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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTAAAGGTGTGAAACCCATGCCTCTTTCTGAGATGGCTAATCTTTTCATGAGCCTTCACTTGGCGGTCGCTCCTGGACTTgtatgtagtttgatatttgtctctctattttgggtcattttgttttttaaacagttgaagttcttgctcttttag

Basic information

species Zea mays
transcript GRMZM2G137236_T01
intron # 24
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G137236_T01 (Zea mays), 5'ss of exon 24
lower sequence: LOC_Os03g02150.1 (Oryza sativa), 5'ss of exon 24
GTTAAAGGTGTGAAACCCATGCCTCTTTCTGAGATGGCTAATCTTTTCATGAGCCTTCACTTGGCGGTCGCTCCTGGACTTgtatgtagtttgatatttgtctc-----tctattttgggtc---attttgt-tttttaaacagttgaagttcttgctc--ttttag
|||||||||||||||||  | |||||| ||||||| |||| ||||||||||||||||||||||||||| |||||||||||||||||| || |||| ||||||||     ||   |||  ||    |||       |||  ||  ||||| |||||| ||  ||||||
GTTAAAGGTGTGAAACCATTACCTCTTCCTGAGATAGCTAGTCTTTTCATGAGCCTTCACTTGGCGGTTGCTCCTGGACTTgtatgttgtgtgatttttgtctcagttttcagctttcagttcaaattccaagccttttcacttttgaacttcttgttcctttttag
















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|211430870|gb|FL250418.1|FL250418
EST:     AGATGGCTAATCTTTTCATGAGCCTTCACTTGGCGGTCGCTCCTGGACTT                         GATAACAACCCGAACAATCTGGTTGCATGCACGACATTCTTTTCTGAAGCA
genomic: AGATGGCTAATCTTTTCATGAGCCTTCACTTGGCGGTCGCTCCTGGACTTgtatgtagtt ... gctcttttagGATAACAACCCGAACAATCTGGTTGCATGCACGACATTCTTTTCTGAAGCA
EST: gi|37395386|gb|CF634973.1|CF634973
EST:     AGATGGCTAATCTTTTCATGAGCCTTCACTTGGCGGTCGCTCCTGGACTT                         GATAACAACCCGAACAATCTGGTTGCATGCACGACATTCTTTTCTGAAGCA
genomic: AGATGGCTAATCTTTTCATGAGCCTTCACTTGGCGGTCGCTCCTGGACTTgtatgtagtt ... gctcttttagGATAACAACCCGAACAATCTGGTTGCATGCACGACATTCTTTTCTGAAGCA
EST: gi|40336758|gb|CK370828.1|CK370828
EST:     AGATGGCTAATCTTTTCATGAGCCTTCACTTGGCGGTCGCTCCTGGACTT                         GATAACAACCCGAACAATCTGGTTGCATGCACGACATTCTTTTCTGAAGCA
genomic: AGATGGCTAATCTTTTCATGAGCCTTCACTTGGCGGTCGCTCCTGGACTTgtatgtagtt ... gctcttttagGATAACAACCCGAACAATCTGGTTGCATGCACGACATTCTTTTCTGAAGCA
EST: gi|38502665|gb|CF972525.1|CF972525
EST:     GATGGCTAATCTTTTCATGAGCCTTCCCTTGGGCGGTCGCTCCTGGACTT                         GATA-CAACCCGAATAATCTGGTTGCATGCACGA
genomic: GATGGCTAATCTTTTCATGAGCCTTCACTTGG-CGGTCGCTCCTGGACTTgtatgtagtt ... gctcttttagGATAACAACCCGAACAATCTGGTTGCATGCACGA
EST: gi|113704027|gb|EE681531.1|EE681531
EST:     AGATGGCTAATCTTTTCATGAGCCTTCACTTGGCGGTCGCTCCTGGACTT                         GATAACAACCCGAACAATCTGGTTGCATGCACGACATTCTTTTCTGAAGCA
genomic: AGATGGCTAATCTTTTCATGAGCCTTCACTTGGCGGTCGCTCCTGGACTTgtatgtagtt ... gctcttttagGATAACAACCCGAACAATCTGGTTGCATGCACGACATTCTTTTCTGAAGCA
EST: gi|67018440|gb|CO447189.1|CO447189
EST:     AGATGGCTAATCTTTTCATGAGCCTTCACTTGGCGGTCGCTCCTGGACTT                         GATAACAACCCGAACAATCTGGTTGCATGCACGACATTCTTTTCTGAAGCA
genomic: AGATGGCTAATCTTTTCATGAGCCTTCACTTGGCGGTCGCTCCTGGACTTgtatgtagtt ... gctcttttagGATAACAACCCGAACAATCTGGTTGCATGCACGACATTCTTTTCTGAAGCA
EST: gi|211430871|gb|FL250419.1|FL250419
EST:     AGATGGCTAATCTTTTCATGAGCCTTCACTTGGCGGTCGCTCCTGGACTT                         GATAACAACCCGAACAATCTGGTTGCATGCACGACATTCTTTTCTGAAGCA
genomic: AGATGGCTAATCTTTTCATGAGCCTTCACTTGGCGGTCGCTCCTGGACTTgtatgtagtt ... gctcttttagGATAACAACCCGAACAATCTGGTTGCATGCACGACATTCTTTTCTGAAGCA
EST: gi|213169610|gb|FM186192.1|FM186192
EST:     AGATGGCTAATCTTTTCATGAGCCTTCACTTGGCGGTCGCTCCTGGACTT                         GATAACAACCCGAACAATCTGGTTGCATGCACGACATTCTTTTCTGAAGCA
genomic: AGATGGCTAATCTTTTCATGAGCCTTCACTTGGCGGTCGCTCCTGGACTTgtatgtagtt ... gctcttttagGATAACAACCCGAACAATCTGGTTGCATGCACGACATTCTTTTCTGAAGCA

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: 49 (upstream exon), 49 (downstream exon)
Score: 300

GTTAAAGGTGTGAAACCCATGCCTCTTTCTGAGATGGCTAATCTTTTCATGAGCCTTCACTTGGCGGTCGCTCCTGGACTTgtatgtagtt ... gctcttttagGATAACAACCCGAACAATCTGGTTGCATGCACGACATTCTTTTCTGAAGCAACACGTGCCATGCTTTGTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 252

GTTAAAGGTGTGAAACCCATGCCTCTTTCTGAGATGGCTAATCTTTTCATGAGCCTTCACTTGGCGGTCGCTCCTGGACTTgtatgtagtt ... gctcttttagGATAACAACCCGAACAATCTGGTTGCATGCACGACATTCTTTTCTGAAGCAACACGTGCCATGCTTTGTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 330

GTTAAAGGTGTGAAACCCATGCCTCTTTCTGAGATGGCTAATCTTTTCATGAGCCTTCACTTGGCGGTCGCTCCTGGACTTgtatgtagtt ... gctcttttagGATAACAACCCGAACAATCTGGTTGCATGCACGACATTCTTTTCTGAAGCAACACGTGCCATGCTTTGTCTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 198

GTTAAAGGTGTGAAACCCATGCCTCTTTCTGAGATGGCTAATCTTTTCATGAGCCTTCACTTGGCGGTCGCTCCTGGACTTgtatgtagtt ... gctcttttagGATAACAACCCGAACAATCTGGTTGCATGCACGACATTCTTTTCTGAAGCAACACGTGCCATGCTTTGTCTG