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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctgaaatgttttgcatactcttttgcctactgcatcgtctctttatttgttgttttcaattctttaacatcaccaattttcagGCCAAAGCTCTAGCTGAAAAGAATATGCGGGACATGCTGGCTCAGAGAGAGCAAGCAGAGAGACAT

Basic information

species Oryza sativa
transcript LOC_Os01g44310.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g44310.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G316635_T03 (Zea mays), 3'ss of exon 3
-------------------------------------------------gtatgctgaaatgttttgcatactcttttgcctactgcatcgtctctttatttgttgttttcaattctttaacatcaccaattttcagGCCAAAGCTCTAGCTGAAAAGAATATGCGGGACATGCTGGCTCAGAGAGAGCAAGCAGAGAGACAT
                                                 |||| ||  |||| | |   | || | |||| | || | | || | |||   |    | |   | || | | ||| |||||||||||||| ||||| || |||||||||||||||||||| |||||||  ||||| ||||| || |||| ||||
acgacataaagcaaaattggaaaggcaccaacgcacagctgagcgagcggtatacttcaatgctat---tgctatgttgcattctac-ttgtttgtttgcctagCCTGTGGCAGTCCTCATCATTACCAATTTTCAGGCGAAAGCCCTTGCTGAAAAGAATATGCGGGATATGCTGGTGCAGAGGGAGCATGCTGAGAAACAT

upper sequence: LOC_Os01g44310.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G316635_T02 (Zea mays), 3'ss of exon 4
gtatgctgaaatgttttgcatactcttttgcctactgcatcgtctctttatttgttgttttcaattctttaacatcaccaattttcagGCCAAAGCTCTAGCTGAAAAGAATATGCGGGACATGCTGGCTCAGAGAGAGCAAGCAGAGAGACAT
|||| ||  |||| | |   | || | |||| | || | | || | |||   |    | |   | || | | ||| |||||||||||||| ||||| || |||||||||||||||||||| |||||||  ||||| ||||| || |||| ||||
gtatacttcaatgctat---tgctatgttgcattctac-ttgtttgtttgcctagcctgtggcagtcctcatcattaccaattttcagGCGAAAGCCCTTGCTGAAAAGAATATGCGGGATATGCTGGTGCAGAGGGAGCATGCTGAGAAACAT

upper sequence: LOC_Os01g44310.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G316635_T01 (Zea mays), 3'ss of exon 4
gtatgctgaaatgttttgcatactcttttgcctactgcatcgtctctttatttgttgttttcaattctttaacatcaccaattttcagGCCAAAGCTCTAGCTGAAAAGAATATGCGGGACATGCTGGCTCAGAGAGAGCAAGCAGAGAGACAT----------------------------------
|||| ||  |||| | |   | || | |||| | || | | || | |||   |    | |   | || | | ||| |||||||||||||| ||||| || |||||||||||||||||||| |||||||  ||||| ||||| || |||| ||||                                  
gtatacttcaatgctat---tgctatgttgcattctac-ttgtttgtttgcctagcctgtggcagtcctcatcattaccaattttcagGCGAAAGCCCTTGCTGAAAAGAATATGCGGGATATGCTGGTGCAGAGGGAGCATGCTGAGAAACATGTAAGATAGTTGGTCATCAGGAAAGAAAAACATA

upper sequence: LOC_Os01g44310.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv18s0001g12770.t01 (Vitis vinifera), 3'ss of exon 3
---------------gtatgctgaaatgttttgcatactcttttgcctactgcatcgtctctttatttgttgttttcaattctttaacatcaccaattttcagGCCAAAGCTCTAGCTGAAAAGAATATGCGGGACATGCTGGCTCAGAGAGAGCAAGCAGAGAGACAT
                | | | ||   |   | || |    ||    |   ||   |||   | |   |||      ||  | ||  | |   |   | |||||| |||| ||| |  || ||||||||||||||  | || ||||||| |||||||||||||||| | 
gtatacttcctgcttctgtccagattcgggattcaaatctgttgatatgtggc--tgtcaagtaacaggtttgacataacgccttttc-tggtcttgtctcagGCAAAAGTTCTTGAGGAGAAGAATATGCGGGATCTACTTGCTCAGAAAGAGCAAGCAGAGAGAAAC

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|33653814|gb|CF276428.1|CF276428
EST:     TGAGACATAAAGCAAGATCTGAGAGGGAACATCGCACAGCTGAGCGAGCG                         GCCAAAGCTCTAGCTGAAAAGAATATGCGGGACATGCTGGCTCAGAGAGAG
genomic: TGAGACATAAAGCAAGATCTGAGAGGGAACATCGCACAGCTGAGCGAGCGgtatgctgaa ... caattttcagGCCAAAGCTCTAGCTGAAAAGAATATGCGGGACATGCTGGCTCAGAGAGAG
EST: gi|29617071|gb|CB622083.1|CB622083
EST:     TGAGACATAAAGCAAGATCTGAGAGGGAACATCGCACAGCTGAGCGAGCG                         GCCAAAGCTCTAGCTGAAAAGAATATGCGGGACATGCTGGCTCAGAGAGAG
genomic: TGAGACATAAAGCAAGATCTGAGAGGGAACATCGCACAGCTGAGCGAGCGgtatgctgaa ... caattttcagGCCAAAGCTCTAGCTGAAAAGAATATGCGGGACATGCTGGCTCAGAGAGAG
EST: gi|29621424|gb|CB626435.1|CB626435
EST:     AGAGGGAACATCGCACAGCTGAGCGAGCG                         GCCAAAGCTCTAGCTGAAAAGAATATGCGGGACATGCTGGCTCAGAGAGAG
genomic: AGAGGGAACATCGCACAGCTGAGCGAGCGgtatgctgaa ... caattttcagGCCAAAGCTCTAGCTGAAAAGAATATGCGGGACATGCTGGCTCAGAGAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgcatcgtctctttatttgttgttttcaattctttaacatcaccaattttcagGCCAAAGCTCTAGCTGAAAAGAATATGCGGGACATGCTGGCTCAGAGAGAGCAAGCAGAGAGACAT
                                 ctttaac  putative branch site (score: 3)
                                                ttttc  putative PPT
             tttatttgttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctgaaatgttttgcatactcttttgcctactgcatcgtctctttatttgttgttttcaattctttaacatcaccaattttcagGCCAAAGCTCTAGCTGAAAAGAATATGCGGGACATGCTGGCTCAGAGAGAGCAAGCAGAGAGACAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG