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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtcaggccttctttattattttcccccttattttcggagcaactagcttaccatctatcagagtcgtacttcaactgtgatattattctgtggcagATCGACAGCAACACTGATGGTCTTGTGGACTTTGAAGAGTTTGTAGCAGCAACCCTCCATATACATCAAATGGCTGAGCTTGACTCTGAAAGGTGGGGCC

Basic information

species Oryza sativa
transcript LOC_Os02g03410.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g03410.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G157068_T01 (Zea mays), 3'ss of exon 10
----------------gtaagtgtcaggccttctttattattttcccccttattttcggagcaactagcttaccat-ctatcagagtcgtacttcaactgtgatattattctgtggcagATCGACAGCAACACTGATGGTCTTGTGGACTTTGAAGAGTTTGTAGCAGCAACCCTCCATATACATCAAATGGCTGAGCTTGACTCTGAAAGGTGGGGCC
                 |  |  ||  ||| | | | || ||  ||||||| ||| |  || || |||||  || |  | | || ||   ||   |||||  || ||||| ||||| |||| ||||||||||||||||| || ||||||||  | |||||||| || ||||| |||||||| || || ||||| ||||| ||||| |||||||||||| 
gtaagtttgagccttcttctggatccagccctttct-ttgttaccccccttgtttcca-agaaaatagctggccttgttctgagggtataaccaaaactgc-atcttattttgtggtagATTGACAGCAACACTGATGGGCTCGTGGACTTCAAGGAGTTTGTTGCGGCAACTCTCCATATCCACCAGATGGCGGAGCTCGACTCAGAAAGGTGGGGCA
















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|87024700|gb|CI259415.1|CI259415
EST:     ATCTTCCTTGGAGATTGAAGGGCCCCCGTGTTCTCGAGATTATCCAAGCA                         ATCGACAGCAACACTGATGGTCTTGTGGACTTTGAAGAGTTTGTAGCAGCA
genomic: ATCTTCCTTGGAGATTGAAGGGCCCCCGTGTTCTCGAGATTATCCAAGCAgtaagtgtca ... tctgtggcagATCGACAGCAACACTGATGGTCTTGTGGACTTTGAAGAGTTTGTAGCAGCA
EST: gi|87027206|gb|CI278238.1|CI278238
EST:     ATCTTCCTTGGAGATTGAAGGGCCCCCGTGTTCTCGAGATTATCCAAGCA                         ATCGACAGCAACACTGATGGTCTTGTGGACTTTGAAGAGTTTGTAGCAGCA
genomic: ATCTTCCTTGGAGATTGAAGGGCCCCCGTGTTCTCGAGATTATCCAAGCAgtaagtgtca ... tctgtggcagATCGACAGCAACACTGATGGTCTTGTGGACTTTGAAGAGTTTGTAGCAGCA
EST: gi|29680387|gb|CB676662.1|CB676662
EST:     ATCTTCCTTGGAGATTGAAGGGCCCCCGTGTTCTCGAGATTATCCAAGCA                         ATCGACAGCAACACTGATGGTCTTGTGGACTTTGAAGAGTTTGTAGCAGCA
genomic: ATCTTCCTTGGAGATTGAAGGGCCCCCGTGTTCTCGAGATTATCCAAGCAgtaagtgtca ... tctgtggcagATCGACAGCAACACTGATGGTCTTGTGGACTTTGAAGAGTTTGTAGCAGCA
EST: gi|44675829|gb|CR289263.1|CR289263
EST:     ATCTTCCTTGGAGATTGAAGGGCCCCCGTGTTCTCGAGATTATCCAAGCA                         ATCGACAGCAACACTGATGGTCTTGTGGACTTTGAAGAGTTTGTAGCAGCA
genomic: ATCTTCCTTGGAGATTGAAGGGCCCCCGTGTTCTCGAGATTATCCAAGCAgtaagtgtca ... tctgtggcagATCGACAGCAACACTGATGGTCTTGTGGACTTTGAAGAGTTTGTAGCAGCA
EST: gi|88576337|gb|CI670482.1|CI670482
EST:     ATCTTCCTTGGAGATTGAAGGGCCCCCGTGTTCTCGAGATTATCCAAGCA                         ATCGACAGCAACACTGATGGTCTTGTGGACTTTGAAGAGTTTGTAGCAGCA
genomic: ATCTTCCTTGGAGATTGAAGGGCCCCCGTGTTCTCGAGATTATCCAAGCAgtaagtgtca ... tctgtggcagATCGACAGCAACACTGATGGTCTTGTGGACTTTGAAGAGTTTGTAGCAGCA
EST: gi|29657421|gb|CB653696.1|CB653696
EST:     ATCTTCCTTGGAGATTGAAGGGCCCCGGTGTTCTCGAGATTATCCAAGCA                         ATCGACAGCAACACTGATGGTCTTGTGGACTTTGAAGAGTTTGTAGCAGCA
genomic: ATCTTCCTTGGAGATTGAAGGGCCCCCGTGTTCTCGAGATTATCCAAGCAgtaagtgtca ... tctgtggcagATCGACAGCAACACTGATGGTCTTGTGGACTTTGAAGAGTTTGTAGCAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actagcttaccatctatcagagtcgtacttcaactgtgatattattctgtggcagATCGACAGCAACACTGATGGTCTTGTGGACTTTGAAGAGTTTGTAGCAGCAACCCTCCATATACATCAAATGGCTGAGCTTGACTCTGAAAGGTGGGGCC
   agcttac  putative branch site (score: 3)
                                         ttattct  putative PPT
                                    tgatattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgtcaggccttctttattattttcccccttattttcggagcaactagcttaccatctatcagagtcgtacttcaactgtgatattattctgtggcagATCGACAGCAACACTGATGGTCTTGTGGACTTTGAAGAGTTTGTAGCAGCAACCCTCCATATACATCAAATGGCTGAGCTTGACTCTGAAAGGTGGGGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT