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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtgagaagctcactcatattcctccccttttcacattcctgcctatttagatttgcttttatgtcacaccatgctcacttcgttccccaatggtgtagCTGCTGAGAACCTAGTAAAAGGCTGTGCTGGGAAGTATGCAACAGGAGATGAAGTCCGATTG

Basic information

species Oryza sativa
transcript LOC_Os02g35590.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g35590.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G102488_T01 (Zea mays), 3'ss of exon 2
ttgtgagaagctcactcatattcctccccttttcacattcctgcctatttagatttgc----ttttatgtcacaccatgctcacttcgttccccaatggtgtagCTGCTGAGAACCTAGTA------AAAGGCTGTGCTGGGAAGTATGCAACAGGAGATGAAGTCCGATTG--------------------------------
   |  | || ||  |  |||| | || || || | ||||   | || ||   || |     |  |||     |   ||||| |||   |||| |||||| |||||  |||||||||  ||      ||||| || || |||||||||||||||||||||||||||| ||||                                
-gctttgcagttctgttgtattacaccactattgaaattcactcatagttcccttagtagcttgctatcctgtaatgtgctcgctt---tccctaatggtttagCTATTGAGAACCTGATACAACTAAAAGGATGCGCCGGGAAGTATGCAACAGGAGATGAAGTCCAATTGGTACATTTGCTCGCCATTTGTCACCTTTTTTT
















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|88520540|gb|CI448194.1|CI448194
EST:     AGGGGAGAGCATCCCATGGACTCAACAACAGATCGACAGAGGTTTCGCAG                         CTGCTGAGAACCTAGTAAAAGGCTGTGCTGGGAAGTATGCAACAGGAGATG
genomic: AGGGGAGAGCATCCCATGGACTCAACAACAGATCGACAGAGGTTTCGCAGgttctcctca ... aatggtgtagCTGCTGAGAACCTAGTAAAAGGCTGTGCTGGGAAGTATGCAACAGGAGATG
EST: gi|88251938|gb|CI350366.1|CI350366
EST:     AGGGGAGAGCATCCCATGGACTCAACAACAGATCGACAGAGGTTTCGCAGG                         CTGCTGAGAACCTAGTAAAAGGCTGTGCTGGGAAGTATGCAACAGGAGAT
genomic: AGGGGAGAGCATCCCATGGACTCAACAACAGATCGACAGAGGTTTCGCA-Ggttctcctca ... aatggtgtagCTGCTGAGAACCTAGTAAAAGGCTGTGCTGGGAAGTATGCAACAGGAGAT
EST: gi|88263359|gb|CI367133.1|CI367133
EST:     AGGGGAGAGCATCCCATGGACTCAACAACAGATCGACAGAGGTTTCGCAG                         CTGCTGAGAACCTAGTAAAAGGCTGTGCTGGGAAGTATGCAACAGGAGATG
genomic: AGGGGAGAGCATCCCATGGACTCAACAACAGATCGACAGAGGTTTCGCAGgttctcctca ... aatggtgtagCTGCTGAGAACCTAGTAAAAGGCTGTGCTGGGAAGTATGCAACAGGAGATG
EST: gi|88368430|gb|CI561504.1|CI561504
EST:     AGATCGACAGAGGTTTCGCAG                         CTGCTGAGAACCTAGTAAAAGGCTGTGCTGGGAAGTATGCAACAGGAGATG
genomic: AGATCGACAGAGGTTTCGCAGgttctcctca ... aatggtgtagCTGCTGAGAACCTAGTAAAAGGCTGTGCTGGGAAGTATGCAACAGGAGATG
EST: gi|88456348|gb|CI560951.1|CI560951
EST:     GGGGAGAGCATCCCATGGACTCAACAACAGATCGACAGAGGTTTCGCAG                         CTGCTGAGAACCTAGTAAAAGGCTGTGCTGGGAAGTATGCAACAGGAGATG
genomic: GGGGAGAGCATCCCATGGACTCAACAACAGATCGACAGAGGTTTCGCAGgttctcctca ... aatggtgtagCTGCTGAGAACCTAGTAAAAGGCTGTGCTGGGAAGTATGCAACAGGAGATG
EST: gi|163927722|gb|EG712482.1|EG712482
EST:     AGGGGAGAGCATCCCATGGACTCAACAACAGATCGACAGAGGTTTCGCAG                         CTGCTGAGAACCTAGTAAAAGGCTGTGCTGGGAAGTATGCAACAGGAGATG
genomic: AGGGGAGAGCATCCCATGGACTCAACAACAGATCGACAGAGGTTTCGCAGgttctcctca ... aatggtgtagCTGCTGAGAACCTAGTAAAAGGCTGTGCTGGGAAGTATGCAACAGGAGATG
EST: gi|88503640|gb|CI431146.1|CI431146
EST:     TCAACAACAGATCGACAGAGGTTTCGCAG                         CTGCTGAGAACCTAGTAAAAGGCTGTGCTGGGAAGTATGCAACAGGAGATG
genomic: TCAACAACAGATCGACAGAGGTTTCGCAGgttctcctca ... aatggtgtagCTGCTGAGAACCTAGTAAAAGGCTGTGCTGGGAAGTATGCAACAGGAGATG
EST: gi|88512762|gb|CI440268.1|CI440268
EST:     AGGGGAGAGCATCCCATGGACTCAACAACAGATCGACAGAGGTTTCGCAG                         CTGCTGAGAACCTAGTAAAAGGCTGTGCTGGGAAGTATGCAACAGGAGATG
genomic: AGGGGAGAGCATCCCATGGACTCAACAACAGATCGACAGAGGTTTCGCAGgttctcctca ... aatggtgtagCTGCTGAGAACCTAGTAAAAGGCTGTGCTGGGAAGTATGCAACAGGAGATG
EST: gi|88521271|gb|CI448453.1|CI448453
EST:     AGGGGAGAGCATCCCATGGACTCAACAACAGATCGACAGAGGTTTCGCAG                         CTGCTGAGAACCTAGTAAAAGGGCTGTGCTGGGAAGTATGCAACAGGAGAT
genomic: AGGGGAGAGCATCCCATGGACTCAACAACAGATCGACAGAGGTTTCGCAGgttctcctca ... aatggtgtagCTGCTGAGAACCTAGTAAAA-GGCTGTGCTGGGAAGTATGCAACAGGAGAT
EST: gi|88508803|gb|CI436309.1|CI436309
EST:     AGGGGAGAGCATCCCATGGACTCAACAACAGATCGACAGAGGTTTCGCAG                         CTGCTGAGAACCTAGTAAAAGGCTGTGCTGGGAAGTATGCAACAGGAGATG
genomic: AGGGGAGAGCATCCCATGGACTCAACAACAGATCGACAGAGGTTTCGCAGgttctcctca ... aatggtgtagCTGCTGAGAACCTAGTAAAAGGCTGTGCTGGGAAGTATGCAACAGGAGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttagatttgcttttatgtcacaccatgctcacttcgttccccaatggtgtagCTGCTGAGAACCTAGTAAAAGGCTGTGCTGGGAAGTATGCAACAGGAGATGAAGTCCGATTG
                            tgctcac  putative branch site (score: 2)
                                       ttcccca  putative PPT
             ttttatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtgagaagctcactcatattcctccccttttcacattcctgcctatttagatttgcttttatgtcacaccatgctcacttcgttccccaatggtgtagCTGCTGAGAACCTAGTAAAAGGCTGTGCTGGGAAGTATGCAACAGGAGATGAAGTCCGATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG