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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGTCTGCAGTTTCATATGTTGGAAGCTATTTGTCTCGGGCAAGGTTCATTTCTGCTGATACGGTGGTTGGTATACTCAAAAGgtggttgttacgctgtagtgtctgcatccatatatgtcttgagtaatatggtttggtatttgaatatctttgtacttcttttggcag

Basic information

species Oryza sativa
transcript LOC_Os06g47350.2
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g47350.2 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G415846_T01 (Zea mays), 5'ss of exon 11
AATGTCTGCAGTTTCATATGTTGGAAGCTATTTGTCTCGGGCAAGGTTCATTTCTGCTGATACGGTGGTTGGTATACTCAAAAGgtggttgttacgctgtagtgtctgcatccatatatgtcttgagtaatatggtttggtatttgaatatctttgtacttcttttg-gcag-----------------------------
| ||||||||||||||||||||||||||||| |||| ||||||||||||||||| |   |||  || |||  | |||||||||||||| |    | ||| |   |    |   |||| ||| ||||| |        || ||| | |  || |||| |  | || ||  ||                              
AGTGTCTGCAGTTTCATATGTTGGAAGCTATCTGTCCCGGGCAAGGTTCATTTCCGTAAATATAGTTGTTTCTGTACTCAAAAGgtggctacc-ctctg-aacatacaaa---atatttgttttgagcacctcacagtg-tatct-atgatttttgcatctgttctgtacatctgcgatttatgttatgttatgtgcttag
















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|58676719|gb|CK065406.1|CK065406
EST:     TCTCGGGCAAGGTTCATTTCTGCTGATACGGTGGTTGGTATACTCAAAAG                         GTTAGTGGACTGGTGTGTTGACTATTGTGACCTCCAGAACAACATAGGGAT
genomic: TCTCGGGCAAGGTTCATTTCTGCTGATACGGTGGTTGGTATACTCAAAAGgtggttgtta ... cttttggcagGTTAGTGGACTGGTGTGTTGACTATTGTGACCTCCAGAACAACATAAGGAT
EST: gi|58668152|gb|CK056838.1|CK056838
EST:     TCTCGGGCAAGGTTCATTTCTGCTGATACGGTGGTTGGTATACTCAAAAG                         GTTAGTGGACTGGTGTGTTGACTATTGTGACCTCCAGAACAACATAGGGAT
genomic: TCTCGGGCAAGGTTCATTTCTGCTGATACGGTGGTTGGTATACTCAAAAGgtggttgtta ... cttttggcagGTTAGTGGACTGGTGTGTTGACTATTGTGACCTCCAGAACAACATAAGGAT
EST: gi|218504600|gb|FG967431.1|FG967431
EST:     CATTTCTGCTGATACGG-GG-TGGTATACTCAAAAG                         GTTAGTGGACTGGTGTGTTGACTATTGTGACCTCCAGAACAACATAGGGAT
genomic: CATTTCTGCTGATACGGTGGTTGGTATACTCAAAAGgtggttgtta ... cttttggcagGTTAGTGGACTGGTGTGTTGACTATTGTGACCTCCAGAACAACATAAGGAT
EST: gi|33812524|gb|CF332150.1|CF332150
EST:     TCTCGGGC-AGGTTCATTTCTGCTGATACGGTGGTTGGTATACTCAAAAG                         GTTAGTGGACTGGTGTGTTGACTATTGTGACCTCCAGAACAACATAAGGAT
genomic: TCTCGGGCAAGGTTCATTTCTGCTGATACGGTGGTTGGTATACTCAAAAGgtggttgtta ... cttttggcagGTTAGTGGACTGGTGTGTTGACTATTGTGACCTCCAGAACAACATAAGGAT
EST: gi|66922574|gb|CX109422.1|CX109422
EST:     TCTCGGGCAAGGTTCATTTCTGCTGATACGGTGGTTGGTATACTCAAAAG                         GTTAGTGGACTGGTGTGTTGACTATTGTGACCTCCAGAACAACATAGGGAT
genomic: TCTCGGGCAAGGTTCATTTCTGCTGATACGGTGGTTGGTATACTCAAAAGgtggttgtta ... cttttggcagGTTAGTGGACTGGTGTGTTGACTATTGTGACCTCCAGAACAACATAAGGAT
EST: gi|29628119|gb|CB633130.1|CB633130
EST:     TCTCGGGCAAGGTTCATTTCTGCTGATACGGTGGTTGGTATACTCAAAAG                         GTTAGTGGACTGGTGTGTTGACTATTGTGACCTCCAGAACAACATANGGAT
genomic: TCTCGGGCAAGGTTCATTTCTGCTGATACGGTGGTTGGTATACTCAAAAGgtggttgtta ... cttttggcagGTTAGTGGACTGGTGTGTTGACTATTGTGACCTCCAGAACAACATAAGGAT
EST: gi|29689750|gb|CB686025.1|CB686025
EST:     CTCGGGNCA-GGTTCATTTCTGCTGATACGGTGGTTGGTATACTCAAAAG                         GTTAGTGGACTGGTGTGTTGACTA
genomic: CTCGGG-CAAGGTTCATTTCTGCTGATACGGTGGTTGGTATACTCAAAAGgtggttgtta ... cttttggcagGTTAGTGGACTGGTGTGTTGACTA
EST: gi|58668829|gb|CK057515.1|CK057515
EST:     TCTCGGGCAA-GTTCATTTCTGCTGATACGGTGGTTGGTATACTCAAAAG                         GTTAGTGGACTGGTGTGTTGACTATTGTGACCTCCAGAACAACATAGGGAT
genomic: TCTCGGGCAAGGTTCATTTCTGCTGATACGGTGGTTGGTATACTCAAAAGgtggttgtta ... cttttggcagGTTAGTGGACTGGTGTGTTGACTATTGTGACCTCCAGAACAACATAAGGAT
EST: gi|58680790|gb|CK069477.1|CK069477
EST:     GGGCAAGGTTCATTTCTGCTGATACGGTGGTTGGTATACTCAAAAG                         GTTAGTGGACTGGTGTGTTGACTATTGTGACCTCCAGAACAACATAGGGAT
genomic: GGGCAAGGTTCATTTCTGCTGATACGGTGGTTGGTATACTCAAAAGgtggttgtta ... cttttggcagGTTAGTGGACTGGTGTGTTGACTATTGTGACCTCCAGAACAACATAAGGAT
EST: gi|218492292|gb|FG954140.1|FG954140
EST:     TCTCGGGCAAGGTTCATTTCTGCTGATACGGTGGTTGGTATACTCAAAAG                         GTTAGTGGACTGGTGTGTTGACTATTGTGACCTCCAGAACAACATAGGGAT
genomic: TCTCGGGCAAGGTTCATTTCTGCTGATACGGTGGTTGGTATACTCAAAAGgtggttgtta ... cttttggcagGTTAGTGGACTGGTGTGTTGACTATTGTGACCTCCAGAACAACATAAGGAT

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: 73 (upstream exon), 74 (downstream exon)
Score: 83

AATGTCTGCAGTTTCATATGTTGGAAGCTATTTGTCTCGGGCAAGGTTCATTTCTGCTGATACGGTGGTTGGTATACTCAAAAGgtggttgtta ... cttttggcagGTTAGTGGACTGGTGTGTTGACTATTGTGACCTCCAGAACAACATAAGGATAACAACCAAGCCTATAAATCATCAAATATTTTACGCAAGCTGTCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATGTCTGCAGTTTCATATGTTGGAAGCTATTTGTCTCGGGCAAGGTTCATTTCTGCTGATACGGTGGTTGGTATACTCAAAAGgtggttgttacgctgtagtgtctgcatccatatatgtcttgagtaatatggtttggtatttgaatatctttgtacttcttttggcag

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