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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgttaacagtctgtggtaattttggatgtaataatccccttacatcatttttgtcttgtgtgtagCCTACTATACCTTCAGATGGTAAATCGATTCCCAAAATTGGGAATATTGGTCACATGACAAGAATAACCAACAAGCTTATTCAGTTGGGAAGCAGTAACG

Basic information

species Oryza sativa
transcript LOC_Os01g40340.3
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g40340.3 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G149321_T01 (Zea mays), 3'ss of exon 4
gtaagttgttaacagtctgtggtaattttggatgtaat-----------aatccccttacatcatttt---tgtcttgtgtgt--agCCTACTATACCTTCAGATGGTAAATCGATTCCCAAAATTGGGAATATTGGTCACATGACAAGAATAACCAACAAGCTTATTCAGTTGGGAAGCAGTAACG
||||||| | || |  ||||    |||||  |  | ||           |||||| ||  ||  | |    |||||| | ||   |||||||| | || || || || ||| |   ||| | |||||| ||| |||||||||||||||||||| |||| || |||||||||||||| |  |||||| 
gtaagttatcaatacactgtaactattttttactttatcacagagacctaatccctttttattttctggtgtgtcttctatgctcagCCTACTGTTCCCTCTGAAGGGAAAACCCCTCCAAGAATTGGAAATGTTGGTCACATGACAAGAATAGCCAATAAACTTATTCAGTTGGGCAATAGTAACA
















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|58679221|gb|CK067908.1|CK067908
EST:     GGAAAAACTTTCTTCTTTGTCAACAGAGTCTACTGGG                         CCTACTATACCTTCAGATGGTAAATCGATTCCCAAAATTGGGAATATTGGT
genomic: GGAAAAACTTTCTTCTTTGTCAACAGAGTCTACTGGGgtaagttgtt ... ttgtgtgtagCCTACTATACCTTCAGATGGTAAATCGATTCCCAAAATTGGGAATATTGGT
EST: gi|29680806|gb|CB677081.1|CB677081
EST:     AAATTCTTGCCGCGGAAAAACTTTCTTCTTTGTCAACAGAGTCTACTGGG                         CCTACTATACCTTCAGATGGTAAATCGATTCCCAAAATTGGGAATATTGGT
genomic: AAATTCTTGCCGCGGAAAAACTTTCTTCTTTGTCAACAGAGTCTACTGGGgtaagttgtt ... ttgtgtgtagCCTACTATACCTTCAGATGGTAAATCGATTCCCAAAATTGGGAATATTGGT
EST: gi|29612947|gb|CB617960.1|CB617960
EST:     AAATTCTTGCCGCGGAAAAACTTTCTTCTTTGTCAACAGAGTCTACTGGG                         CCTACTATACCTTCAGATGGTAAATCGATTCCCAAAATTGGGAATATTGGT
genomic: AAATTCTTGCCGCGGAAAAACTTTCTTCTTTGTCAACAGAGTCTACTGGGgtaagttgtt ... ttgtgtgtagCCTACTATACCTTCAGATGGTAAATCGATTCCCAAAATTGGGAATATTGGT
EST: gi|88717309|gb|CI740819.1|CI740819
EST:     AAATTCTTGCCGCGGAAAAACTTTCTTCTTTGTCAACAGAGTCTACTGGG                         CCTACTATACCTTCAGATGGTAAATCGATTCCCAAAATTGGGAATATTGGT
genomic: AAATTCTTGCCGCGGAAAAACTTTCTTCTTTGTCAACAGAGTCTACTGGGgtaagttgtt ... ttgtgtgtagCCTACTATACCTTCAGATGGTAAATCGATTCCCAAAATTGGGAATATTGGT
EST: gi|88417264|gb|CI576338.1|CI576338
EST:     AAATTCTTGCCGCGGAAAAACTTTCTTCTTTGTCAACAGAGTCTACTGGG                         CCTACTATACCTTCAGATGGTAAATCGATTCCCAAAATTGGGAATATTGGT
genomic: AAATTCTTGCCGCGGAAAAACTTTCTTCTTTGTCAACAGAGTCTACTGGGgtaagttgtt ... ttgtgtgtagCCTACTATACCTTCAGATGGTAAATCGATTCCCAAAATTGGGAATATTGGT
EST: gi|58689270|gb|CK077957.1|CK077957
EST:     AAATTCTTGCCGCGGAAAAACTTTCTTCTTTGTCAACAGAGTCTACTGGG                         CCTACTATACCTTCAGATGGTAAATCGATTCCCAAAATTGGGAATATTGGT
genomic: AAATTCTTGCCGCGGAAAAACTTTCTTCTTTGTCAACAGAGTCTACTGGGgtaagttgtt ... ttgtgtgtagCCTACTATACCTTCAGATGGTAAATCGATTCCCAAAATTGGGAATATTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtggtaattttggatgtaataatccccttacatcatttttgtcttgtgtgtagCCTACTATACCTTCAGATGGTAAATCGATTCCCAAAATTGGGAATATTGGTCACATGACAAGAATAACCAACAAGCTTATTCAGTTGGGAAGCAGTAACG
                          cccttac  putative branch site (score: 3)
                                     tttttgtctt  putative PPT
               atgtaataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttgttaacagtctgtggtaattttggatgtaataatccccttacatcatttttgtcttgtgtgtagCCTACTATACCTTCAGATGGTAAATCGATTCCCAAAATTGGGAATATTGGTCACATGACAAGAATAACCAACAAGCTTATTCAGTTGGGAAGCAGTAACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT