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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGTGCAGAGGGAGGAGAAGAAGGTGGAGAAGTCCATCAGGGAGGCCGCCAAGCGCAACGACATCGGATCGGCCAAGgtacccctacgcttccatccattcgattcgattccacttgtttgcggtttgctgatgcgcattcgtgttgggttttggtcag

Basic information

species Oryza sativa
transcript LOC_Os03g01810.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g01810.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G042552_T02 (Zea mays), 5'ss of exon 2
-----------------------ATGTGCAGAGGGAGGAGAAGAAGGTGGAGAAGTCCATCAGGGAGGCCGCCAAGCGCAACGACATCGGATCGGCCAAGgtacccctacgcttccatccattcgatt------cgattccacttgtttgcggtttgctgatgcgc-attcgt---gttgggttttggtcag-
                       |||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||| ||||| |||||||||  |   |   || |  || ||  ||      ||||        ||  |  ||  | ||  |    || ||   ||   |  ||  |||  
CCCTCGACCTCGATGTGCTGCAGATGTGCAGAGGGAGGAGAAGAAGGTGGAGAAGGCCATCAGGGAGGCCGCCAAGCGCAACGACATGGGATCCGCCAAGgtaggcacccatctcgaatcaatctgttgacggacgatctgttggtttcacttttcaccgaccccttgtttgtctggtgatgccttcttcaag

upper sequence: LOC_Os03g01810.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G042552_T01 (Zea mays), 5'ss of exon 2
ATGTGCAGAGGGAGGAGAAGAAGGTGGAGAAGTCCATCAGGGAGGCCGCCAAGCGCAACGACATCGGATCGGCCAAGgtacccctacgcttccatccattcgatt------cgattccacttgtttgcggtttgctgatgcgc-attcgt---gttgggttttggtcag-
|||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||| ||||| |||||||||  |   |   || |  || ||  ||      ||||        ||  |  ||  | ||  |    || ||   ||   |  ||  |||  
ATGTGCAGAGGGAGGAGAAGAAGGTGGAGAAGGCCATCAGGGAGGCCGCCAAGCGCAACGACATGGGATCCGCCAAGgtaggcacccatctcgaatcaatctgttgacggacgatctgttggtttcacttttcaccgaccccttgtttgtctggtgatgccttcttcaag
















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|95100648|gb|CI692355.1|CI692355
EST:     AGAAGTCCATCAGGGAGGCCGCCAAGCGCAACGACATCGGATCGGCCAAG                         GCGCTGGCCAAGGAGGTGGTGAGGTCCAGGAAGGCGGTCAACCGCCTCTAC
genomic: AGAAGTCCATCAGGGAGGCCGCCAAGCGCAACGACATCGGATCGGCCAAGgtacccctac ... ttttggtcagGCGCTGGCCAAGGAGGTGGTGAGGTCCAGGAAGGCGGTCAACCGCCTCTAC
EST: gi|27547715|gb|CA767395.2|CA767395
EST:     AGAAGTCCATCAGGGAGGCCGCCAAGCGCAACGACATCGGATCGGCCAAG                         GCGCTGGCCAAGGAGGTGGTGAGGTCCAGGAAGGCGGTCAACCGCCTCTAC
genomic: AGAAGTCCATCAGGGAGGCCGCCAAGCGCAACGACATCGGATCGGCCAAGgtacccctac ... ttttggtcagGCGCTGGCCAAGGAGGTGGTGAGGTCCAGGAAGGCGGTCAACCGCCTCTAC
EST: gi|95101417|gb|CI693165.1|CI693165
EST:     AGAAGTCCATCAGGGAGGCCGCCAAGCGCAACGACATCGGATCGGCCAAG                         GCGCTGGCCAAGGAGGTGGTGAGGTCCAGGAAGGCGGTCAACCGCCTCTAC
genomic: AGAAGTCCATCAGGGAGGCCGCCAAGCGCAACGACATCGGATCGGCCAAGgtacccctac ... ttttggtcagGCGCTGGCCAAGGAGGTGGTGAGGTCCAGGAAGGCGGTCAACCGCCTCTAC
EST: gi|88310672|gb|CI672535.1|CI672535
EST:     AGAAGTCCATCAGGGAGGCCGCCAAGCGCAACGACATCGGATCGGCCAAG                         GCGCTGGCCAAGGAGGTGGTGAGGTCCAGGAAGGCGGTCAACCGCCTCTAC
genomic: AGAAGTCCATCAGGGAGGCCGCCAAGCGCAACGACATCGGATCGGCCAAGgtacccctac ... ttttggtcagGCGCTGGCCAAGGAGGTGGTGAGGTCCAGGAAGGCGGTCAACCGCCTCTAC
EST: gi|27576250|gb|CA998944.1|CA998944
EST:     AGAAGTCCATCAGGGAGGCCGCCAAGCGCAACGACATCGGATCGGCCAAG                         GCGCTGGCCAAGGAGGTGGTGAGGTCCAGGAAGGCGGTCAACCGCCTCTAC
genomic: AGAAGTCCATCAGGGAGGCCGCCAAGCGCAACGACATCGGATCGGCCAAGgtacccctac ... ttttggtcagGCGCTGGCCAAGGAGGTGGTGAGGTCCAGGAAGGCGGTCAACCGCCTCTAC
EST: gi|58686936|gb|CK075623.1|CK075623
EST:     AGAAGTCCATCAGGGAGGCCGCCAAGCGCAACGACATCGGATCGGCCAAT                         GCGCTGGCCAAGGAGGTGGTGAGGTCCAGGAAGGCGGTCAACCGCCTCTAC
genomic: AGAAGTCCATCAGGGAGGCCGCCAAGCGCAACGACATCGGATCGGCCAAGgtacccctac ... ttttggtcagGCGCTGGCCAAGGAGGTGGTGAGGTCCAGGAAGGCGGTCAACCGCCTCTAC
EST: gi|88587132|gb|CI704860.1|CI704860
EST:     AGAAGTCCATCAGGGAGGCCGCCAAGCGCAACGACATCGGATCGGCCAAG                         GCGCTGGCCAAGGAGGTGGTGAGGTCCAGGAAGGCGGTCAACCGCCTCTAC
genomic: AGAAGTCCATCAGGGAGGCCGCCAAGCGCAACGACATCGGATCGGCCAAGgtacccctac ... ttttggtcagGCGCTGGCCAAGGAGGTGGTGAGGTCCAGGAAGGCGGTCAACCGCCTCTAC
EST: gi|88382928|gb|CI683023.1|CI683023
EST:     AGAAGTCCATCAGGGAGGCCGCCAAGCGCAACGACATCGGATCGGCCAAG                         GCGCTGGCCAAGGAGGTGGTGAGGTCCAGGAAGGCGGTCAACCGCCTCTAC
genomic: AGAAGTCCATCAGGGAGGCCGCCAAGCGCAACGACATCGGATCGGCCAAGgtacccctac ... ttttggtcagGCGCTGGCCAAGGAGGTGGTGAGGTCCAGGAAGGCGGTCAACCGCCTCTAC
EST: gi|88408489|gb|CI685983.1|CI685983
EST:     AGAAGTCCATCAGGGAGGCCGNCAAGCGCAACGACATCGGATCGGCCAAG                         GCGCTGGCCAAGGAGGTGGTGAGGTCCAGGAAGGCGGTCAACCGCCTCTAG
genomic: AGAAGTCCATCAGGGAGGCCGCCAAGCGCAACGACATCGGATCGGCCAAGgtacccctac ... ttttggtcagGCGCTGGCCAAGGAGGTGGTGAGGTCCAGGAAGGCGGTCAACCGCCTCTAC
EST: gi|112785790|gb|EE591423.1|EE591423
EST:     AGAAGTCCATCAGGGAGGCCGCCAAGCGCAACGACATCGGATCGGCCAAG                         GCGCTGGCCAAGGAGGTGGTGAGGTCCAGGAAGGCGGTCAACCGCCTCTAC
genomic: AGAAGTCCATCAGGGAGGCCGCCAAGCGCAACGACATCGGATCGGCCAAGgtacccctac ... ttttggtcagGCGCTGGCCAAGGAGGTGGTGAGGTCCAGGAAGGCGGTCAACCGCCTCTAC
EST: gi|33666695|gb|CF297662.1|CF297662
EST:     AGAAGTCCATCAGGGAGGCCGCCAAGCGCAACGACATCGGATCGGCCAAG                         GCGCTGGCCAAGGAGGTGGTGAGGTCCAGGAAGGCGGTCAACCGCCTCTAC
genomic: AGAAGTCCATCAGGGAGGCCGCCAAGCGCAACGACATCGGATCGGCCAAGgtacccctac ... ttttggtcagGCGCTGGCCAAGGAGGTGGTGAGGTCCAGGAAGGCGGTCAACCGCCTCTAC
EST: gi|88580269|gb|CI697183.1|CI697183
EST:     AGAAGTCCATCAGGGAGGCCGCCAAGCGCAACGACATCGGATCGGCCAAG                         GCGCTGGCCAAGGAGGTGGTGAGGTCCAGGAAGGCGGTCAACCGCCTCTAC
genomic: AGAAGTCCATCAGGGAGGCCGCCAAGCGCAACGACATCGGATCGGCCAAGgtacccctac ... ttttggtcagGCGCTGGCCAAGGAGGTGGTGAGGTCCAGGAAGGCGGTCAACCGCCTCTAC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 69 (upstream exon), 61 (downstream exon)
Score: 9

ATGTGCAGAGGGAGGAGAAGAAGGTGGAGAAGTCCATCAGGGAGGCCGCCAAGCGCAACGACATCGGATCGGCCAAGgtacccctac ... ttttggtcagGCGCTGGCCAAGGAGGTGGTGAGGTCCAGGAAGGCGGTCAACCGCCTCTACGAGAACAAGGCCCAGCTCAACTCCATCTCCATGCACCTTGGCGAGATCG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGTGCAGAGGGAGGAGAAGAAGGTGGAGAAGTCCATCAGGGAGGCCGCCAAGCGCAACGACATCGGATCGGCCAAGgtacccctacgcttccatccattcgattcgattccacttgtttgcggtttgctgatgcgcattcgtgttgggttttggtcag

- - - - - - - - - - - - -  AGAAGT