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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGTCTGGCAACCCAACCGGCCAAGGGCCAACCCCGTCCCCGGACCCCGACTCCCCGAGGGCCAACCGGCCAAGGCACAACCGCTGAACCGCACAATGCAgtgagagaccgagggtgattattttttatttgaatagaaataaaataacgtgtctaatccaatatattttcactgtgatactag

Basic information

species Zea mays
transcript GRMZM2G144716_T02
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|71429836|gb|DR810886.1|DR810886
EST:     CTCCCCGAGGGCCAACCGGCCAAGGCACGACCGCTGAACCGCACAATGCA                         TATTTAGTCGCCTACTCGCCTAGGCCTATTATTTCCCTCTCAGACTCAAAT
genomic: CTCCCCGAGGGCCAACCGGCCAAGGCACAACCGCTGAACCGCACAATGCAgtgagagacc ... gtgatactagTATTTAGTCGCCTACTCGCCTAGGCCTATTATTTCCCTCTCAAACTCAAAT
EST: gi|93283064|gb|EB675328.1|EB675328
EST:     CTCCCCGAGGGCCAACCGGCCAAGGCACAACCGCTGAACCGCACAATGCA                         TATTTAGTCGCCTACTCGCCTAGGCCTATTATTTCCCTCTCAAACTCAAAT
genomic: CTCCCCGAGGGCCAACCGGCCAAGGCACAACCGCTGAACCGCACAATGCAgtgagagacc ... gtgatactagTATTTAGTCGCCTACTCGCCTAGGCCTATTATTTCCCTCTCAAACTCAAAT
EST: gi|78085402|gb|DV513795.1|DV513795
EST:     TCCCCGAGGGCCACCCGGCCCAAGGCACAACCGCTGAACCGCACAATGCA                         TATTTAGTCGCCTACTCGCCTAGGCCTATTAT
genomic: TCCCCGAGGGCCAACCGGCC-AAGGCACAACCGCTGAACCGCACAATGCAgtgagagacc ... gtgatactagTATTTAGTCGCCTACTCGCCTAGGCCTATTAT
EST: gi|32798293|gb|CD950529.1|CD950529
EST:     CTCCCCGAGGGCCAACTGGCCAAGGCACAACCGCTGAACCGCACAATGCA                         TATTTAGTCGCCTACTCGCCTAGGCCTATTCTTTCCCTCTCAAACTCAAAT
genomic: CTCCCCGAGGGCCAACCGGCCAAGGCACAACCGCTGAACCGCACAATGCAgtgagagacc ... gtgatactagTATTTAGTCGCCTACTCGCCTAGGCCTATTATTTCCCTCTCAAACTCAAAT
EST: gi|211197040|gb|FL177610.1|FL177610
EST:     CTCCCCGAGGGCCAACCGGCCAAGGCACAACCGCTGAACCGCACAATGCA                         TATTTAGTCGCCTACTCGCCTAGGCCTATTATTTCCCTCTCAAACTCAAAT
genomic: CTCCCCGAGGGCCAACCGGCCAAGGCACAACCGCTGAACCGCACAATGCAgtgagagacc ... gtgatactagTATTTAGTCGCCTACTCGCCTAGGCCTATTATTTCCCTCTCAAACTCAAAT
EST: gi|211180004|gb|FL285245.1|FL285245
EST:     CTCCCCAAGGGCCAACCGGCCAAGGCACAACCGCTGAACCGCACAATGCA                         TATTTAGTCGCCTACTCGCCTAGGCCTATTCTTTCCCTCTCAAACTCAAAT
genomic: CTCCCCGAGGGCCAACCGGCCAAGGCACAACCGCTGAACCGCACAATGCAgtgagagacc ... gtgatactagTATTTAGTCGCCTACTCGCCTAGGCCTATTATTTCCCTCTCAAACTCAAAT

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: 46 (upstream exon), 39 (downstream exon)
Score: 42

CCGTCTGGCAACCCAACCGGCCAAGGGCCAACCCCGTCCCCGGACCCCGACTCCCCGAGGGCCAACCGGCCAAGGCACAACCGCTGAACCGCACAATGCAgtgagagacc ... gtgatactagTATTTAGTCGCCTACTCGCCTAGGCCTATTATTTCCCTCTCAAACTCAAATTCTTCCTGGAATCCACCAAAGCCCTGCCTCCCCTCTACTGATTCTGAAA


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 29

CCGTCTGGCAACCCAACCGGCCAAGGGCCAACCCCGTCCCCGGACCCCGACTCCCCGAGGGCCAACCGGCCAAGGCACAACCGCTGAACCGCACAATGCAgtgagagacc ... gtgatactagTATTTAGTCGCCTACTCGCCTAGGCCTATTATTTCCCTCTCAAACTCAAATTCTTCCTGGAATCCACCAAAGCCCTGCCTCCCCTCTACTGATTCTGAAA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 25

CCGTCTGGCAACCCAACCGGCCAAGGGCCAACCCCGTCCCCGGACCCCGACTCCCCGAGGGCCAACCGGCCAAGGCACAACCGCTGAACCGCACAATGCAgtgagagacc ... gtgatactagTATTTAGTCGCCTACTCGCCTAGGCCTATTATTTCCCTCTCAAACTCAAATTCTTCCTGGAATCCACCAAAGCCCTGCCTCCCCTCTACTGATTCTGAAA


Block sizes: 46 (upstream exon), 40 (downstream exon)
Score: 37

CCGTCTGGCAACCCAACCGGCCAAGGGCCAACCCCGTCCCCGGACCCCGACTCCCCGAGGGCCAACCGGCCAAGGCACAACCGCTGAACCGCACAATGCAgtgagagacc ... gtgatactagTATTTAGTCGCCTACTCGCCTAGGCCTATTATTTCCCTCTCAAACTCAAATTCTTCCTGGAATCCACCAAAGCCCTGCCTCCCCTCTACTGATTCTGAAA