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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGGCCGGGCGAGGCGGACTGCGCCTACTACCTCCGCACGGGCGCCTGCGGCTACGGGGAGCGCTGCCGCTACAACCACCCCCGCGATCGGCCGGCCCCGgtgagaaccagcctaatccacgccgctcccccacccctatccctgctctgctctgtttttgtgtctcgtgctcagctcgatggttactggtgagctaagc...

Basic information

species Zea mays
transcript GRMZM2G069009_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069009_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g15350.1 (Oryza sativa), 5'ss of exon 2
GCGGCCGGGCGAGGCGGACTGCGCCTACTACCTCCGCACGGGCGCCTGCGGCTACGGGGAGCGCTGCCGCTACAACCACCCCCGCGATCGGCCGGCCCCGgtgagaaccagc-ctaatccacgc---cgctcccccacccctatccctgctctgctctgtttttgtgtctcgtgctcagctcgatggttac--tggtgagctaagc
      ||| ||||||||||||| |||||||||||||||||| || |||||||||||||||  |||||||||||||||||| ||||||||  | ||| | |        ||| | ||| | | |   |||| | | || ||| |   |  | |  ||   |  ||  | | |         | |||    |  |  ||   || | 
------GGGGGAGGCGGACTGCGTCTACTACCTCCGCACGGGGGCTTGCGGCTACGGGGAGAACTGCCGCTACAACCACCCGCGCGATCGCGCCGCCGCAGCAGTGgtgagcaccaattccccctctcgctgctctactcctctttttttttttttcacctcctgactttagctacggtgacaatgaccgccctattggattacgt
















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|78082473|gb|DV510885.1|DV510885
EST:     GCTACGGGGAGCGCTGCCGCTACAACCACCCCCGCGATCGGCCGGCCCCG                         GTTAATGGAGTTGGAAAGACCGCAGTTACAGTGGAGTACCCAGAGCGTCCT
genomic: GCTACGGGGAGCGCTGCCGCTACAACCACCCCCGCGATCGGCCGGCCCCGgtgagaacca ... tgttttccagGTTAATGGAGTTGGAAAGACCGCAGTTACAGTGGAGTACCCAGAGCGTCCT
EST: gi|94476471|gb|EB705429.1|EB705429
EST:     GCTACGGGGAGCGCTGCCGCTACAACCACCCCCGCGATCGGCCGGCCCCG                         GTTAATGGAGTTGGAAAGACCGCAGTTACAGTGGAGTACCCAGAGCGTCCT
genomic: GCTACGGGGAGCGCTGCCGCTACAACCACCCCCGCGATCGGCCGGCCCCGgtgagaacca ... tgttttccagGTTAATGGAGTTGGAAAGACCGCAGTTACAGTGGAGTACCCAGAGCGTCCT
EST: gi|149005039|gb|EE039564.2|EE039564
EST:     GCTACGGGGAGCGCTGCCGCTACAACCACCCCCGCGATCGGCCGGCCCCG                         GTTAATGGAGTTGGAAAGACCGCAGTTACAGTGGAGTACCCAGAGCGTCCT
genomic: GCTACGGGGAGCGCTGCCGCTACAACCACCCCCGCGATCGGCCGGCCCCGgtgagaacca ... tgttttccagGTTAATGGAGTTGGAAAGACCGCAGTTACAGTGGAGTACCCAGAGCGTCCT
EST: gi|91049855|gb|EB160273.1|EB160273
EST:     GCTACGGGGAGCGCTGCCGCTACAACCACCCCCGCGATCGGCCGGCCCCG                         GTTAATGGAGTTGGAAAGACCGCAGTTACAGTGGAGTACCCAGAGCGTCCT
genomic: GCTACGGGGAGCGCTGCCGCTACAACCACCCCCGCGATCGGCCGGCCCCGgtgagaacca ... tgttttccagGTTAATGGAGTTGGAAAGACCGCAGTTACAGTGGAGTACCCAGAGCGTCCT
EST: gi|148956932|gb|EC902865.2|EC902865
EST:     GCTACGGGGAGCGCTGCCGCTACAACCACCCCCGCGATCGGCCGGCCCCG                         GTTAATGGAGTTGGAAAGACCGCAGTTACAGTGGAGTACCCAGAGCGTCCT
genomic: GCTACGGGGAGCGCTGCCGCTACAACCACCCCCGCGATCGGCCGGCCCCGgtgagaacca ... tgttttccagGTTAATGGAGTTGGAAAGACCGCAGTTACAGTGGAGTACCCAGAGCGTCCT
EST: gi|149094715|gb|EE180267.2|EE180267
EST:     GCTACGGGGAGCGCTGCCGCTACAACCACCCCCGCGATCGGCCGGCCCCG                         GTTAATGGAGTTGGAAAGACCGCAGTTACAGTGGAGTACCCAGAGCGTCCT
genomic: GCTACGGGGAGCGCTGCCGCTACAACCACCCCCGCGATCGGCCGGCCCCGgtgagaacca ... tgttttccagGTTAATGGAGTTGGAAAGACCGCAGTTACAGTGGAGTACCCAGAGCGTCCT
EST: gi|78082860|gb|DV511253.1|DV511253
EST:     GCTACGGGGAGCGCTGCCGCTACAACCACCCCCGCGATCGGCCGGCCCCG                         GTTAATGGAGTTGGAAAGACCGCAGTTACAGTGGAGTACCCAGAGCGTCCT
genomic: GCTACGGGGAGCGCTGCCGCTACAACCACCCCCGCGATCGGCCGGCCCCGgtgagaacca ... tgttttccagGTTAATGGAGTTGGAAAGACCGCAGTTACAGTGGAGTACCCAGAGCGTCCT
EST: gi|71418361|gb|DR804412.1|DR804412
EST:     GCTACGGGGAGCGCTGCCGCTACAACCACCCCCGCGATCGGCCGGCCCCG                         GTTAATGGAGTTGGAAAGACCGCAGTTACAGTGGAGTACCCAGAGCGTCCT
genomic: GCTACGGGGAGCGCTGCCGCTACAACCACCCCCGCGATCGGCCGGCCCCGgtgagaacca ... tgttttccagGTTAATGGAGTTGGAAAGACCGCAGTTACAGTGGAGTACCCAGAGCGTCCT
EST: gi|76937022|gb|DV175010.1|DV175010
EST:     GCTACGGGGAGCGCTGCCGCTACAACCACCCCCGCGATCGGCCGGCCCCG                         GTTAATGGAGTTGGAAAGACCGCAGTTACAGTGGAGTACCCAGAGCGTCCT
genomic: GCTACGGGGAGCGCTGCCGCTACAACCACCCCCGCGATCGGCCGGCCCCGgtgagaacca ... tgttttccagGTTAATGGAGTTGGAAAGACCGCAGTTACAGTGGAGTACCCAGAGCGTCCT
EST: gi|74232341|gb|DT640255.1|DT640255
EST:     GCTACGGGGAGCGCTGCCGCTACAACCACCCCCGCGATCGGCCGGCCCCG                         GTTAATGGAGTTGGAAAGACCGCAGTTACAGTGGAGTACCCAGAGCGTCCT
genomic: GCTACGGGGAGCGCTGCCGCTACAACCACCCCCGCGATCGGCCGGCCCCGgtgagaacca ... tgttttccagGTTAATGGAGTTGGAAAGACCGCAGTTACAGTGGAGTACCCAGAGCGTCCT
EST: gi|149087101|gb|EE176640.2|EE176640
EST:     GCTACGGGGAGCGCTGCCGCTACAACCACCCCCGCGATCGGCCGGCCCCG                         GTTAATGGAGTTGGAAAGACCGCAGTTACAGTGGAGTACCCAGAGCGTCCT
genomic: GCTACGGGGAGCGCTGCCGCTACAACCACCCCCGCGATCGGCCGGCCCCGgtgagaacca ... tgttttccagGTTAATGGAGTTGGAAAGACCGCAGTTACAGTGGAGTACCCAGAGCGTCCT
EST: gi|76286604|gb|DV026172.1|DV026172
EST:     GCTACGGGGAGCGCTGCCGCTACAACCACCCCCGCGATCGGCCGGCCCCG                         GTTAATGGAGTTGGAAAGACCGCAGTTACAGTGGAGTACCCAGAGCGTCCT
genomic: GCTACGGGGAGCGCTGCCGCTACAACCACCCCCGCGATCGGCCGGCCCCGgtgagaacca ... tgttttccagGTTAATGGAGTTGGAAAGACCGCAGTTACAGTGGAGTACCCAGAGCGTCCT
EST: gi|149102933|gb|EE288285.2|EE288285
EST:     GCTACGGGGAGCGCTGCCGCTACAACCACCCCCGCGATCGGCCGGCCCCG                         GTTAATGGAGTTGGAAAGACCGCAGTTACAGTGGAGTACCCAGAGCGTCCT
genomic: GCTACGGGGAGCGCTGCCGCTACAACCACCCCCGCGATCGGCCGGCCCCGgtgagaacca ... tgttttccagGTTAATGGAGTTGGAAAGACCGCAGTTACAGTGGAGTACCCAGAGCGTCCT
EST: gi|78114960|gb|DV533348.1|DV533348
EST:     GCTACGGGGAGCGCTGCCGCTACAACCACCCCCGCGATCGGCCGGCCCCG                         GTTAATGGAGTTGGAAAGACCGCAGTTACAGTGGAGTACCCAGAGCGTCCT
genomic: GCTACGGGGAGCGCTGCCGCTACAACCACCCCCGCGATCGGCCGGCCCCGgtgagaacca ... tgttttccagGTTAATGGAGTTGGAAAGACCGCAGTTACAGTGGAGTACCCAGAGCGTCCT

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: 47 (upstream exon), 47 (downstream exon)
Score: 98

GCGGCCGGGCGAGGCGGACTGCGCCTACTACCTCCGCACGGGCGCCTGCGGCTACGGGGAGCGCTGCCGCTACAACCACCCCCGCGATCGGCCGGCCCCGgtgagaacca ... tgttttccagGTTAATGGAGTTGGAAAGACCGCAGTTACAGTGGAGTACCCAGAGCGTCCTGGACAGCCTCTCTGTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 121

GCGGCCGGGCGAGGCGGACTGCGCCTACTACCTCCGCACGGGCGCCTGCGGCTACGGGGAGCGCTGCCGCTACAACCACCCCCGCGATCGGCCGGCCCCGgtgagaacca ... tgttttccagGTTAATGGAGTTGGAAAGACCGCAGTTACAGTGGAGTACCCAGAGCGTCCTGGACAGCCTCTCTGTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 93

GCGGCCGGGCGAGGCGGACTGCGCCTACTACCTCCGCACGGGCGCCTGCGGCTACGGGGAGCGCTGCCGCTACAACCACCCCCGCGATCGGCCGGCCCCGgtgagaacca ... tgttttccagGTTAATGGAGTTGGAAAGACCGCAGTTACAGTGGAGTACCCAGAGCGTCCTGGACAGCCTCTCTGTGAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 76

GCGGCCGGGCGAGGCGGACTGCGCCTACTACCTCCGCACGGGCGCCTGCGGCTACGGGGAGCGCTGCCGCTACAACCACCCCCGCGATCGGCCGGCCCCGgtgagaacca ... tgttttccagGTTAATGGAGTTGGAAAGACCGCAGTTACAGTGGAGTACCCAGAGCGTCCTGGACAGCCTCTCTGTGAG


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGGCCGGGCGAGGCGGACTGCGCCTACTACCTCCGCACGGGCGCCTGCGGCTACGGGGAGCGCTGCCGCTACAACCACCCCCGCGATCGGCCGGCCCCGgtgagaaccagcctaatccacgccgctcccccacccctatccctgctctgctctgtttttgtgtctcgtgctcagctcgatggttactggtgagctaagc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccacgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctccccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccctatc