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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtaggccctcgcgcgcgcggggtgcctccttccaccccgcctcagcttttgatgtcgttcgcccctccgatcctttggctgaaatcggctgtggatgatggcagCGGAGATGCTGGTCGGCCCGACCAAGGTCTTGTTCATGGACGAGATATCCACCGGCCTGGACAGCTCCACCACCTTCCAGATCATCAGGTGCATCCAGCA

Basic information

species Oryza sativa
transcript LOC_Os01g52560.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g52560.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G000614_T02 (Zea mays), 3'ss of exon 4
gtacgtaggccctcgcgcgcgcggggtgcctccttccaccccgcctcagcttttgatgtcgttcgcccctccgatcctttggctgaaatcggctgtggatgatggcagCGGAGATGCTGGTCGGCCCGACCAAGGTCTTGTTCATGGACGAGATATCCACCGGCCTGGACAGCTCCACCACCTTCCAGATCATCAGGTGCATCCAGCA
    |||  ||||| | | |         |  | || | |||  |   || | || ||| |      |||||| | |  | |||  || ||   |||  || |  ||| |||||||||||||||||||||||||||  | |||||||||||||| ||||| ||||| |||||||||||||||||||||||  ||| ||||||||||||
----gtac-ccctccctctcctt---catccgcctcaaacccatccgcgcgtctgctgttg------cctccgttaccgttgctacaaccgcgcgtgtttggtttcagGGGAGATGCTGGTCGGCCCGACCAAGGTGCTATTCATGGACGAGATCTCCACGGGCCTCGACAGCTCCACCACCTTCCAGATTGTCAAGTGCATCCAGCA
















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|88321740|gb|CI672882.1|CI672882
EST:     CGAGCTGCGGCGCGGCATCTCCGGCGGCCAGAAGAAGCGCCTCACCACAG                         CGGAGATGCTGGTCGGCCCGACCAAGGTCTTGTTCATGGACGAGATATCCA
genomic: CGAGCTGCGGCGCGGCATCTCCGGCGGCCAGAAGAAGCGCCTCACCACAGgtacgtaggc ... atgatggcagCGGAGATGCTGGTCGGCCCGACCAAGGTCTTGTTCATGGACGAGATATCCA
EST: gi|88434150|gb|CI587028.1|CI587028
EST:     CGAGCTGCGGCGCGGCATCTCCGGCGGCCAGAAGAAGCGCCTCACCACAG                         CGGAGATTGCTGGTCGGCCCGACCAAGGTCTTGTTCATGGACGAGATATCC
genomic: CGAGCTGCGGCGCGGCATCTCCGGCGGCCAGAAGAAGCGCCTCACCACAGgtacgtaggc ... atgatggcagCGGAGAT-GCTGGTCGGCCCGACCAAGGTCTTGTTCATGGACGAGATATCC
EST: gi|88349106|gb|CI678074.1|CI678074
EST:     CGAGCTGCGGCGCGGCATCTCCGGCGGCCAGAAAAAGCGCCTCACCACAG                         CGGAGATGCTGGTCGGCCCGACCAAGGTCTTGTTCATGGACGAGATATCCA
genomic: CGAGCTGCGGCGCGGCATCTCCGGCGGCCAGAAGAAGCGCCTCACCACAGgtacgtaggc ... atgatggcagCGGAGATGCTGGTCGGCCCGACCAAGGTCTTGTTCATGGACGAGATATCCA
EST: gi|88425662|gb|CI689310.1|CI689310
EST:     CGAGCTGCGGCGCGGCATCTCCGGCGGCCAGAAGAAGCGCCTCACCACAG                         CGGAGATGCTGGTCGGCCCGACCAAGGTCTTGTTCATGGACGAGATATCCA
genomic: CGAGCTGCGGCGCGGCATCTCCGGCGGCCAGAAGAAGCGCCTCACCACAGgtacgtaggc ... atgatggcagCGGAGATGCTGGTCGGCCCGACCAAGGTCTTGTTCATGGACGAGATATCCA
EST: gi|88369653|gb|CI582848.1|CI582848
EST:     CGAGCTGCGGCGCGGCATCTCCGGCGGCCAGAAGAAGCGCCTCACCACAG                         CGGAGATGCTGGTCGGCCCGACCAAGGTCTTGTTCATGGACGAGATATCCA
genomic: CGAGCTGCGGCGCGGCATCTCCGGCGGCCAGAAGAAGCGCCTCACCACAGgtacgtaggc ... atgatggcagCGGAGATGCTGGTCGGCCCGACCAAGGTCTTGTTCATGGACGAGATATCCA
EST: gi|88352918|gb|CI678950.1|CI678950
EST:     CGAGCTGCGGCGCGGCATCTCCGGCGGCCAGAAGAAGCGCCTCACCACAG                         CGGAGATGCTGGTCGGCCCGACCAAGGTCTTGTTCATGGACGA
genomic: CGAGCTGCGGCGCGGCATCTCCGGCGGCCAGAAGAAGCGCCTCACCACAGgtacgtaggc ... atgatggcagCGGAGATGCTGGTCGGCCCGACCAAGGTCTTGTTCATGGACGA
EST: gi|88306308|gb|CI636693.1|CI636693
EST:     CGAGCTGCGGCGCGGCATCTCCGGCGGCCAGAAGAAGCGCCTCACCACAG                         CGGAGATGCTGGTCGGCCCGACCAAGGTCTTGTTCATGGACGAGATATCCA
genomic: CGAGCTGCGGCGCGGCATCTCCGGCGGCCAGAAGAAGCGCCTCACCACAGgtacgtaggc ... atgatggcagCGGAGATGCTGGTCGGCCCGACCAAGGTCTTGTTCATGGACGAGATATCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatgtcgttcgcccctccgatcctttggctgaaatcggctgtggatgatggcagCGGAGATGCTGGTCGGCCCGACCAAGGTCTTGTTCATGGACGAGATATCCACCGGCCTGGACAGCTCCACCACCTTCCAGATCATCAGGTGCATCCAGCA
 ttttgat  putative branch site (score: 4)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtaggccctcgcgcgcgcggggtgcctccttccaccccgcctcagcttttgatgtcgttcgcccctccgatcctttggctgaaatcggctgtggatgatggcagCGGAGATGCTGGTCGGCCCGACCAAGGTCTTGTTCATGGACGAGATATCCACCGGCCTGGACAGCTCCACCACCTTCCAGATCATCAGGTGCATCCAGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA