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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcggccacccacgccacattccctatttccgcatctcaatctgcaaggcttgctgcacagttgcgggtagatttggtccgcgttctttttccccctcacagtcccaactcgaaattgagggtttcgttttctctttgttgcggagGCTCCTAGGCGACAGATCGCCGTTCACGCAGCAGAACTGGCAGGGGGATAGCCTCGACCGCGACGAGGAGAACAGCAGGATCCAAC

Basic information

species Oryza sativa
transcript LOC_Os01g64920.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g64920.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G075101_T03 (Zea mays), 3'ss of exon 1
gtacgcggccacccacgccacattccctatttccgcatctcaatctgcaaggcttgctgcacagttgcgggtagatttggtccgcgttctttttccccctcacagtcccaactcgaaattgagggtttcgttttctctttgttgcggagGCTCCTAGGCGACAGATCGCCGTTCACGCAGCAGAACTGGCAGGGGGATAGCCTCGACCGCGACGAGGAGAACAGCAGGATCCAAC
|||||||     || |    | || ||| |   |   ||    | |    |    ||||     |  | | | | ||||| |  ||    ||||     ||    |   ||||     |       || | | | |    ||| |||||||||||||||||||||||||| |||||||||||||||||||| ||||||||||| ||||||||||||||||||| |||||||||||
gtacgcg-----ccgcatttcctttcctctccgcttctcctgctttctggga---gctgtgatctctctgctgggtttggccttcga---ttttgggattcgggctaggaactgacggtctgctcgtttggtgtgtgcgcgttccggagGCTCCTAGGCGACAGATCGCCCTTCACGCAGCAGAACTGGCAAGGGGATAGCCTGGACCGCGACGAGGAGAACAACAGGATCCAAC
















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|88312953|gb|CI592237.1|CI592237
EST:     CTCTTCGCCGGCGTCGAGCGCTACCGCCTCCTCGAGTGGCTCTTCTTCCG                         GCTCCTAGGCGACAGATCGCCGTTCACGCAGCAGAACTGGCAGGGGGATAG
genomic: CTCTTCGCCGGCGTCGAGCGCTACCGCCTCCTCGAGTGGCTCTTCTTCCGgtacgcggcc ... tgttgcggagGCTCCTAGGCGACAGATCGCCGTTCACGCAGCAGAACTGGCAGGGGGATAG
EST: gi|88346773|gb|CI657324.1|CI657324
EST:     TCTTCGCCGGCGTCGAGCGCTNAC-GCCTCCTCGAGTGGCTCTTCTTCCG                         GCTCCTAGGCGACAGATCGCCGTTCACGCAGCAGAACTGGCAGGGGGATAG
genomic: TCTTCGCCGGCGTCGAGCGCT-ACCGCCTCCTCGAGTGGCTCTTCTTCCGgtacgcggcc ... tgttgcggagGCTCCTAGGCGACAGATCGCCGTTCACGCAGCAGAACTGGCAGGGGGATAG
EST: gi|88372509|gb|CI610832.1|CI610832
EST:     CTCTTCGCCGGCGTCGAGCGCTACCGCCTCCTCGAGTGGCTCTTCTTCCG                         GCTCCTAGGCGACAGATCGCCGTTCACGCAGCAGAACTGGCAGGGGGATAG
genomic: CTCTTCGCCGGCGTCGAGCGCTACCGCCTCCTCGAGTGGCTCTTCTTCCGgtacgcggcc ... tgttgcggagGCTCCTAGGCGACAGATCGCCGTTCACGCAGCAGAACTGGCAGGGGGATAG
EST: gi|87009560|gb|CI309081.1|CI309081
EST:     CTCTTCGCCGGCGTCGAGCGCTACCGCCTCCTCGAGTGGCTCTTCTTCCG                         GCTCCTAGGCGACAGATCGCCGTTCACGCAGCAGAACTGGCAGGGGGATAG
genomic: CTCTTCGCCGGCGTCGAGCGCTACCGCCTCCTCGAGTGGCTCTTCTTCCGgtacgcggcc ... tgttgcggagGCTCCTAGGCGACAGATCGCCGTTCACGCAGCAGAACTGGCAGGGGGATAG
EST: gi|29687390|gb|CB683665.1|CB683665
EST:     CTCTTCGCCGGCGTCGAGCGCTACCGCCTCCTCGAGTGGCTCTTCTTCCG                         GCTCCTAGGCGACAGATCGCCGTTCACGCAGCAGAACTGGCAGGGGGATAG
genomic: CTCTTCGCCGGCGTCGAGCGCTACCGCCTCCTCGAGTGGCTCTTCTTCCGgtacgcggcc ... tgttgcggagGCTCCTAGGCGACAGATCGCCGTTCACGCAGCAGAACTGGCAGGGGGATAG
EST: gi|88695588|gb|CI737626.1|CI737626
EST:     CTCTTCGCCGGCGTCGAGCGCTACCGCCTCCTCGAGTGGCTCTTCTTCCG                         GCTCCTAGGCGACAGATCGCCGTTCACGCAGCAGAACTGGCAGGGGGATAG
genomic: CTCTTCGCCGGCGTCGAGCGCTACCGCCTCCTCGAGTGGCTCTTCTTCCGgtacgcggcc ... tgttgcggagGCTCCTAGGCGACAGATCGCCGTTCACGCAGCAGAACTGGCAGGGGGATAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccccctcacagtcccaactcgaaattgagggtttcgttttctctttgttgcggagGCTCCTAGGCGACAGATCGCCGTTCACGCAGCAGAACTGGCAGGGGGATAGCCTCGACCGCGACGAGGAGAACAGCAGGATCCAAC
  ccctcac  putative branch site (score: 3)
                               tttcgttttctctttg  putative PPT
                     aaattga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgcggccacccacgccacattccctatttccgcatctcaatctgcaaggcttgctgcacagttgcgggtagatttggtccgcgttctttttccccctcacagtcccaactcgaaattgagggtttcgttttctctttgttgcggagGCTCCTAGGCGACAGATCGCCGTTCACGCAGCAGAACTGGCAGGGGGATAGCCTCGACCGCGACGAGGAGAACAGCAGGATCCAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA