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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgctggtgtttgttcgtcttctagtagcagtattgctgtacgatacgaagtgtaagccggttctggacatgatctgcgacagGTGCGTCCAAATGCTGTTGCGCTGGTTGATGCCTTCAACTACACAGACCACTACCTGGGGTCTGTGCTGGGGCGGTACGATGGGAATGTGTACCCAGCGC

Basic information

species Zea mays
transcript GRMZM5G864319_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G864319_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os06g01390.1 (Oryza sativa), 3'ss of exon 13
gtacgctggtgtttgttcgtcttctagtagcagtattgctgtacgatacgaagtgtaagccggttctggacatgatctgcgacagGTGCGTCCAAATGCTGTTGCGCTGGTTGATGCCTTCAACTACACAGACCACTACCTGGGGTCTGTGCTGGGGCGGTACGATGGGAATGTGTACCCAGCGC
        || |    || ||      |  || | |        |||  |||    |     |     ||||    |     |||||||| || || || || |||||||| || || ||||||||||| ||||||||||||||||| ||||||||||| ||||| || ||||| ||||| ||||
--------gtatggtgtcctccgtcgatgtcaatgtcaaaagtggatgagaaactgagaaatg----agacaaatgcaaatgcagGTGCGGCCGAACGCGGTGGCGCTGGTGGACGCGTTCAACTACACCGACCACTACCTGGGGTCGGTGCTGGGGCGCTACGACGGCAATGTTTACCCGGCGC
















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|78092060|gb|DV520434.1|DV520434
EST:     CCAAGCAGGGAGCGCTGGCAAACGAGCAGCTGGGCAAGCTTTACGCACAG                         GTGCGTCCAAATGCTGTTGCGCTGGTTGATGCCTTCAACTACACAGACCAC
genomic: CCAAGCAGGGAGCGCTGGCAAACGAGCAGCTGGGCAAGCTTTACGCACAGgtacgctggt ... tctgcgacagGTGCGTCCAAATGCTGTTGCGCTGGTTGATGCCTTCAACTACACAGACCAC
EST: gi|78089951|gb|DV518325.1|DV518325
EST:     CCAAGCAGGGAGCGCTGGCAAACGAGCAGCTGGGCAAGCTTTACGCACAG                         GTGCGTCCAAATGCTGTTGCGCTGGTTGATGCCTTCAACTACACAGACCAC
genomic: CCAAGCAGGGAGCGCTGGCAAACGAGCAGCTGGGCAAGCTTTACGCACAGgtacgctggt ... tctgcgacagGTGCGTCCAAATGCTGTTGCGCTGGTTGATGCCTTCAACTACACAGACCAC
EST: gi|71759064|gb|DR957001.1|DR957001
EST:     CCAAGCAGGGAGCGCTGGCAAACGAGCAGCTGGGCAAGCTTTACGCACAG                         GTGCGTCCAAATGCTGTTGCGCTGGTTGATGCCTTCAACTACACAGACCAC
genomic: CCAAGCAGGGAGCGCTGGCAAACGAGCAGCTGGGCAAGCTTTACGCACAGgtacgctggt ... tctgcgacagGTGCGTCCAAATGCTGTTGCGCTGGTTGATGCCTTCAACTACACAGACCAC
EST: gi|32835294|gb|CD974972.1|CD974972
EST:     CCAAGCAGGGAGCGCTGGCAAACGAGCAGCTGGACAAGCTTTACGCACAG                         GTGCGTCCAAATGCTGTTGCGCTGGTTGATGCCTTCAACTACACAGACCAC
genomic: CCAAGCAGGGAGCGCTGGCAAACGAGCAGCTGGGCAAGCTTTACGCACAGgtacgctggt ... tctgcgacagGTGCGTCCAAATGCTGTTGCGCTGGTTGATGCCTTCAACTACACAGACCAC
EST: gi|149044449|gb|EE047570.2|EE047570
EST:     CCAAGCAGGGAGCGCTGGCAAACGAGCAGCTGGGCAAGCTTTACGCACAG                         GTGCGTCCAAATGCTGTTGCGCTGGTTGATGCCTTCAACTACACAGACCAC
genomic: CCAAGCAGGGAGCGCTGGCAAACGAGCAGCTGGGCAAGCTTTACGCACAGgtacgctggt ... tctgcgacagGTGCGTCCAAATGCTGTTGCGCTGGTTGATGCCTTCAACTACACAGACCAC
EST: gi|32834719|gb|CD974397.1|CD974397
EST:     CCAAGCAGGGAGCGCTGGCAAACGAGCAGCTGGGCAAGCTTTACGCACAG                         GTGCGTCCAAATGCTGTTGCGCTGGTTGATGCCTTCAACTACACAGACCAC
genomic: CCAAGCAGGGAGCGCTGGCAAACGAGCAGCTGGGCAAGCTTTACGCACAGgtacgctggt ... tctgcgacagGTGCGTCCAAATGCTGTTGCGCTGGTTGATGCCTTCAACTACACAGACCAC
EST: gi|84908462|gb|DW404340.1|DW404340
EST:     CCAAGCAGGGAGCGCTGGCAAACGAGCAGCTGGGCAAGCTTTACGCACAG                         GTGCGTCCAAATGCTGTTGCGCTGGTTGATGCCTTCAACTACACAGACCAC
genomic: CCAAGCAGGGAGCGCTGGCAAACGAGCAGCTGGGCAAGCTTTACGCACAGgtacgctggt ... tctgcgacagGTGCGTCCAAATGCTGTTGCGCTGGTTGATGCCTTCAACTACACAGACCAC
EST: gi|113703173|gb|EE680677.1|EE680677
EST:     CCAAGCAGGGAGCGCTGGCAAACGAGCAGCTGGGCAAGCTTTACGCACAG                         GTGCGTCCAAATGCTGTTGCGCTGGTTGATGCCTTCAACTACACAGACCAC
genomic: CCAAGCAGGGAGCGCTGGCAAACGAGCAGCTGGGCAAGCTTTACGCACAGgtacgctggt ... tctgcgacagGTGCGTCCAAATGCTGTTGCGCTGGTTGATGCCTTCAACTACACAGACCAC
EST: gi|60395837|gb|DN228707.1|DN228707
EST:     CCAAGCAGGGAGCGCTGGCAAACGAGCAGCTGGGCAAGCTTTACGCACAG                         GTGCGTCCAAATGCTGTTGCGCTGGTTGATGCCTTCAACTACACAGACCAC
genomic: CCAAGCAGGGAGCGCTGGCAAACGAGCAGCTGGGCAAGCTTTACGCACAGgtacgctggt ... tctgcgacagGTGCGTCCAAATGCTGTTGCGCTGGTTGATGCCTTCAACTACACAGACCAC
EST: gi|31558693|gb|CD527905.1|CD527905
EST:     CCAAGCAGGGAGCGCTGGCAAACGAGCAGCTGGGCAAGCTTTACGCACAG                         GTGCGTCCAAATGCTGTTGCGCTGGTTGATGCCTTCAACTACACAGACCAC
genomic: CCAAGCAGGGAGCGCTGGCAAACGAGCAGCTGGGCAAGCTTTACGCACAGgtacgctggt ... tctgcgacagGTGCGTCCAAATGCTGTTGCGCTGGTTGATGCCTTCAACTACACAGACCAC
EST: gi|60356985|gb|DN223958.1|DN223958
EST:     CCAAGCAGGGAGCGCTGGCAAACGAGCAGCTGGGCAAGCTTTACGCACAG                         GTGCGTCCAAATGCTGTTGCGCTGGTTGATGCCTTCAACTACACAGACCAC
genomic: CCAAGCAGGGAGCGCTGGCAAACGAGCAGCTGGGCAAGCTTTACGCACAGgtacgctggt ... tctgcgacagGTGCGTCCAAATGCTGTTGCGCTGGTTGATGCCTTCAACTACACAGACCAC
EST: gi|31405924|gb|CD484656.1|CD484656
EST:     CCAAGCAGGGAGCGCTGGCAAACGAGCAGCTGGGCAAGCTTTACGCACAG                         GTGCGTCCAAATGCTGTTGCGCTGGTTGATGCCTTCAACTACACAGACCAC
genomic: CCAAGCAGGGAGCGCTGGCAAACGAGCAGCTGGGCAAGCTTTACGCACAGgtacgctggt ... tctgcgacagGTGCGTCCAAATGCTGTTGCGCTGGTTGATGCCTTCAACTACACAGACCAC
EST: gi|44901346|gb|CK827891.1|CK827891
EST:     CCAAGCAGGGAGCGCTGGCAAACGAGCAGCTGGGCAAGCTTTACGCACAG                         GTGCGTCCAAATGCTGTTGCGCTGGTTGATGCCTTCAACTACACAGACCAC
genomic: CCAAGCAGGGAGCGCTGGCAAACGAGCAGCTGGGCAAGCTTTACGCACAGgtacgctggt ... tctgcgacagGTGCGTCCAAATGCTGTTGCGCTGGTTGATGCCTTCAACTACACAGACCAC
EST: gi|71315287|gb|DR794255.1|DR794255
EST:     CCAAGCAGGGAGCGCTGGCAAACGAGCAGCTGGGCAAGCTTTACGCACAG                         GTGCGTCCAAATGCTGTTGCGCTGGTTGATGCCTTCAACTACACAGACCAC
genomic: CCAAGCAGGGAGCGCTGGCAAACGAGCAGCTGGGCAAGCTTTACGCACAGgtacgctggt ... tctgcgacagGTGCGTCCAAATGCTGTTGCGCTGGTTGATGCCTTCAACTACACAGACCAC
EST: gi|95107827|gb|EB740056.1|EB740056
EST:     GGCAAGCTTTACGCACAG                         GTGCGTCCAAATGCTGTTGCGCTGGTTGATGCCTTCAACTACACAGACCAC
genomic: GGCAAGCTTTACGCACAGgtacgctggt ... tctgcgacagGTGCGTCCAAATGCTGTTGCGCTGGTTGATGCCTTCAACTACACAGACCAC
EST: gi|9732140|gb|BE510892.1|BE510892
EST:     CCAAGCAGGGAGCGCTGGCAAACGAGCAGCTGGGCAAGCTTTACGCACAG                         GTGCGTCCAAATG
genomic: CCAAGCAGGGAGCGCTGGCAAACGAGCAGCTGGGCAAGCTTTACGCACAGgtacgctggt ... tctgcgacagGTGCGTCCAAATG
EST: gi|78109869|gb|DV528285.1|DV528285
EST:     CCAAGCAGGGAGCGCTGGCAAACGAGCAGCTGGGCAAGCTTTACGCACAG                         GTGCGTCCAAATGCTGTTGCGCTGGTTGATGCCTTCAACTACACAGACCAC
genomic: CCAAGCAGGGAGCGCTGGCAAACGAGCAGCTGGGCAAGCTTTACGCACAGgtacgctggt ... tctgcgacagGTGCGTCCAAATGCTGTTGCGCTGGTTGATGCCTTCAACTACACAGACCAC
EST: gi|47962349|gb|CN845058.1|CN845058
EST:     CCAAGCAGGGAGCGCTGGCAAACGAGCAGCTGGGCAAGCTTTACGCACAG                         GTGCGTCCAAATGCTGTTGCGCTGGTTGATGCCTTCAACTACACAGACCAC
genomic: CCAAGCAGGGAGCGCTGGCAAACGAGCAGCTGGGCAAGCTTTACGCACAGgtacgctggt ... tctgcgacagGTGCGTCCAAATGCTGTTGCGCTGGTTGATGCCTTCAACTACACAGACCAC
EST: gi|37385402|gb|CF629841.1|CF629841
EST:     CCAAGCAGGGAGCGCTGGCAAACGAGCAGCTGGGCAAGCTTTACGCACAG                         GTGCGTCCAAATGCTGTTGCGCTGGTTGATGCCTTCAACTACACAGACCAC
genomic: CCAAGCAGGGAGCGCTGGCAAACGAGCAGCTGGGCAAGCTTTACGCACAGgtacgctggt ... tctgcgacagGTGCGTCCAAATGCTGTTGCGCTGGTTGATGCCTTCAACTACACAGACCAC
EST: gi|51592617|gb|CV071763.1|CV071763
EST:     CCAAGCAGGGAGCGCTGGCAAACGAGCAGCTGGGCAAGCTTTACGCACAG                         GTGCGTCCAAATGCTGTTGCGCTGGTTGATGCCTTCAACTACACAGACCAC
genomic: CCAAGCAGGGAGCGCTGGCAAACGAGCAGCTGGGCAAGCTTTACGCACAGgtacgctggt ... tctgcgacagGTGCGTCCAAATGCTGTTGCGCTGGTTGATGCCTTCAACTACACAGACCAC
EST: gi|14204220|gb|BG837897.1|BG837897
EST:     CCAAGCAGGGAGCGCTGGCAAACGAGCAGCTGGGCAAGCTTTACGCACAG                         GTGCGTCCAAATGCTGTTGCGCTGGTTGATGCCTTCAACTACACAGACCAC
genomic: CCAAGCAGGGAGCGCTGGCAAACGAGCAGCTGGGCAAGCTTTACGCACAGgtacgctggt ... tctgcgacagGTGCGTCCAAATGCTGTTGCGCTGGTTGATGCCTTCAACTACACAGACCAC

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), 48 (downstream exon)
Score: 74

CATTCTCCACAAGCACCTGGGCGACTTCCTGGCAACCGGGTGCATCACACCCAAGCAGGGAGCGCTGGCAAACGAGCAGCTGGGCAAGCTTTACGCACAGgtacgctggt ... tctgcgacagGTGCGTCCAAATGCTGTTGCGCTGGTTGATGCCTTCAACTACACAGACCACTACCTGGGGTCTGTGCTGGGGCGGTACGATGGGAATGTGTACCCAGCGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 224

CATTCTCCACAAGCACCTGGGCGACTTCCTGGCAACCGGGTGCATCACACCCAAGCAGGGAGCGCTGGCAAACGAGCAGCTGGGCAAGCTTTACGCACAGgtacgctggt ... tctgcgacagGTGCGTCCAAATGCTGTTGCGCTGGTTGATGCCTTCAACTACACAGACCACTACCTGGGGTCTGTGCTGGGGCGGTACGATGGGAATGTGTACCCAGCGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 371

CATTCTCCACAAGCACCTGGGCGACTTCCTGGCAACCGGGTGCATCACACCCAAGCAGGGAGCGCTGGCAAACGAGCAGCTGGGCAAGCTTTACGCACAGgtacgctggt ... tctgcgacagGTGCGTCCAAATGCTGTTGCGCTGGTTGATGCCTTCAACTACACAGACCACTACCTGGGGTCTGTGCTGGGGCGGTACGATGGGAATGTGTACCCAGCGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 284

CATTCTCCACAAGCACCTGGGCGACTTCCTGGCAACCGGGTGCATCACACCCAAGCAGGGAGCGCTGGCAAACGAGCAGCTGGGCAAGCTTTACGCACAGgtacgctggt ... tctgcgacagGTGCGTCCAAATGCTGTTGCGCTGGTTGATGCCTTCAACTACACAGACCACTACCTGGGGTCTGTGCTGGGGCGGTACGATGGGAATGTGTACCCAGCGC