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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGGCCGTCTGCTACTTCTGTGATCTCTCCTCCCCCGTCTTTCGTCTCCGGTTGCATCCCCGACGTCCTCGCCTGCGgtgagcgactcccgctcccgccccccgcccaactgaccgcggatctttcggccggccgaaatccccgtccttcttggacgccgctctctcctctcctgtt...

Basic information

species Zea mays
transcript GRMZM2G104449_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|148983373|gb|EE029360.2|EE029360
EST:     TCCTCCCCCGTCTTTCGTCTCCGGTTGCATCCCCGACGTCCTCGCCTGCG                         GTGGGAGGGCGGGGCGGACGAGCTGGAGGTTCCTGGTAGCGGCTGCCGCCG
genomic: TCCTCCCCCGTCTTTCGTCTCCGGTTGCATCCCCGACGTCCTCGCCTGCGgtgagcgact ... ggcgtgctagGTGGGAGGGCGGGGCGGAGGAGCTGGAGGTTCCTGGTAGCGGCTGCCGCCG
EST: gi|149078013|gb|EE166751.2|EE166751
EST:     GTCTCCGGTTGCATCCCCGACGTCCTCGCCTGCG                         GTGGGAGGGCGGGGCGGAGGAGCTGGAGGTTCCTGGTAGCGGCTGCCGCCG
genomic: GTCTCCGGTTGCATCCCCGACGTCCTCGCCTGCGgtgagcgact ... ggcgtgctagGTGGGAGGGCGGGGCGGAGGAGCTGGAGGTTCCTGGTAGCGGCTGCCGCCG
EST: gi|71429317|gb|DR810367.1|DR810367
EST:     CGTCTCCGGTTGCATCCCCGACGTCCTCGCCTGCG                         GTGGGAGGGCGGGGCGGAGGAGCTGGAGGTTCCTGGTAGCGGCTGCCGCCG
genomic: CGTCTCCGGTTGCATCCCCGACGTCCTCGCCTGCGgtgagcgact ... ggcgtgctagGTGGGAGGGCGGGGCGGAGGAGCTGGAGGTTCCTGGTAGCGGCTGCCGCCG
EST: gi|76014645|gb|DT941815.1|DT941815
EST:     CGTCTCCGGTTGCATCCCCGACGTCCTCGCCTGCG                         GTGGGAGGGCGGGGCGGAGGAGCTGGAGGTTCCTGGTAGCGGCTGCCGCCG
genomic: CGTCTCCGGTTGCATCCCCGACGTCCTCGCCTGCGgtgagcgact ... ggcgtgctagGTGGGAGGGCGGGGCGGAGGAGCTGGAGGTTCCTGGTAGCGGCTGCCGCCG
EST: gi|211453618|gb|FL253931.1|FL253931
EST:     TCCTCCCCCGTCTTTCGTCTCCGGTTGCATCCCCGACGTCCTCGCCTGCG                         GTGGGAGGGCGGGGCGGAGGAGCTGGAGGTTCCTGGTAGCGGCTGCCGCCG
genomic: TCCTCCCCCGTCTTTCGTCTCCGGTTGCATCCCCGACGTCCTCGCCTGCGgtgagcgact ... ggcgtgctagGTGGGAGGGCGGGGCGGAGGAGCTGGAGGTTCCTGGTAGCGGCTGCCGCCG
EST: gi|149084046|gb|EE173442.2|EE173442
EST:     TCCTCCCCCGTCTTTCGTCTCCGGTTGCATCCCCGACGTCCTCGCCTGCG                         GTGGGAGGGCGGGGCGGAGGAGCTGGAGGTTCCTGGTAGCGGCTGCCGCCG
genomic: TCCTCCCCCGTCTTTCGTCTCCGGTTGCATCCCCGACGTCCTCGCCTGCGgtgagcgact ... ggcgtgctagGTGGGAGGGCGGGGCGGAGGAGCTGGAGGTTCCTGGTAGCGGCTGCCGCCG
EST: gi|93284538|gb|EB676802.1|EB676802
EST:     TCCTCCCCCGTCTTTCGTCTCCGGTTGCATCCCCGACGTCCTCGCCTGCG                         GTGGGAGGGCGGGGCGGAGGAGCTGGAGGTTCCTGGTAGCGGCTGCCGCCG
genomic: TCCTCCCCCGTCTTTCGTCTCCGGTTGCATCCCCGACGTCCTCGCCTGCGgtgagcgact ... ggcgtgctagGTGGGAGGGCGGGGCGGAGGAGCTGGAGGTTCCTGGTAGCGGCTGCCGCCG

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: 26

GCGGCCGTCTGCTACTTCTGTGATCTCTCCTCCCCCGTCTTTCGTCTCCGGTTGCATCCCCGACGTCCTCGCCTGCGgtgagcgact ... ggcgtgctagGTGGGAGGGCGGGGCGGAGGAGCTGGAGGTTCCTGGTAGCGGCTGCCGCCGGCCATGGAGAAGAGGAAGCGGATCCTGGAGCTGCGGGATCGGCTGGACC


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 36

GCGGCCGTCTGCTACTTCTGTGATCTCTCCTCCCCCGTCTTTCGTCTCCGGTTGCATCCCCGACGTCCTCGCCTGCGgtgagcgact ... ggcgtgctagGTGGGAGGGCGGGGCGGAGGAGCTGGAGGTTCCTGGTAGCGGCTGCCGCCGGCCATGGAGAAGAGGAAGCGGATCCTGGAGCTGCGGGATCGGCTGGACC


Block sizes: 49 (upstream exon), 38 (downstream exon)
Score: 19

GCGGCCGTCTGCTACTTCTGTGATCTCTCCTCCCCCGTCTTTCGTCTCCGGTTGCATCCCCGACGTCCTCGCCTGCGgtgagcgact ... ggcgtgctagGTGGGAGGGCGGGGCGGAGGAGCTGGAGGTTCCTGGTAGCGGCTGCCGCCGGCCATGGAGAAGAGGAAGCGGATCCTGGAGCTGCGGGATCGGCTGGACC


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 15

GCGGCCGTCTGCTACTTCTGTGATCTCTCCTCCCCCGTCTTTCGTCTCCGGTTGCATCCCCGACGTCCTCGCCTGCGgtgagcgact ... ggcgtgctagGTGGGAGGGCGGGGCGGAGGAGCTGGAGGTTCCTGGTAGCGGCTGCCGCCGGCCATGGAGAAGAGGAAGCGGATCCTGGAGCTGCGGGATCGGCTGGACC