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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGTTCACCCCGCGTCGTCTTCGCTCTCACGATCCCTCGGCAGTCGGCGACGGCTGGGCGACCGCCACTTCCGCCTTCTCTTCCTACTGAGCGTCTCCAGgtactccaccccttctacctgctgtgcgaaaccgagcacccaaaccctaacttaaactttttttgttcggatctggtctaataacaaatatatgtacattcatactgacctttttgcaaaaaaaaaaattcggatgtactcccgtgtcctccactgcttctag

Basic information

species Zea mays
transcript GRMZM2G106574_T01
intron # 1
splice site 5'
intron type U2

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|14243476|gb|BG841204.2|BG841204
EST:     GGCTGGGCGACCGCCACTTCCGCCTTCTTCTTCCTACTGAGCGTCTCCAG                         GCACGCTTCTGAATTCGGAGTTGCCAGCATTCGCTCGAGGTGCCGGACCAG
genomic: GGCTGGGCGACCGCCACTTCCGCCTTC-TCTTCCTACTGAGCGTCTCCAGgtactccacc ... ctgcttctagGCACGCTTCTGAATTCGGAGTTGCCAGCATTCGCTCGAGGTGCCGGACCAG
EST: gi|76912105|gb|DV164577.1|DV164577
EST:     CGGCTGGGCGACCGCCACTTCCGCCTTCTCTTCCTACTGAGCGTCTCCAG                         GCACGCTTCTGAATTCGGAGTTGCCAGCATTCGCTCGAGGTGCCGGACCAG
genomic: CGGCTGGGCGACCGCCACTTCCGCCTTCTCTTCCTACTGAGCGTCTCCAGgtactccacc ... ctgcttctagGCACGCTTCTGAATTCGGAGTTGCCAGCATTCGCTCGAGGTGCCGGACCAG
EST: gi|4730361|gb|AI649527.1|AI649527
EST:     CGGCTGGGCGACCGCCACTTCCGCCTTCTCTTCCTACTGAGCGTCTCCAG                         GCACGCTTTTGAATTCGGAGTTGCCAGCATTCGCTCGAGGTGCCGGACCAG
genomic: CGGCTGGGCGACCGCCACTTCCGCCTTCTCTTCCTACTGAGCGTCTCCAGgtactccacc ... ctgcttctagGCACGCTTCTGAATTCGGAGTTGCCAGCATTCGCTCGAGGTGCCGGACCAG
EST: gi|213169581|gb|FM186027.1|FM186027
EST:     CGGCTGGGCGACCGCCGCTGCCGCCTTCTCTTCCTACCGAGCGTCTCCAG                         GCACGCTTCTGAATTCGGAGTTGCCAGCATTCGCTCGAGGTGCCGGACCAG
genomic: CGGCTGGGCGACCGCCACTTCCGCCTTCTCTTCCTACTGAGCGTCTCCAGgtactccacc ... ctgcttctagGCACGCTTCTGAATTCGGAGTTGCCAGCATTCGCTCGAGGTGCCGGACCAG
EST: gi|32855389|gb|CD995070.1|CD995070
EST:     CGGCTGGGCGACCGCCGCTGCCGCCTTCTCTTCCTACCGAGCGTCTCCAG                         GCACGCTTCTGAATTCGGAGTTGCCAGCATTCGCTCGAGGTGCCGGACCAG
genomic: CGGCTGGGCGACCGCCACTTCCGCCTTCTCTTCCTACTGAGCGTCTCCAGgtactccacc ... ctgcttctagGCACGCTTCTGAATTCGGAGTTGCCAGCATTCGCTCGAGGTGCCGGACCAG
EST: gi|33285604|gb|CF075399.1|CF075399
EST:     CGGCTGGGCGACCGCCGCTGCCGCCTTCTCTTCTTACCGAGCGTCTCCAG                         GCACGCTTCTGAATTCGGAGTTGCCAGCATTCGCTCGAGGNGCCGGACCAG
genomic: CGGCTGGGCGACCGCCACTTCCGCCTTCTCTTCCTACTGAGCGTCTCCAGgtactccacc ... ctgcttctagGCACGCTTCTGAATTCGGAGTTGCCAGCATTCGCTCGAGGTGCCGGACCAG
EST: gi|60338673|gb|DN205646.1|DN205646
EST:     CGGCTGGGCGACCGCCACTTCCGCCTTCTCTTCCTACTGAGCGTCTCCAG                         GCACGCTTCTGAATTCGGAGTTGCCAGCATTCGCTCGAGGTGCCGGACCAG
genomic: CGGCTGGGCGACCGCCACTTCCGCCTTCTCTTCCTACTGAGCGTCTCCAGgtactccacc ... ctgcttctagGCACGCTTCTGAATTCGGAGTTGCCAGCATTCGCTCGAGGTGCCGGACCAG
EST: gi|60358045|gb|DN225018.1|DN225018
EST:     CGGCTGGGCGACCGCCACTTCCGCCTTCTCTTCCTACTGAGCGTCTCCAG                         GCACGCTTCTGAATTCGGAGTTGCCAGCATTCGCTCGAGGTGCCGGACCAG
genomic: CGGCTGGGCGACCGCCACTTCCGCCTTCTCTTCCTACTGAGCGTCTCCAGgtactccacc ... ctgcttctagGCACGCTTCTGAATTCGGAGTTGCCAGCATTCGCTCGAGGTGCCGGACCAG
EST: gi|37391857|gb|CF633173.1|CF633173
EST:     CGGCTGGGCGACCGCCGCTGCCGCCTTCTCTTCCTACCGAGCGTCTCCAG                         GCACGCTTCTGAATTCGGAGTTGCCAGCATTCGCTCGAGGTGCCGGACCAG
genomic: CGGCTGGGCGACCGCCACTTCCGCCTTCTCTTCCTACTGAGCGTCTCCAGgtactccacc ... ctgcttctagGCACGCTTCTGAATTCGGAGTTGCCAGCATTCGCTCGAGGTGCCGGACCAG
EST: gi|32907954|gb|CF012767.1|CF012767
EST:     CGGCTGGGCGACCGCCGCTGCCGCCTTCTCTTCCTACCGAGCGTCTCCAG                         GCACGCTTCTGAATTCGGAGTTGCCAGCATTCGCTCGAGGTGCCGGACCAG
genomic: CGGCTGGGCGACCGCCACTTCCGCCTTCTCTTCCTACTGAGCGTCTCCAGgtactccacc ... ctgcttctagGCACGCTTCTGAATTCGGAGTTGCCAGCATTCGCTCGAGGTGCCGGACCAG
EST: gi|116819876|gb|EC863043.1|EC863043
EST:     CGGCTGGGCGACCGCCACTTCCGCCTTCTCTTCCTACTGAGCGTCTCCAG                         GCACGCTTCTGAATTCGGAGTTGCCAGCATTCGCTCCGAGGTGCCGGACCA
genomic: CGGCTGGGCGACCGCCACTTCCGCCTTCTCTTCCTACTGAGCGTCTCCAGgtactccacc ... ctgcttctagGCACGCTTCTGAATTCGGAGTTGCCAGCATTCGCT-CGAGGTGCCGGACCA
EST: gi|213179135|gb|FM184923.1|FM184923
EST:     CGGCTGGGCGACCGCCGCTGCCGCCTTCTCTTCCTACCGAGCGTCTCCAG                         GCACGCTTCTGAATTCGGAGTTGCCAGCATTCGCTCGAGGTGCCGGACCAG
genomic: CGGCTGGGCGACCGCCACTTCCGCCTTCTCTTCCTACTGAGCGTCTCCAGgtactccacc ... ctgcttctagGCACGCTTCTGAATTCGGAGTTGCCAGCATTCGCTCGAGGTGCCGGACCAG
EST: gi|116829615|gb|EC870229.1|EC870229
EST:     CGGCTGGGCGACCGCCGCTGCCGCCTTCTCTT-CTACCGAGCGTCTCCAG                         GCACGCTTCTGAATTCGGAGTTGCCAGCATTCGCTCGAGGTGCCGGACCAG
genomic: CGGCTGGGCGACCGCCACTTCCGCCTTCTCTTCCTACTGAGCGTCTCCAGgtactccacc ... ctgcttctagGCACGCTTCTGAATTCGGAGTTGCCAGCATTCGCTCGAGGTGCCGGACCAG
EST: gi|211218119|gb|FL199938.1|FL199938
EST:     CGGCTGGGCGACCGCCGCTGCCGCCTTCTCTTCCTACCGAGCGTCTCCAG                         GCACGCTTCTGAATTCGGAGTTGCCAGCATTCGCTCGAGGTGCCGGACCAG
genomic: CGGCTGGGCGACCGCCACTTCCGCCTTCTCTTCCTACTGAGCGTCTCCAGgtactccacc ... ctgcttctagGCACGCTTCTGAATTCGGAGTTGCCAGCATTCGCTCGAGGTGCCGGACCAG
EST: gi|211218118|gb|FL199937.1|FL199937
EST:     CGGCTGGGCGACCGCCGCTGCCGCCTTCTCTTCCTACCGAGCGTCTCCAG                         GCACGCTTCTGAATTCGGAGTTGCCAGCATTCGCTCGAGGTGCCGGACCAG
genomic: CGGCTGGGCGACCGCCACTTCCGCCTTCTCTTCCTACTGAGCGTCTCCAGgtactccacc ... ctgcttctagGCACGCTTCTGAATTCGGAGTTGCCAGCATTCGCTCGAGGTGCCGGACCAG

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: 394

CTGTTCACCCCGCGTCGTCTTCGCTCTCACGATCCCTCGGCAGTCGGCGACGGCTGGGCGACCGCCACTTCCGCCTTCTCTTCCTACTGAGCGTCTCCAGgtactccacc ... ctgcttctagGCACGCTTCTGAATTCGGAGTTGCCAGCATTCGCTCGAGGTGCCGGACCAGATCTCACCATCATGCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 332

CTGTTCACCCCGCGTCGTCTTCGCTCTCACGATCCCTCGGCAGTCGGCGACGGCTGGGCGACCGCCACTTCCGCCTTCTCTTCCTACTGAGCGTCTCCAGgtactccacc ... ctgcttctagGCACGCTTCTGAATTCGGAGTTGCCAGCATTCGCTCGAGGTGCCGGACCAGATCTCACCATCATGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 338

CTGTTCACCCCGCGTCGTCTTCGCTCTCACGATCCCTCGGCAGTCGGCGACGGCTGGGCGACCGCCACTTCCGCCTTCTCTTCCTACTGAGCGTCTCCAGgtactccacc ... ctgcttctagGCACGCTTCTGAATTCGGAGTTGCCAGCATTCGCTCGAGGTGCCGGACCAGATCTCACCATCATGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 384

CTGTTCACCCCGCGTCGTCTTCGCTCTCACGATCCCTCGGCAGTCGGCGACGGCTGGGCGACCGCCACTTCCGCCTTCTCTTCCTACTGAGCGTCTCCAGgtactccacc ... ctgcttctagGCACGCTTCTGAATTCGGAGTTGCCAGCATTCGCTCGAGGTGCCGGACCAGATCTCACCATCATGCAG