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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAGACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAAgtaatacaccttgaaccgatgccttctctggcggttttattcggatctgtttcagccgggggtttcactcgtttggattcctgcag

Basic information

species Zea mays
transcript GRMZM2G147882_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147882_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g09300.2 (Oryza sativa), 5'ss of exon 6
TAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAGACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAAgtaa-tacaccttgaaccgatgccttctctggcggtt---ttattcggatctgtttcagccggg-ggtttcactcgtttggattcctgcag
||| || ||| |||||||| |||| ||||  ||||| || |||||||| || || ||||| || ||||| ||||||||||||||||||||||| |||||||||| | || |||||| |||  |||| ||    | ||   | |||    |   ||  |       |||     ||  |  || |  |||||
TAAAGTATCAAATCCTGCAGAGGGAGTTTTTGGAGCAGGTGCCCATTCTGATTATGGCCTAATCACTCTACTGGCAACCGATGATGTAGTTGGTCTCCAAgtaaatgcatcttgaatcgacaccttatcaaatgtttcattgattttcgtgacttctaataaaatggtagttttccatctgaattatgcag
















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|32924156|gb|CF028968.1|CF028968
EST:     ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAA                         ATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
genomic: ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAAgtaatacacc ... attcctgcagATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
EST: gi|32858736|gb|CD998417.1|CD998417
EST:     ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAA                         ATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
genomic: ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAAgtaatacacc ... attcctgcagATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
EST: gi|78117759|gb|DV536146.1|DV536146
EST:     CTACGGCCTGATAACTCTCCTNGGCA-CCGATGATGTAGTTGGGCTCCAA                         ATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
genomic: CTACGGCCTGATAACTCTCCT-GGCAACCGATGATGTAGTTGGGCTCCAAgtaatacacc ... attcctgcagATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
EST: gi|93014970|gb|EB640490.1|EB640490
EST:     CTACGGCCTGATAACTCTCCTGGGCA-CCGATGATGTAGTTGGGCTCCAA                         ATATGCAAGGAC
genomic: CTACGGCCTGATAACTCTCCTGG-CAACCGATGATGTAGTTGGGCTCCAAgtaatacacc ... attcctgcagATATGCAAGGAC
EST: gi|32924110|gb|CF028922.1|CF028922
EST:     ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAA                         ATATGCAAGGACAAGAACGCTCAGCCTCAGCTGTGGGAATACGTAGCTCCG
genomic: ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAAgtaatacacc ... attcctgcagATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG

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: 36 (upstream exon), 46 (downstream exon)
Score: 20

TAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAGACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAAgtaatacacc ... attcctgcagATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGG


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

TAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAGACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAAgtaatacacc ... attcctgcagATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 495

TAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAGACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAAgtaatacacc ... attcctgcagATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGG


Block sizes: 37 (upstream exon), 44 (downstream exon)
Score: 13

TAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAGACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAAgtaatacacc ... attcctgcagATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGG