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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCATTTGTGATTGCATTTTCTCTTGGCTTGGGAGCGATTCCGTGGATCATTATGTCTGAGgtatagtttgttcttgctttttatattatacagagcttttaattcgctaatgtgtctttgctatcttatctttatgtaattattatgagtgccacttagc...

Basic information

species Zea mays
transcript GRMZM2G097768_T01
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G097768_T01 (Zea mays), 5'ss of exon 16
lower sequence: LOC_Os05g50280.1 (Oryza sativa), 5'ss of exon 15
GCATTTGTGATTGCATTTTCTCTTGGCTTGGGAGCGATTCCGTGGATCATTATGTCTGAGgtatagtttg-ttcttgctttttatattatacagagcttttaattcg---ctaatgtgtctttgctatcttatct--ttatgtaattattatgagtgccactta-gc------
|||||||||||| ||||||||||||| |||||||| || || |||||||| ||||||||||||| || |  | ||| ||  | ||||||        | ||| |      |||  |    |||  | |   || |   |  |  |||  | |   ||||    | ||      
GCATTTGTGATTTCATTTTCTCTTGGTTTGGGAGCCATACCATGGATCATAATGTCTGAGgtattgtataatccttcctgctaatattagctgagattattactgaaggcctagagcaaatttattgttgaatttgactgggagattgatgtatttgccttgcatgccttcag
















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|71772624|gb|DR970552.1|DR970552
EST:     TTGCATTTTCTCTTGGCTTGGGAGCGATTCCGTGGATCATTATGTCTGAG                         ATCCTTCCTGTTAACATCAAGAGCCTTGCTGGAAGTGTTGCGACCCTGGCG
genomic: TTGCATTTTCTCTTGGCTTGGGAGCGATTCCGTGGATCATTATGTCTGAGgtatagtttg ... ttcctttcagATCCTTCCTGTTAACATCAAGAGCCTTGCTGGAAGTGTTGCGACCCTGGCG
EST: gi|71772625|gb|DR970553.1|DR970553
EST:     TTGCATTTTCTCTTGGCTTGGGAGCGATTCCGTGGATCATTATGTCTGAG                         ATCCTTCCTTGT-AACATCAAAAGCCTTGCTGGA
genomic: TTGCATTTTCTCTTGGCTTGGGAGCGATTCCGTGGATCATTATGTCTGAGgtatagtttg ... ttcctttcagATCCTTCCT-GTTAACATCAAGAGCCTTGCTGGA
EST: gi|193503179|gb|AM937591.1|AM937591
EST:     TTGCATTTTCTCTTGGCTTGGGAGCGATTCCGTGGATCATTATGTCTGAG                         ATCCTTCCTGTTAACATCAAGAGCCTTGCTGGAAGTGTTGCGACCCTGGCG
genomic: TTGCATTTTCTCTTGGCTTGGGAGCGATTCCGTGGATCATTATGTCTGAGgtatagtttg ... ttcctttcagATCCTTCCTGTTAACATCAAGAGCCTTGCTGGAAGTGTTGCGACCCTGGCG

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), 47 (downstream exon)
Score: 124

GCATTTGTGATTGCATTTTCTCTTGGCTTGGGAGCGATTCCGTGGATCATTATGTCTGAGgtatagtttg ... ttcctttcagATCCTTCCTGTTAACATCAAGAGCCTTGCTGGAAGTGTTGCGACCCTGGCGAACTGGCTGACAGCATGGGCCATTACAATGACGGCAAGCCTGATGTTGA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 219

GCATTTGTGATTGCATTTTCTCTTGGCTTGGGAGCGATTCCGTGGATCATTATGTCTGAGgtatagtttg ... ttcctttcagATCCTTCCTGTTAACATCAAGAGCCTTGCTGGAAGTGTTGCGACCCTGGCGAACTGGCTGACAGCATGGGCCATTACAATGACGGCAAGCCTGATGTTGA


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 152

GCATTTGTGATTGCATTTTCTCTTGGCTTGGGAGCGATTCCGTGGATCATTATGTCTGAGgtatagtttg ... ttcctttcagATCCTTCCTGTTAACATCAAGAGCCTTGCTGGAAGTGTTGCGACCCTGGCGAACTGGCTGACAGCATGGGCCATTACAATGACGGCAAGCCTGATGTTGA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 215

GCATTTGTGATTGCATTTTCTCTTGGCTTGGGAGCGATTCCGTGGATCATTATGTCTGAGgtatagtttg ... ttcctttcagATCCTTCCTGTTAACATCAAGAGCCTTGCTGGAAGTGTTGCGACCCTGGCGAACTGGCTGACAGCATGGGCCATTACAATGACGGCAAGCCTGATGTTGA