaggctccc ... tccatcgcagGATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
EST: gi|88305179|gb|CI651976.1|CI651976
EST:     CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATG                         GATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
genomic: CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATGgtaggctccc ... tccatcgcagGATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
EST: gi|88731371|gb|CI754984.1|CI754984
EST:     CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATG                         GATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
genomic: CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATGgtaggctccc ... tccatcgcagGATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
EST: gi|88330185|gb|CI658490.1|CI658490
EST:     CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATG                         GATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
genomic: CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATGgtaggctccc ... tccatcgcagGATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
EST: gi|88592435|gb|CI710537.1|CI710537
EST:     CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATG                         GATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
genomic: CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATGgtaggctccc ... tccatcgcagGATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
EST: gi|88341776|gb|CI642920.1|CI642920
EST:     CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATG                         GATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
genomic: CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATGgtaggctccc ... tccatcgcagGATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
EST: gi|88717504|gb|CI741014.1|CI741014
EST:     CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATG                         GATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGGGCC
genomic: CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATGgtaggctccc ... tccatcgcagGATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
EST: gi|29643625|gb|CB648632.1|CB648632
EST:     CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATG                         GATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
genomic: CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATGgtaggctccc ... tccatcgcagGATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
EST: gi|86909359|gb|CI304636.1|CI304636
EST:     CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATG                         GATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
genomic: CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATGgtaggctccc ... tccatcgcagGATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
EST: gi|88294215|gb|CI667189.1|CI667189
EST:     CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATG                         GATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
genomic: CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATGgtaggctccc ... tccatcgcagGATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
EST: gi|88328228|gb|CI651236.1|CI651236
EST:     CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATG                         GATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
genomic: CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATGgtaggctccc ... tccatcgcagGATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
EST: gi|88574595|gb|CI666364.1|CI666364
EST:     CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATG                         GATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
genomic: CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATGgtaggctccc ... tccatcgcagGATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
EST: gi|66932263|gb|CX119111.1|CX119111
EST:     CTTCCCTTCCCTTCCGACGCGCGCGACGCCGTCTCCGGGGAGAAAATATG                         GATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC
genomic: CTTCCCTTCCCTTCCGACGCGCGCGACGCCTTCTCCGGGGAGAAAATATGgtaggctccc ... tccatcgcagGATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgagccataaatccccgagaaaccctaactaacaagtgattttccatcgcagGATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCCAACCTCGTCGTCATCAACCCAG
                             aactaac  putative branch site (score: 1)
                                          ttttccatc  putative PPT
         ataaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggctccccatggcttctctcccctctcaatcgcggccaaaattccactgggttttctgctacttttgagccataaatccccgagaaaccctaactaacaagtgattttccatcgcagGATTACCTCAAGACGGTGGTTCCATCACAGCTGATGGCCGAGCGCGGCGCCAACCTCGTCGTCATCAACCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT