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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACTGTGTGCGCGGTCGGTCGCTTCCCTTCCCTTTTGTCCGCGATCTGGGCTGGCCCTCGTGGCCTCGTCCCGTCTCCGATTCCGGCGTCCGAACCAGgtgagcgacctctccagtctcccaccccccgtctcaactacttcttcgcacgcgccgaattgtagaggcctagaggggcggaatctgacgcgagtttcattggattcggtgcag

Basic information

species Zea mays
transcript GRMZM2G451882_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|211076796|gb|FL055833.1|FL055833
EST:     GACTGGCCCTCGTGGCCTCGTCCCGTCTCCGATTCCGGCGTCCGAACCAG                         ATTCGCCCGGGCCTTCGTGCCAGCGATGAAGGAGAAGCGTGGGCTCGAGGA
genomic: GGCTGGCCCTCGTGGCCTCGTCCCGTCTCCGATTCCGGCGTCCGAACCAGgtgagcgacc ... ttcggtgcagATTCGCCCGGGCCTTCGTGCCAGCGATGAAGGAGAAGCGTGGGCTCGAGGA
EST: gi|148941980|gb|EC886967.2|EC886967
EST:     GGCTGGCCCTCGTGGCCTCGTCCCGTCTCCGATTCCGGCGTCCGAACCAG                         ATTCGCCCGGGCCTTCGTGCCAGCGATGAAGGAGAAGCGTGGGCTCGAGGA
genomic: GGCTGGCCCTCGTGGCCTCGTCCCGTCTCCGATTCCGGCGTCCGAACCAGgtgagcgacc ... ttcggtgcagATTCGCCCGGGCCTTCGTGCCAGCGATGAAGGAGAAGCGTGGGCTCGAGGA
EST: gi|211079522|gb|FL055834.1|FL055834
EST:     GACTGGCCCTCGTGGCCTCGTCCCGTCTCCGATTCCGGCGTCCGAACCAG                         ATTCGCCCGGGCCTTCGTGCCAGCGATGAAGGAGAAGCGTGGGCTCGAGGA
genomic: GGCTGGCCCTCGTGGCCTCGTCCCGTCTCCGATTCCGGCGTCCGAACCAGgtgagcgacc ... ttcggtgcagATTCGCCCGGGCCTTCGTGCCAGCGATGAAGGAGAAGCGTGGGCTCGAGGA
EST: gi|149013593|gb|EE043063.2|EE043063
EST:     GGCTGGCCCTCGTGGCCTCGTCCCGTCTCCGATTCCGGCGTCCGAACCAG                         ATTCGCCCGGGCCTTCGTGCCAGCGATGAAGGAGAAGCGTGGGCTCGAGGA
genomic: GGCTGGCCCTCGTGGCCTCGTCCCGTCTCCGATTCCGGCGTCCGAACCAGgtgagcgacc ... ttcggtgcagATTCGCCCGGGCCTTCGTGCCAGCGATGAAGGAGAAGCGTGGGCTCGAGGA
EST: gi|211355831|gb|FL403692.1|FL403692
EST:     GGCTGGCCCTCGTGGCCTCGTCCCGTCTCCGATTCCGGCGTCCGAACCAG                         ATTCGCCCGGGCCTTCGTGCCAGCGATGAAGGAGAAGCGTGGGCTCGAGGA
genomic: GGCTGGCCCTCGTGGCCTCGTCCCGTCTCCGATTCCGGCGTCCGAACCAGgtgagcgacc ... ttcggtgcagATTCGCCCGGGCCTTCGTGCCAGCGATGAAGGAGAAGCGTGGGCTCGAGGA
EST: gi|211076795|gb|FL055832.1|FL055832
EST:     GACTGGCCCTCGTGGCCTCGTCCCGTCTCCGATTCCGGCGTCCGAACCAG                         ATTCGCCCGGGCCTTCGTGCCAGCGATGAAGGAGAAGCGTGGGCTCGAGGA
genomic: GGCTGGCCCTCGTGGCCTCGTCCCGTCTCCGATTCCGGCGTCCGAACCAGgtgagcgacc ... ttcggtgcagATTCGCCCGGGCCTTCGTGCCAGCGATGAAGGAGAAGCGTGGGCTCGAGGA
EST: gi|71771244|gb|DR969181.1|DR969181
EST:     GGCTGGCCCTCGTGGCCTCGTCCCGTCTCCGATTCCGGCGTCCGAACCAG                         ATTCGCCCGGGCCTTCGTGCCAGCGATGAAGGAGAAGCGTGGGCTCGAGGA
genomic: GGCTGGCCCTCGTGGCCTCGTCCCGTCTCCGATTCCGGCGTCCGAACCAGgtgagcgacc ... ttcggtgcagATTCGCCCGGGCCTTCGTGCCAGCGATGAAGGAGAAGCGTGGGCTCGAGGA

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: 41 (upstream exon), 49 (downstream exon)
Score: 95

AACTGTGTGCGCGGTCGGTCGCTTCCCTTCCCTTTTGTCCGCGATCTGGGCTGGCCCTCGTGGCCTCGTCCCGTCTCCGATTCCGGCGTCCGAACCAGgtgagcgacc ... ttcggtgcagATTCGCCCGGGCCTTCGTGCCAGCGATGAAGGAGAAGCGTGGGCTCGAGGACGCCGGCGGGGGCGCCGGCGACGGACGTCCTGATGCCAAGAGGTCGCGG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 83

AACTGTGTGCGCGGTCGGTCGCTTCCCTTCCCTTTTGTCCGCGATCTGGGCTGGCCCTCGTGGCCTCGTCCCGTCTCCGATTCCGGCGTCCGAACCAGgtgagcgacc ... ttcggtgcagATTCGCCCGGGCCTTCGTGCCAGCGATGAAGGAGAAGCGTGGGCTCGAGGACGCCGGCGGGGGCGCCGGCGACGGACGTCCTGATGCCAAGAGGTCGCGG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 94

AACTGTGTGCGCGGTCGGTCGCTTCCCTTCCCTTTTGTCCGCGATCTGGGCTGGCCCTCGTGGCCTCGTCCCGTCTCCGATTCCGGCGTCCGAACCAGgtgagcgacc ... ttcggtgcagATTCGCCCGGGCCTTCGTGCCAGCGATGAAGGAGAAGCGTGGGCTCGAGGACGCCGGCGGGGGCGCCGGCGACGGACGTCCTGATGCCAAGAGGTCGCGG


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 60

AACTGTGTGCGCGGTCGGTCGCTTCCCTTCCCTTTTGTCCGCGATCTGGGCTGGCCCTCGTGGCCTCGTCCCGTCTCCGATTCCGGCGTCCGAACCAGgtgagcgacc ... ttcggtgcagATTCGCCCGGGCCTTCGTGCCAGCGATGAAGGAGAAGCGTGGGCTCGAGGACGCCGGCGGGGGCGCCGGCGACGGACGTCCTGATGCCAAGAGGTCGCGG