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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcttttaggtcgagctctcccagatacgcgcgcaggcgcaggggactcattgactgacggacgggtatgcgtgtttcagGCCACCGTGAGCGTTGGTGGGCGCACGCACAGCGCCATGTCCATCGAGCATTTCATCCTGAGGCTGCCCTACAGCGCCAAGCAG

Basic information

species Zea mays
transcript GRMZM2G066516_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G066516_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os09g28850.2 (Oryza sativa), 3'ss of exon 6
------------gtgagcttttaggtcgagctctcccagatacgcgcgcaggcgcaggggactcattga----ctgacggacgggta---tgcgtgtttc-------------agGCCACCGTGAGCGTTGGTGGGCGCACGCACAGCGCCATGTCCATCGAGCATTTCATCCTGAGGCTGCCCTACAGCGCCAAGCAG
            || |  | ||      ||| |        | ||||    |   |  | | | ||  |    ||||||   | ||    | ||||||||             |||| ||  | |  || |||||||||||||||||||||||||| |||||||||||||||||| |||||||||||||||  ||||| 
gtatagcactaagtaacttcttgcaagcagcacaaatcatgatgcgccggtgattaacgaagtaatcaagtctctgacgagagagtgatctccgtgtttcgctctctgttttcagGCGACAATAAATGTGGGTGGGCGCACGCACAGCGCCATGTCGATCGAGCATTTCATCCTGCGGCTGCCCTACAGCGTGAAGCAT
















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|74234141|gb|DT642055.1|DT642055
EST:     AGCATGGGATACCTACCACCCCGCAAATGCTCGTGGCGATGATGCCCAAG                         GCCACCGTGAGCGTTGGTGGGCGCACGCACAGCGCCATGTCCATCGAGCAT
genomic: AGCATGGGATACCTACCACCCCGCAAATGCTCGTGGCGATGATGCCCAAGgtgagctttt ... cgtgtttcagGCCACCGTGAGCGTTGGTGGGCGCACGCACAGCGCCATGTCCATCGAGCAT
EST: gi|149101218|gb|EE187329.2|EE187329
EST:     AGCATGGGATACCTACCACCCCGCAAATGCTCGTGGCGATGATGCCCAAG                         GCCACCGTGAGCGTTGGTGGGCGCACGCACAGCGCCATGTCCATCGAGCAT
genomic: AGCATGGGATACCTACCACCCCGCAAATGCTCGTGGCGATGATGCCCAAGgtgagctttt ... cgtgtttcagGCCACCGTGAGCGTTGGTGGGCGCACGCACAGCGCCATGTCCATCGAGCAT
EST: gi|67015405|gb|CO444154.1|CO444154
EST:     AGCATGGGATACCTACCACCCCGCAAATGCTCGTGGCGATGATGCCCAAG                         GCCACCGTGAGCGTTGGTGGGCGCACGCACAGCGCCATGTCCATCGAGCAT
genomic: AGCATGGGATACCTACCACCCCGCAAATGCTCGTGGCGATGATGCCCAAGgtgagctttt ... cgtgtttcagGCCACCGTGAGCGTTGGTGGGCGCACGCACAGCGCCATGTCCATCGAGCAT
EST: gi|149101219|gb|EE187330.2|EE187330
EST:     AGCATGGGATACCTACCACCCCGCAAATGCTCGTGGCGATGATGCCCAAG                         GCCACCGTGAGCGTTGGTGGGCGCACGCACAGCGCCATGTCCATCGAGCAT
genomic: AGCATGGGATACCTACCACCCCGCAAATGCTCGTGGCGATGATGCCCAAGgtgagctttt ... cgtgtttcagGCCACCGTGAGCGTTGGTGGGCGCACGCACAGCGCCATGTCCATCGAGCAT
EST: gi|94478763|gb|EB707721.1|EB707721
EST:     AGCATGGGATACCTACCACCCCGCAAATGCTCGTGGCGATGATGCCCAAG                         GCCACCGTGAGCGTTGGTGGGCGCACGCACAGCGCCATGTCCATCGAGCAT
genomic: AGCATGGGATACCTACCACCCCGCAAATGCTCGTGGCGATGATGCCCAAGgtgagctttt ... cgtgtttcagGCCACCGTGAGCGTTGGTGGGCGCACGCACAGCGCCATGTCCATCGAGCAT
EST: gi|88749193|gb|DY533334.1|DY533334
EST:     AGCATGGGATACCTACCACCCCGCAAATGCTCGTGGCGATGATGCCCAAG                         GCCACCGTGAGCGTTGGTGGGCGCACGCACAGCGCCATGTCCATCGAGCAT
genomic: AGCATGGGATACCTACCACCCCGCAAATGCTCGTGGCGATGATGCCCAAGgtgagctttt ... cgtgtttcagGCCACCGTGAGCGTTGGTGGGCGCACGCACAGCGCCATGTCCATCGAGCAT
EST: gi|148956148|gb|EC901923.2|EC901923
EST:     AGCATGGGATACCTACCACCCCGCAAATGCTCGTGGCGATGATGCCCAAG                         GCCACCGTGAGCGTTGGTGGGCGCACGCACAGCGCCATGTCCATCGAGCAT
genomic: AGCATGGGATACCTACCACCCCGCAAATGCTCGTGGCGATGATGCCCAAGgtgagctttt ... cgtgtttcagGCCACCGTGAGCGTTGGTGGGCGCACGCACAGCGCCATGTCCATCGAGCAT

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 5 RNA-Seq libraries.


Block sizes: 45 (upstream exon), 26 (downstream exon)
Score: 7

GCGTTCCTGGAGCATGGGATACCTACCACCCCGCAAATGCTCGTGGCGATGATGCCCAAGgtgagctttt ... cgtgtttcagGCCACCGTGAGCGTTGGTGGGCGCACGCACAGCGCCATGTCCATCGAGCATTTCATCCTGAGGCTGCCCTACAGCGCCAAGCAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 13

GCGTTCCTGGAGCATGGGATACCTACCACCCCGCAAATGCTCGTGGCGATGATGCCCAAGgtgagctttt ... cgtgtttcagGCCACCGTGAGCGTTGGTGGGCGCACGCACAGCGCCATGTCCATCGAGCATTTCATCCTGAGGCTGCCCTACAGCGCCAAGCAG


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 6

GCGTTCCTGGAGCATGGGATACCTACCACCCCGCAAATGCTCGTGGCGATGATGCCCAAGgtgagctttt ... cgtgtttcagGCCACCGTGAGCGTTGGTGGGCGCACGCACAGCGCCATGTCCATCGAGCATTTCATCCTGAGGCTGCCCTACAGCGCCAAGCAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 10

GCGTTCCTGGAGCATGGGATACCTACCACCCCGCAAATGCTCGTGGCGATGATGCCCAAGgtgagctttt ... cgtgtttcagGCCACCGTGAGCGTTGGTGGGCGCACGCACAGCGCCATGTCCATCGAGCATTTCATCCTGAGGCTGCCCTACAGCGCCAAGCAG


Block sizes: 44 (upstream exon), 27 (downstream exon)
Score: 12

GCGTTCCTGGAGCATGGGATACCTACCACCCCGCAAATGCTCGTGGCGATGATGCCCAAGgtgagctttt ... cgtgtttcagGCCACCGTGAGCGTTGGTGGGCGCACGCACAGCGCCATGTCCATCGAGCATTTCATCCTGAGGCTGCCCTACAGCGCCAAGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacgcgcgcaggcgcaggggactcattgactgacggacgggtatgcgtgtttcagGCCACCGTGAGCGTTGGTGGGCGCACGCACAGCGCCATGTCCATCGAGCATTTCATCCTGAGGCTGCCCTACAGCGCCAAGCAG
                           gactgac  putative branch site (score: 12)