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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTATTGCATTGATAGTTACAGTCATCCAAATTGTGAGAGTACCTAACCTCAAGgtactcaaaccactcttgacttttttttgtctttcggctttctcttgctatggcctttgttgataatatttagttgaggtacgagttttgtttgtcatgatcag

Basic information

species Zea mays
transcript GRMZM2G165351_T04
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165351_T03 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os06g51430.1 (Oryza sativa), 5'ss of exon 9
GGTATTGCATTGATAGTTACAGTCATCCAAATTGTGAGAGTACCTAACCTCAAGgtactcaaaccactcttgacttt----tttttgtctttcggctttctcttgctatggcctttgttgataatattta---gttgaggtacgagttttgtttgt---------catgatcag
||||||||| ||||| |||| || ||||||||||| ||||||||||||||||||||| || | |  |||||||||||    ||| |   |   || | |      | || ||   | || ||  || ||    || |  || | |||| | |||||         ||||| |||
GGTATTGCACTGATAATTACTGTTATCCAAATTGTTAGAGTACCTAACCTCAAGgtaatctagctgctcttgacttttgactttctacatgatggatgttaagctccattgcaagttttcattttactttagcgtggttgttcaagttatctttgtaactgaggccatgaacag
















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|67025992|gb|CO454741.1|CO454741
EST:     TTGCATTGATAGTTACAGTCATCCAAATTGTGAGAGTACCTAACCTCAAG                         GTGGGTTCGGTTCTTCTTGGCTGTGCCTTCCTGTATGATATCTTCTGGGTG
genomic: TTGCATTGATAGTTACAGTCATCCAAATTGTGAGAGTACCTAACCTCAAGgtactcaaac ... tcatgatcagGTGGGTTCGGTTCTTCTCGGCTGTGCCTTCCTGTATGATATCTTCTGGGTG
EST: gi|32843028|gb|CD982709.1|CD982709
EST:     GTACCTAACCTCAAG                         GTGGGTTCGGTTCTTCTTGGCTGTGCCTTCCTGTATGATATCTTCTGGGTG
genomic: GTACCTAACCTCAAGgtactcaaac ... tcatgatcagGTGGGTTCGGTTCTTCTCGGCTGTGCCTTCCTGTATGATATCTTCTGGGTG
EST: gi|74234147|gb|DT642061.1|DT642061
EST:     AAATTGTGAGAGTACCTAACCTCAAG                         GTGGGTTCGGTTCTTCTCGGCTGTGCCTTCCTGTATGATATCTTCTGGGTG
genomic: AAATTGTGAGAGTACCTAACCTCAAGgtactcaaac ... tcatgatcagGTGGGTTCGGTTCTTCTCGGCTGTGCCTTCCTGTATGATATCTTCTGGGTG
EST: gi|67024697|gb|CO453446.1|CO453446
EST:     TTGCATTGATAGTTACAGTCATCCAAATTGTGAGAGTACCTAACCTCAAG                         GTGGGTTCGGTTCTTCTTGGCTGTGCCTTCCTGTATTATATCTTCTGGGTG
genomic: TTGCATTGATAGTTACAGTCATCCAAATTGTGAGAGTACCTAACCTCAAGgtactcaaac ... tcatgatcagGTGGGTTCGGTTCTTCTCGGCTGTGCCTTCCTGTATGATATCTTCTGGGTG
EST: gi|32848049|gb|CD987730.1|CD987730
EST:     ACCTAACCTCAAG                         GTGGGTTCGGTTCTTCTTGGCTGTGCCTTCCTGCATGATATCTTCTGGGTG
genomic: ACCTAACCTCAAGgtactcaaac ... tcatgatcagGTGGGTTCGGTTCTTCTCGGCTGTGCCTTCCTGTATGATATCTTCTGGGTG
EST: gi|67017568|gb|CO446317.1|CO446317
EST:     TTGCATTGATAGTTACAGTCATCCAAATTGTGAGAGTACCTAACCTCAAG                         GTGGGTTCGGTTCTTCTTGGCTGTGCCTTCCTGTATGA-ATCTTCTGGGTG
genomic: TTGCATTGATAGTTACAGTCATCCAAATTGTGAGAGTACCTAACCTCAAGgtactcaaac ... tcatgatcagGTGGGTTCGGTTCTTCTCGGCTGTGCCTTCCTGTATGATATCTTCTGGGTG

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: 35 (upstream exon), 49 (downstream exon)
Score: 157

GGTATTGCATTGATAGTTACAGTCATCCAAATTGTGAGAGTACCTAACCTCAAGgtactcaaac ... tcatgatcagGTGGGTTCGGTTCTTCTCGGCTGTGCCTTCCTGTATGATATCTTCTGGGTGTTTATCTCCAAGAGATGGTTTCATGAGAGCGTGATGATTGTG


Block sizes: 35 (upstream exon), 49 (downstream exon)
Score: 147

GGTATTGCATTGATAGTTACAGTCATCCAAATTGTGAGAGTACCTAACCTCAAGgtactcaaac ... tcatgatcagGTGGGTTCGGTTCTTCTCGGCTGTGCCTTCCTGTATGATATCTTCTGGGTGTTTATCTCCAAGAGATGGTTTCATGAGAGCGTGATGATTGTG


Block sizes: 35 (upstream exon), 49 (downstream exon)
Score: 163

GGTATTGCATTGATAGTTACAGTCATCCAAATTGTGAGAGTACCTAACCTCAAGgtactcaaac ... tcatgatcagGTGGGTTCGGTTCTTCTCGGCTGTGCCTTCCTGTATGATATCTTCTGGGTGTTTATCTCCAAGAGATGGTTTCATGAGAGCGTGATGATTGTG


Block sizes: 35 (upstream exon), 49 (downstream exon)
Score: 164

GGTATTGCATTGATAGTTACAGTCATCCAAATTGTGAGAGTACCTAACCTCAAGgtactcaaac ... tcatgatcagGTGGGTTCGGTTCTTCTCGGCTGTGCCTTCCTGTATGATATCTTCTGGGTGTTTATCTCCAAGAGATGGTTTCATGAGAGCGTGATGATTGTG