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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgcaaccaaagttcattaattgtgactttgtgagaccctgaatattggatttactactgtaaattttctcttaactgcttcttctaatatataaaagtcttctgaaattttgaacagGAGGAAATAATAATGCTGCAAGATTGGTAGGAGCATGCAATGCACCAGATAAGTTTGAGATGTTGGATCTAGTCCATCCCCTTGTCTGGAGGCAGTCTAC

Basic information

species Oryza sativa
transcript LOC_Os08g42470.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g42470.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM5G882527_T03 (Zea mays), 3'ss of exon 7
---------------------------------------------------------gtactgcaaccaaagttcattaattgtgact--ttgtgagaccctgaatattggattta--ctactgtaaattttctcttaactgcttcttctaata------tataaaagtcttctg-------aaattttgaacagGAGGAAATAATAATGCTGCAAGATT-GGTAGGAGCATGCAATGCACCAGATAAGTTTGAGATGTTGGATCTAGTCCATCCCCTTGTCTGGAGGCAGTCTAC--
                                                             | |  |     | ||    | ||| ||  |     | | ||||| |||  | ||   ||||| | | |    | | |     |  | |||||       | ||| |   || ||           | || |||||| | ||  |||||||||| ||||| ||||||||||||||  | ||||||| |||||||||||||||||||||||||||||||||||||||    |       
gtacggtactattgcaagctaagttcattgattgggaggaggcctacatcctactaaaagtttcctctgtcatgcacctctggtgtctggtctcatgtctctgaaaattacacttcacctactctgattgaattatcaggccatcatgctaatgcccccgtttaataacattttgctttgctggtctctggacagGAAGGAA--ATAATGCTGCGAGATTTGGTAGGAGCATGCA-CGTACCAGATGAGTTTGAGATGTTGGATCTAGTCCATCCCCTTGTCTGGATTTGGAGAGAGC
















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|88518978|gb|CI446632.1|CI446632
EST:     GGGAAGAGTGACAGAGAAAGCAAGAAAAAAGGACCCCACATTGACAATAG                         GAGGAAATAATAATGCTGCAAGATTGGTAGGAGCATGCAATGCACCAGATA
genomic: GGGAAGAGTGACAGAGAAAGCAAGAAAAAAGGACCCCACATTGACAATAGgtactgcaac ... ttttgaacagGAGGAAATAATAATGCTGCAAGATTGGTAGGAGCATGCAATGCACCAGATA
EST: gi|58601809|gb|CK012337.1|CK012337
EST:     GGGAAGAGTGACAGAGAAAGCAAGAAAAAAGGACCCCACATTGACAATAG                         GAGGAAATAATAATGCTGCAAGATTGGTAGGAGCATGCAATGCACCAGATA
genomic: GGGAAGAGTGACAGAGAAAGCAAGAAAAAAGGACCCCACATTGACAATAGgtactgcaac ... ttttgaacagGAGGAAATAATAATGCTGCAAGATTGGTAGGAGCATGCAATGCACCAGATA
EST: gi|16574090|gb|BI801386.1|BI801386
EST:     GGTAAGAGTGACAGAGAAAGCAAG--AAAAGGACCCCACATTGACAATAG                         GAGGAAATAATAATGCTGCAAGATTGGTAGGAGCATGCAATGCACCAGATA
genomic: GG-AAGAGTGACAGAGAAAGCAAGAAAAAAGGACCCCACATTGACAATAGgtactgcaac ... ttttgaacagGAGGAAATAATAATGCTGCAAGATTGGTAGGAGCATGCAATGCACCAGATA
EST: gi|88488916|gb|CI426187.1|CI426187
EST:     GGGAAGAGTGACAGAGAAAGCAAGAAAAAAGGACCCCACATTGACAATAG                         GAGGAAATAATAATGCTGCAAGATTGGTAGGAGCATGCAATGCACCAGATA
genomic: GGGAAGAGTGACAGAGAAAGCAAGAAAAAAGGACCCCACATTGACAATAGgtactgcaac ... ttttgaacagGAGGAAATAATAATGCTGCAAGATTGGTAGGAGCATGCAATGCACCAGATA
EST: gi|88471081|gb|CI408352.1|CI408352
EST:     GGGAAGAGTGACAGAGAAAGCAAGAAAAAAGGACCCCACATTGACAATAG                         GAGGAAATAATAATGCTGCAAGATTGGTAGGAGCATGCAATGCACCAGATA
genomic: GGGAAGAGTGACAGAGAAAGCAAGAAAAAAGGACCCCACATTGACAATAGgtactgcaac ... ttttgaacagGAGGAAATAATAATGCTGCAAGATTGGTAGGAGCATGCAATGCACCAGATA
EST: gi|88520643|gb|CI448297.1|CI448297
EST:     GGGAAGAGTGACAGAGAAAGCAAGAAAAAAGGACCCCACATTGACAATAG                         GAGGAAATAATAATGCTGCAAGATTGGTAGGAGCATGCAATGCACCAGATA
genomic: GGGAAGAGTGACAGAGAAAGCAAGAAAAAAGGACCCCACATTGACAATAGgtactgcaac ... ttttgaacagGAGGAAATAATAATGCTGCAAGATTGGTAGGAGCATGCAATGCACCAGATA
EST: gi|58669636|gb|CK058322.1|CK058322
EST:     GGGAAGAGTGACAGAGAAAGCAAGAAAAAAGGACCCCACATTGACAATAG                         GAGGAAATAATAATGCTGCAAGATTGGTAGGAGCATGCAATGCACCAGATA
genomic: GGGAAGAGTGACAGAGAAAGCAAGAAAAAAGGACCCCACATTGACAATAGgtactgcaac ... ttttgaacagGAGGAAATAATAATGCTGCAAGATTGGTAGGAGCATGCAATGCACCAGATA
EST: gi|58600753|gb|CK011281.1|CK011281
EST:     GGGAAGAGTGACAGAGAAAGCAAGAAAAAAGGACCCCACATTGACAATAG                         GAGGAAATAATAATGCTGCAAGATTGGTAGGAGCATGCAATGCACCAGATA
genomic: GGGAAGAGTGACAGAGAAAGCAAGAAAAAAGGACCCCACATTGACAATAGgtactgcaac ... ttttgaacagGAGGAAATAATAATGCTGCAAGATTGGTAGGAGCATGCAATGCACCAGATA
EST: gi|88219040|gb|CI220600.1|CI220600
EST:     GGGAAGAGTGACAGAGAAAGCAAGAAAAAAGGACCCCACATTGACAATAG                         GAGGAAATAATAATGCTGCAAGATTGGTAGGAGCATGCAATGCACCAGATA
genomic: GGGAAGAGTGACAGAGAAAGCAAGAAAAAAGGACCCCACATTGACAATAGgtactgcaac ... ttttgaacagGAGGAAATAATAATGCTGCAAGATTGGTAGGAGCATGCAATGCACCAGATA
EST: gi|88503165|gb|CI430671.1|CI430671
EST:     GGGAAGAGTGACAGAGAAAGCAAGAAAAAAGGACCCCACATTGACAATAG                         GAGGAAATAATAATGCTGCAAGATTGGTAGGAGCATGCAATGCACCAGATA
genomic: GGGAAGAGTGACAGAGAAAGCAAGAAAAAAGGACCCCACATTGACAATAGgtactgcaac ... ttttgaacagGAGGAAATAATAATGCTGCAAGATTGGTAGGAGCATGCAATGCACCAGATA
EST: gi|88469562|gb|CI406833.1|CI406833
EST:     GGGAAGAGTGACAGAGAAAGCAAGAAAAAAGGACCCCACATTGACAATAG                         GAGGAAATAATAATGCTGCAAGATTGGTAGGAGCATGCAATGCACCAGATA
genomic: GGGAAGAGTGACAGAGAAAGCAAGAAAAAAGGACCCCACATTGACAATAGgtactgcaac ... ttttgaacagGAGGAAATAATAATGCTGCAAGATTGGTAGGAGCATGCAATGCACCAGATA
EST: gi|88518576|gb|CI446230.1|CI446230
EST:     GGGAAGAGTGACAGAGAAAGCAAGAAAAAAGGACCCCACATTGACAATAG                         GAGGAAATAATAATGCTGCAAGATTGGTAGGAGCATGCAATGCACCAGATA
genomic: GGGAAGAGTGACAGAGAAAGCAAGAAAAAAGGACCCCACATTGACAATAGgtactgcaac ... ttttgaacagGAGGAAATAATAATGCTGCAAGATTGGTAGGAGCATGCAATGCACCAGATA
EST: gi|15852910|gb|BI805706.1|BI805706
EST:     GGGAAGAGTGACAGAGAAAGCAAGAAAAAAGGACCCCACATTGACAATAG                         GAGGAAATAATAATGCTGCAAGATTGGTAGGAGCATGCAATGCACCAGATA
genomic: GGGAAGAGTGACAGAGAAAGCAAGAAAAAAGGACCCCACATTGACAATAGgtactgcaac ... ttttgaacagGAGGAAATAATAATGCTGCAAGATTGGTAGGAGCATGCAATGCACCAGATA
EST: gi|15852981|gb|BI805777.1|BI805777
EST:     GGGAAGAGTGACAGAGAAAGCAAGAAAAAAGGACCCCACATTGAC-ATAG                         GAGGAAATAATAATGCTGCAAGATTGGTAGGAGCATGCAATGCACCAGATA
genomic: GGGAAGAGTGACAGAGAAAGCAAGAAAAAAGGACCCCACATTGACAATAGgtactgcaac ... ttttgaacagGAGGAAATAATAATGCTGCAAGATTGGTAGGAGCATGCAATGCACCAGATA
EST: gi|88475984|gb|CI413255.1|CI413255
EST:     GGGAAGAGTGACAGAGAAAGCAAGAAAAAAGGACCCCACATTGACAATAG                         GAGGAAATAATAATGCTGCAAGATTGGTAGGAGCATGCAATGCACCAGATA
genomic: GGGAAGAGTGACAGAGAAAGCAAGAAAAAAGGACCCCACATTGACAATAGgtactgcaac ... ttttgaacagGAGGAAATAATAATGCTGCAAGATTGGTAGGAGCATGCAATGCACCAGATA
EST: gi|88972976|gb|CI019595.1|CI019595
EST:     GGGAAGAGTGACAGAGAAAGCAAGAAAAAAGGACCCCACATTGACAATAG                         GAGGAAATAATAATGCTGCAAGATTGGTAGGAGCATGCAATGCACCAGATA
genomic: GGGAAGAGTGACAGAGAAAGCAAGAAAAAAGGACCCCACATTGACAATAGgtactgcaac ... ttttgaacagGAGGAAATAATAATGCTGCAAGATTGGTAGGAGCATGCAATGCACCAGATA
EST: gi|88516755|gb|CI442411.1|CI442411
EST:     GGGAAGAGTGACAGAGAAAGCAAGAAAAAAGGACCCCACATTGACAATAG                         GAGGAAATAATAATGCTGCAAGATTGGTAGGAGCATGCAATGCACCAGATA
genomic: GGGAAGAGTGACAGAGAAAGCAAGAAAAAAGGACCCCACATTGACAATAGgtactgcaac ... ttttgaacagGAGGAAATAATAATGCTGCAAGATTGGTAGGAGCATGCAATGCACCAGATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttctcttaactgcttcttctaatatataaaagtcttctgaaattttgaacagGAGGAAATAATAATGCTGCAAGATTGGTAGGAGCATGCAATGCACCAGATAAGTTTGAGATGTTGGATCTAGTCCATCCCCTTGTCTGGAGGCAGTCTAC
                   ttctaat  putative branch site (score: 2)
                      taatatataaaagtct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgcaaccaaagttcattaattgtgactttgtgagaccctgaatattggatttactactgtaaattttctcttaactgcttcttctaatatataaaagtcttctgaaattttgaacagGAGGAAATAATAATGCTGCAAGATTGGTAGGAGCATGCAATGCACCAGATAAGTTTGAGATGTTGGATCTAGTCCATCCCCTTGTCTGGAGGCAGTCTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG