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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAATCCCATATTTCCGGGAGGTGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAGgtcagtttggttgtcctaccactgttttgtaaataagatttagttacctgactggcacattttgacacttgtggtttcaaaactctcttcctctttgttcaccag

Basic information

species Zea mays
transcript GRMZM2G351582_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G351582_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os08g36774.1 (Oryza sativa), 5'ss of exon 11
AAATCCCATATTTCCGGGAGGTGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAGgtcagtttggttgtcctaccactgttttgtaaataagatttagttacctgac-tggcacattt-tgacacttgtggtttcaaaactctcttcctctttgttcaccag
||||||||||||| || ||||| |||||||||||||||||||| |||||||| || |||||||| |||||||||||||      | |        |    |  ||    |||||  |    |  | | |||||  |||||  | ||   | |||||    ||| | ||  |  | |||
AAATCCCATATTTTCGTGAGGTTATTGTTATGGCAACAACATGCGACATGTGCGGCTATCGCAACTCAGAGgtcagttccagacttccgtagtcatac-atgcatttcttttagaaaaaaaatgttgtacattggtgacaactctgaacttaaaacggctttctttttgttctatcag
















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|60348538|gb|DN215511.1|DN215511
EST:     TGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAG                         CTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGT
genomic: TGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAGgtcagtttgg ... tgttcaccagCTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGT
EST: gi|6445448|gb|AW179366.1|AW179366
EST:     TGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAG                         CTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGT
genomic: TGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAGgtcagtttgg ... tgttcaccagCTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGT
EST: gi|20513026|gb|BQ280212.1|BQ280212
EST:     TATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAG                         CTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGT
genomic: TATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAGgtcagtttgg ... tgttcaccagCTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGT
EST: gi|78544301|gb|DV621799.1|DV621799
EST:     GATTGTTATGGCAACAACATGTGACATGTGTGG-TATTCGCAATTCAGAG                         CTGAAGCCTGGGGGTGAAATTCCAGCTAAAGGGAAGGAAAATTACACTGCG
genomic: GATTGTTATGGCAACAACATGTGACATGTGTGGTTA-TCGCAATTCAGAGgtcagtttgg ... tgttcaccagCTGAAGCCTGGGGGTGAAATTCCAGCT-AAGGGAAAGAAAATTACACTGCG
EST: gi|211367141|gb|FL432366.1|FL432366
EST:     TGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAG                         CTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGT
genomic: TGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAGgtcagtttgg ... tgttcaccagCTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGT
EST: gi|211282780|gb|FL192971.1|FL192971
EST:     TGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAG                         CTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGT
genomic: TGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAGgtcagtttgg ... tgttcaccagCTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGT
EST: gi|88748313|gb|DY532454.1|DY532454
EST:     TGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAG                         CTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGT
genomic: TGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAGgtcagtttgg ... tgttcaccagCTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGT
EST: gi|30306974|gb|CD001647.1|CD001647
EST:     TGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAG                         CTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGT
genomic: TGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAGgtcagtttgg ... tgttcaccagCTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGT
EST: gi|78085694|gb|DV514087.1|DV514087
EST:     TGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAG                         CTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGT
genomic: TGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAGgtcagtttgg ... tgttcaccagCTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGT
EST: gi|31611962|gb|CD568584.1|CD568584
EST:     TGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAG                         CTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGT
genomic: TGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAGgtcagtttgg ... tgttcaccagCTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGT
EST: gi|37401209|gb|CF637968.1|CF637968
EST:     TGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAG                         CTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGT
genomic: TGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAGgtcagtttgg ... tgttcaccagCTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGT
EST: gi|67020485|gb|CO449234.1|CO449234
EST:     TGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAG                         CTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGT
genomic: TGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAGgtcagtttgg ... tgttcaccagCTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGT
EST: gi|60353658|gb|DN220631.1|DN220631
EST:     TGACATGTGTGGTTATCGCAATTCAGAG                         CTGAAGCCTGGGGGTGAAATTCCAGTTAAGGGAAAGAAAATTACACTGCGT
genomic: TGACATGTGTGGTTATCGCAATTCAGAGgtcagtttgg ... tgttcaccagCTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGT
EST: gi|60395671|gb|DN228541.1|DN228541
EST:     TGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAG                         CTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGT
genomic: TGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAGgtcagtttgg ... tgttcaccagCTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGT
EST: gi|29946582|gb|CB816222.1|CB816222
EST:     TGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAG                         CTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGT
genomic: TGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAGgtcagtttgg ... tgttcaccagCTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGT
EST: gi|211282782|gb|FL192973.1|FL192973
EST:     TGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAG                         CTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAWAATTACACTGCGT
genomic: TGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAGgtcagtttgg ... tgttcaccagCTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGT
EST: gi|78543505|gb|DV621003.1|DV621003
EST:     CAACAACATGTGACATGTGTGGTTATCGCAATTCAGAG                         CTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGT
genomic: CAACAACATGTGACATGTGTGGTTATCGCAATTCAGAGgtcagtttgg ... tgttcaccagCTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGT
EST: gi|149027381|gb|EE046513.2|EE046513
EST:     TGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAG                         CTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGT
genomic: TGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAGgtcagtttgg ... tgttcaccagCTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGT
EST: gi|78543967|gb|DV621465.1|DV621465
EST:     TGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAG                         CTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGT
genomic: TGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAGgtcagtttgg ... tgttcaccagCTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGT
EST: gi|60350354|gb|DN217327.1|DN217327
EST:     TGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAG                         CTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGT
genomic: TGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAGgtcagtttgg ... tgttcaccagCTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGT
EST: gi|28568977|gb|CB280852.1|CB280852
EST:     TGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAG                         CTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGT
genomic: TGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAGgtcagtttgg ... tgttcaccagCTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGT
EST: gi|211367140|gb|FL432365.1|FL432365
EST:     TGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAG                         CTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACMCTGSGT
genomic: TGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAGgtcagtttgg ... tgttcaccagCTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGT
EST: gi|7135020|gb|AW497876.1|AW497876
EST:     GCAATTCAGAG                         CTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGT
genomic: GCAATTCAGAGgtcagtttgg ... tgttcaccagCTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGT
EST: gi|60357973|gb|DN224946.1|DN224946
EST:     TGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAG                         CTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGT
genomic: TGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAGgtcagtttgg ... tgttcaccagCTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGT

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 4 RNA-Seq libraries.


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 230

AAATCCCATATTTCCGGGAGGTGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAGgtcagtttgg ... tgttcaccagCTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 110

AAATCCCATATTTCCGGGAGGTGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAGgtcagtttgg ... tgttcaccagCTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 107

AAATCCCATATTTCCGGGAGGTGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAGgtcagtttgg ... tgttcaccagCTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 155

AAATCCCATATTTCCGGGAGGTGATTGTTATGGCAACAACATGTGACATGTGTGGTTATCGCAATTCAGAGgtcagtttgg ... tgttcaccagCTGAAGCCTGGGGGTGAAATTCCAGCTAAGGGAAAGAAAATTACACTGCGTGTTCAAAATGCACAAGACCTTACTCGTGATGTCATAAAG