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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGTCGTCGCCGCCGTCCGACCGTAGGCCGCTCCACTTCGCGGCGTTCCTGCTGCTCGCCGACGCGGCGCTCGTCGCCCTCATCGTCGTCTTCGTCCCGTgtgcgtaccagcatctttttcctccgctttcctcctagccatcgcagctcacctcacggtttcttgcgtgcttgcttcgattctgcag

Basic information

species Oryza sativa
transcript LOC_Os01g07720.4
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g07720.4 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G066362_T02 (Zea mays), 5'ss of exon 1
-GAGTCGTCGCCGCCGTCCGACCGTAGGCCGCTCCACTTCGCGGCGTTCCTGCTGCTCGCCGACGCGGCGCTCGTCGCCCTCATCGTCGTCTTCGTCCCGTgtgcgtacc----agcatctttttcctccgctt--tcctcctagccatcgcagctcacctcacggtttcttgcgtgcttgcttcgattctgcag
  || |   | || ||  | |||| ||| ||||| ||||||| || |||||| |||| |||||||| |||||||||||||||||||||| |||||||||||||  ||| |    |||         |   |||     ||||| | |   ||  | |  || |  |  |||   ||  |||||||   | |||||
CCAGGCAG-GTCGACGGACCACCGGAGGGCGCTCTACTTCGCCGCCTTCCTGGTGCTGGCCGACGCCGCGCTCGTCGCCCTCATCGTCGCCTTCGTCCCGTgtctgtagctccgagcgcgaagcctcattgctcagctctccttgtctctgcgtcgccgctaagcgggtct---gttgttgcttctgat-tgcag
















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|88740960|gb|CI764468.1|CI764468
EST:     GCTGCTCGCCGACGCGGCGCTCGTCGCCCTCATCGTCGTCTTCGTCCCGT                         ATACCAAGATCGACTGGGACGCGTACATGGCTCAG
genomic: GCTGCTCGCCGACGCGGCGCTCGTCGCCCTCATCGTCGTCTTCGTCCCGTgtgcgtacca ... gattctgcagATACCAAGATCGACTGGGACGCGTACATGGCTCAG
EST: gi|88765491|gb|CI774585.1|CI774585
EST:     GCTGCTCGCCGACGCGGCGCTCGTCGCCCTCATCGTCGTCTTCGTCCCGT                         ATACCAAGATCGACTGGGACGCGTACATGGCTCAG
genomic: GCTGCTCGCCGACGCGGCGCTCGTCGCCCTCATCGTCGTCTTCGTCCCGTgtgcgtacca ... gattctgcagATACCAAGATCGACTGGGACGCGTACATGGCTCAG
EST: gi|88734598|gb|CI758106.1|CI758106
EST:     GCTGCTCGCCGACGCGGCGCTCGTCGCCCTCATCGTCGTCTTCGTCCCGT                         ATACCAAGATCGACTGGGACGCGTACATGGCTCAG
genomic: GCTGCTCGCCGACGCGGCGCTCGTCGCCCTCATCGTCGTCTTCGTCCCGTgtgcgtacca ... gattctgcagATACCAAGATCGACTGGGACGCGTACATGGCTCAG
EST: gi|88312323|gb|CI582661.1|CI582661
EST:     GCTGCTCGCCGACGCGGCGCTCGTCGCCCTCATCGTCGTCTTCGTCCCGT                         ATACCAAGATCGACTGGGACGCGTACATGGCTCAG
genomic: GCTGCTCGCCGACGCGGCGCTCGTCGCCCTCATCGTCGTCTTCGTCCCGTgtgcgtacca ... gattctgcagATACCAAGATCGACTGGGACGCGTACATGGCTCAG
EST: gi|88576279|gb|CI670424.1|CI670424
EST:     GCTGCTCGCCGACGCGGCGCTCGTCGCCCTCATCGTCGTCTTCGTCCCGT                         ATACCAAGATCGACTGGGACGCGTACATGGCTCAG
genomic: GCTGCTCGCCGACGCGGCGCTCGTCGCCCTCATCGTCGTCTTCGTCCCGTgtgcgtacca ... gattctgcagATACCAAGATCGACTGGGACGCGTACATGGCTCAG
EST: gi|88309854|gb|CI656988.1|CI656988
EST:     GCTGCTCGCCGACGCGGCGCTCGTCGCCCTCATCGTCGTCTTCGTCCCGT                         ATACCAAGATCGACTGGGACGCGTACATGGCTCAG
genomic: GCTGCTCGCCGACGCGGCGCTCGTCGCCCTCATCGTCGTCTTCGTCCCGTgtgcgtacca ... gattctgcagATACCAAGATCGACTGGGACGCGTACATGGCTCAG
EST: gi|88763364|gb|CI772825.1|CI772825
EST:     GCTGCTCGCCGACGCGGCGCTCGTCGCCCTCATCGTCGTCTTCGTCCCGT                         ATACCAAGATCGACTGGGACGCGTACATGGCTCAG
genomic: GCTGCTCGCCGACGCGGCGCTCGTCGCCCTCATCGTCGTCTTCGTCCCGTgtgcgtacca ... gattctgcagATACCAAGATCGACTGGGACGCGTACATGGCTCAG
EST: gi|88592824|gb|CI710953.1|CI710953
EST:     GCTGCTCGCCGACGCGGCGCTCGTCGCCCTCATCGTCGTCTTCGTCCCGT                         ATACCAAGATCGACTGGGACGCGTACATGGCTCAG
genomic: GCTGCTCGCCGACGCGGCGCTCGTCGCCCTCATCGTCGTCTTCGTCCCGTgtgcgtacca ... gattctgcagATACCAAGATCGACTGGGACGCGTACATGGCTCAG
EST: gi|88449328|gb|CI582200.1|CI582200
EST:     GCTGCTCGCCGACGCGGCGCTCGTCGCCCTCATCGTCGTCTTCGTCCCGT                         ATACCAAGATCGACTGGGACGCGTACATGGCTCAG
genomic: GCTGCTCGCCGACGCGGCGCTCGTCGCCCTCATCGTCGTCTTCGTCCCGTgtgcgtacca ... gattctgcagATACCAAGATCGACTGGGACGCGTACATGGCTCAG
EST: gi|88327935|gb|CI648334.1|CI648334
EST:     GCTGCTCGCCGACGCGGCGCTCGTCGCCCTCATCGTCGTCTTCGTCCCGT                         ATACCAAGATCGACTGGGACGCGTACATGGCTCAG
genomic: GCTGCTCGCCGACGCGGCGCTCGTCGCCCTCATCGTCGTCTTCGTCCCGTgtgcgtacca ... gattctgcagATACCAAGATCGACTGGGACGCGTACATGGCTCAG
EST: gi|88763578|gb|CI773025.1|CI773025
EST:     GCTGCTCGCCGACGCGGCGCTCGTCGCCCTCATCGTCGTCTTCGTCCCGT                         ATACCAAGATCGACTGGGACGCGTACATGGCTCAG
genomic: GCTGCTCGCCGACGCGGCGCTCGTCGCCCTCATCGTCGTCTTCGTCCCGTgtgcgtacca ... gattctgcagATACCAAGATCGACTGGGACGCGTACATGGCTCAG
EST: gi|88741433|gb|CI764941.1|CI764941
EST:     GCTGCTCGCCGACGCGGCGCTCGTCGCCCTCATCGTCGTCTTCGTCCCGT                         ATACCAAGATCGACTGGGACGCGTACATGGCTCAG
genomic: GCTGCTCGCCGACGCGGCGCTCGTCGCCCTCATCGTCGTCTTCGTCCCGTgtgcgtacca ... gattctgcagATACCAAGATCGACTGGGACGCGTACATGGCTCAG
EST: gi|38472084|gb|CF956215.1|CF956215
EST:     GCTGCTCGCCGACGCGGCGCTCGTCGCCCTCATCGTCGCCTTCGTCCCGT                         ATACCAAGATCGACTGGGACGCGTACATGGCTCAG
genomic: GCTGCTCGCCGACGCGGCGCTCGTCGCCCTCATCGTCGTCTTCGTCCCGTgtgcgtacca ... gattctgcagATACCAAGATCGACTGGGACGCGTACATGGCTCAG
EST: gi|88368729|gb|CI645151.1|CI645151
EST:     GCTGCTCGCCGACGCGGCGCTCGTCGCCCTCATCGTCGTCTTCGTCCCGT                         ATACCAAGATCGACTGGGACGCGTACATGGCTCAG
genomic: GCTGCTCGCCGACGCGGCGCTCGTCGCCCTCATCGTCGTCTTCGTCCCGTgtgcgtacca ... gattctgcagATACCAAGATCGACTGGGACGCGTACATGGCTCAG
EST: gi|87008978|gb|CI304921.1|CI304921
EST:     GCTGCTCGCCGACGCGGCGCTCGTCGCCCTCATCGTCGTCTTCGTCCCGT                         ATACCAAGATCGACTGGGACGCGTACATAGCTCAG
genomic: GCTGCTCGCCGACGCGGCGCTCGTCGCCCTCATCGTCGTCTTCGTCCCGTgtgcgtacca ... gattctgcagATACCAAGATCGACTGGGACGCGTACATGGCTCAG
EST: gi|88337341|gb|CI629631.1|CI629631
EST:     CTGCTCGCCGACGCGGCGCCTCGTCGCC-TCATCGTCGTCTTCGTCCCGT                         ATTAC-AAGATCGACTGGGACGCGTACATGGCTCAG
genomic: CTGCTCGCCGACGCGGCGC-TCGTCGCCCTCATCGTCGTCTTCGTCCCGTgtgcgtacca ... gattctgcagAT-ACCAAGATCGACTGGGACGCGTACATGGCTCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGTCGTCGCCGCCGTCCGACCGTAGGCCGCTCCACTTCGCGGCGTTCCTGCTGCTCGCCGACGCGGCGCTCGTCGCCCTCATCGTCGTCTTCGTCCCGTgtgcgtaccagcatctttttcctccgctttcctcctagccatcgcagctcacctcacggtttcttgcgtgcttgcttcgattctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - CGCCGACG