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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCGAGGCCGTTTCTTATCTCGGCACGTACATCAAGTGATACTGAAAATCATTGATAGAGCAATGGCAGCATTTTCTGCTACAGGGATGAACCCTGATAGgtatgttactatctatctgacttgcatctatccttttgcggttaataaatctatttcagtccgactgtatttagtaggaggtgctaatattaatatctat...

Basic information

species Oryza sativa
transcript LOC_Os03g58970.2
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g58970.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA07G00570.1 (Glycine max), 5'ss of exon 8
GGCGAGGCCGTTTCTTATCTCGGCACGTACATCAAGTGATACTGAAAATCATTGATAGAGCAATGGCAGCATTTTCTGCTACAGGGATGAACCCTGATAGgtatgttactatctatctgacttgcat-ctatccttttgcggttaataaa---tctatttcagtccgactgtattta-gtaggaggtgctaatattaatatctat------------------------------
  |  || || | ||| ||| || |  | || | | |  |     | || ||    | ||||||||||||||||||||| ||||||||| | ||  || |||| || ||| |   |   |    ||| ||||| || | |  | || |||   ||| |     | | | ||| |||   |   | ||  |   ||||| |||| |                              
CCCATGGTCGGTACTTGTCTAGGAATTTGCAACGAATTGTCAATGAGATTATAACAAAAGCAATGGCAGCATTTTCTGCAACAGGGATGGATCCATATGGgtaggtcactgttgttgccatcaacattctatcattattctttaaagaaaatatctttgcatttgcaattgtttttctattcaaagttgtggcattaa-atctgtaagagtctgatatgtatattctgttgccag
















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|25807657|gb|CA763618.1|CA763618
EST:     ATTGATAGAGCAATGGCAGCATTTTCTGCTACAGGGATGAACCCTGATAG                         TGTCCTTCCAAGCGACGATTGGTTTATNGACGTTGCTAATGACACTATCAG
genomic: ATTGATAGAGCAATGGCAGCATTTTCTGCTACAGGGATGAACCCTGATAGgtatgttact ... ttctctgcagTGTCCTTCCAAGCGACGATTGGTTCATCGACGTTGCTAATGACACTATCAG
EST: gi|86477481|gb|CI120114.1|CI120114
EST:     ATTGATAGAGCAATGGCAGCGTTTTCTGCTACAGGGATGAACCCTGATAG                         TGTCCTTCCAAGCGACGATTGGTTCATCGACGTTGCTAATGACACTATCAG
genomic: ATTGATAGAGCAATGGCAGCATTTTCTGCTACAGGGATGAACCCTGATAGgtatgttact ... ttctctgcagTGTCCTTCCAAGCGACGATTGGTTCATCGACGTTGCTAATGACACTATCAG
EST: gi|25806473|gb|CA762434.1|CA762434
EST:     ATCGATAGAGCAATGGCAGCATTTTTTGCTACAGGGATGAACCCTGATAG                         TGTCCTTCCAAGCGACGATTGGTTCATNGACGTTGCTAATGACCCTATCAG
genomic: ATTGATAGAGCAATGGCAGCATTTTCTGCTACAGGGATGAACCCTGATAGgtatgttact ... ttctctgcagTGTCCTTCCAAGCGACGATTGGTTCATCGACGTTGCTAATGACACTATCAG
EST: gi|86521349|gb|CI161555.1|CI161555
EST:     ATTGATAGAGCAATGGCAGCATTTTCTGCTACAGGGATGAACCCTGATAG                         TGTCCTTCCAAGCGACGATTGGTTCATCGACGTTGCTAATGACACTATCAG
genomic: ATTGATAGAGCAATGGCAGCATTTTCTGCTACAGGGATGAACCCTGATAGgtatgttact ... ttctctgcagTGTCCTTCCAAGCGACGATTGGTTCATCGACGTTGCTAATGACACTATCAG
EST: gi|218496857|gb|FG966015.1|FG966015
EST:     ATTGATAGAGCAATGGCAGCATTTTCTGCTACAGGGATGAACCCTGATAG                         TGTCCTTCCAAGCGACGATTGGTTCATCGACGTTGCTAATGACACTAT
genomic: ATTGATAGAGCAATGGCAGCATTTTCTGCTACAGGGATGAACCCTGATAGgtatgttact ... ttctctgcagTGTCCTTCCAAGCGACGATTGGTTCATCGACGTTGCTAATGACACTAT
EST: gi|218490678|gb|FG953058.1|FG953058
EST:     ATTGATAGAGCAATGGCAGCATTTTCTGCTACAGGGATGAACCCTGATAG                         TGTCCTTCCAAGCGACGATTGGTTCATCGACGTTGCTAATGACACTATCAG
genomic: ATTGATAGAGCAATGGCAGCATTTTCTGCTACAGGGATGAACCCTGATAGgtatgttact ... ttctctgcagTGTCCTTCCAAGCGACGATTGGTTCATCGACGTTGCTAATGACACTATCAG
EST: gi|86519205|gb|CI159411.1|CI159411
EST:     ATTGATAGAGCAATGGCAGCATTTTCTGCTACAGGGGTGAACCCTGATAG                         TGTCCTTCCAAGCGACGATTGGTTCATCGACGTTGCTAATGACACTATCAG
genomic: ATTGATAGAGCAATGGCAGCATTTTCTGCTACAGGGATGAACCCTGATAGgtatgttact ... ttctctgcagTGTCCTTCCAAGCGACGATTGGTTCATCGACGTTGCTAATGACACTATCAG
EST: gi|27545945|gb|CA767154.2|CA767154
EST:     ATTGATAGAGCAATGGCAGCATTTTCTGCTACAGGGATGAACCCTGATAG                         TGTCCTTCCAAGCGACGATTGGTTCATCGACGTTGCTAATGACACTATCAG
genomic: ATTGATAGAGCAATGGCAGCATTTTCTGCTACAGGGATGAACCCTGATAGgtatgttact ... ttctctgcagTGTCCTTCCAAGCGACGATTGGTTCATCGACGTTGCTAATGACACTATCAG

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: 66 (upstream exon), 74 (downstream exon)
Score: 7

GGCGAGGCCGTTTCTTATCTCGGCACGTACATCAAGTGATACTGAAAATCATTGATAGAGCAATGGCAGCATTTTCTGCTACAGGGATGAACCCTGATAGgtatgttact ... ttctctgcagTGTCCTTCCAAGCGACGATTGGTTCATCGACGTTGCTAATGACACTATCAGTAGGATCAGTGGCAACCCTCGAACTGCCAATGGGGATAGGGAGGTGAAC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCGAGGCCGTTTCTTATCTCGGCACGTACATCAAGTGATACTGAAAATCATTGATAGAGCAATGGCAGCATTTTCTGCTACAGGGATGAACCCTGATAGgtatgttactatctatctgacttgcatctatccttttgcggttaataaatctatttcagtccgactgtatttagtaggaggtgctaatattaatatctat

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