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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGGAAATAGAGGCCACCCAGACAGCAGCCCTCAAGGTTGATGCCTCGCCACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAGgtgaggcagtagtttatcggtagatgctagttcctatgttttaccacatataatcagaaagaataatccaaatatactgcatggcctactgtag

Basic information

species Zea mays
transcript GRMZM2G006130_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006130_T06 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os11g03730.2 (Oryza sativa), 5'ss of exon 2
TTTGGAAATAGAGGCCACCCAGACAGCAGCCCTCAAGGTTGATGCCTCGCCACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAGgtgaggcagtagtt-tatcggtagatgctagttcctatgttttaccacatataatcagaaagaataatccaa-atatactgcatggcctactgtag------------------------------------------------------------------------------------
 ||  |  || | || |||||||| || | |||||||||||||||||| || || ||||| ||  |||||||||| ||||| ||||| |||||||||||||| || |   ||   |||      || ||  ||   |   ||  |    ||| |  | |     |  ||    |  |  |   | |  | ||  ||                                                                                    
GTTACACTTACATGCGACCCAGACTGCGGTCCTCAAGGTTGATGCCTCACCGCAACTTGCTCGACAGATCCCTGACACACTATTTGGAATATTTTTTGAGgtaagccgtgagacatatacagtaattctgtttttcacaatt-gcactgtatcactatatcctttcctctggcacttttttgttaggatgctcaagtgcattagcatgcccagaataatccaggtagattatacatgttccaccatgtcctgatgataatgatcttggctaatattgtag
















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|148950545|gb|EC896122.2|EC896122
EST:     CACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAG                         GAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAAC
genomic: CACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAGgtgaggcagt ... cctactgtagGAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAAC
EST: gi|211169041|gb|FL129153.1|FL129153
EST:     CACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAG                         GAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAAC
genomic: CACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAGgtgaggcagt ... cctactgtagGAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAAC
EST: gi|88755664|gb|DY539805.1|DY539805
EST:     CACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAG                         GAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAAC
genomic: CACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAGgtgaggcagt ... cctactgtagGAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAAC
EST: gi|211170726|gb|FL129169.1|FL129169
EST:     CACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAG                         GAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAAC
genomic: CACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAGgtgaggcagt ... cctactgtagGAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAAC
EST: gi|211170714|gb|FL129157.1|FL129157
EST:     CACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAG                         GAGATCAACCATGCANGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAAC
genomic: CACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAGgtgaggcagt ... cctactgtagGAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAAC
EST: gi|32844992|gb|CD984673.1|CD984673
EST:     CACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAG                         GAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAAC
genomic: CACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAGgtgaggcagt ... cctactgtagGAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAAC
EST: gi|148953656|gb|EC899016.2|EC899016
EST:     CACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAG                         GAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAAC
genomic: CACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAGgtgaggcagt ... cctactgtagGAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAAC
EST: gi|32929289|gb|CF034101.1|CF034101
EST:     CACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAG                         GAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAAC
genomic: CACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAGgtgaggcagt ... cctactgtagGAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAAC
EST: gi|211170722|gb|FL129165.1|FL129165
EST:     CACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAG                         GAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAAC
genomic: CACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAGgtgaggcagt ... cctactgtagGAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAAC
EST: gi|149082080|gb|EE171257.2|EE171257
EST:     CACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAG                         GAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAAC
genomic: CACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAGgtgaggcagt ... cctactgtagGAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAAC
EST: gi|211169040|gb|FL129152.1|FL129152
EST:     CACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAG                         GAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAAC
genomic: CACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAGgtgaggcagt ... cctactgtagGAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAAC
EST: gi|148953586|gb|EC898940.2|EC898940
EST:     CACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAG                         GAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAAC
genomic: CACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAGgtgaggcagt ... cctactgtagGAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAAC
EST: gi|32844324|gb|CD984005.1|CD984005
EST:     CACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAG                         GAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAAC
genomic: CACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAGgtgaggcagt ... cctactgtagGAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAAC
EST: gi|211170721|gb|FL129164.1|FL129164
EST:     CACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAG                         GAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAAC
genomic: CACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAGgtgaggcagt ... cctactgtagGAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAAC
EST: gi|91051534|gb|EB161952.1|EB161952
EST:     CACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAG                         GAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAAC
genomic: CACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAGgtgaggcagt ... cctactgtagGAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAAC
EST: gi|148956552|gb|EC902392.2|EC902392
EST:     CACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAG                         GAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAAC
genomic: CACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAGgtgaggcagt ... cctactgtagGAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAAC
EST: gi|149079201|gb|EE168160.2|EE168160
EST:     CACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAG                         GAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAAC
genomic: CACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAGgtgaggcagt ... cctactgtagGAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAAC
EST: gi|211170720|gb|FL129163.1|FL129163
EST:     CACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAG                         GAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAAC
genomic: CACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAGgtgaggcagt ... cctactgtagGAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAAC
EST: gi|149100793|gb|EE186887.2|EE186887
EST:     CACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAG                         GAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAAC
genomic: CACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAGgtgaggcagt ... cctactgtagGAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAAC
EST: gi|60399112|gb|DN231926.1|DN231926
EST:     CACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAG                         GAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAAC
genomic: CACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAGgtgaggcagt ... cctactgtagGAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAAC
EST: gi|211169043|gb|FL129155.1|FL129155
EST:     CACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAG                         GAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAAC
genomic: CACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAGgtgaggcagt ... cctactgtagGAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAAC

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), 49 (downstream exon)
Score: 183

TTTGGAAATAGAGGCCACCCAGACAGCAGCCCTCAAGGTTGATGCCTCGCCACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAGgtgaggcagt ... cctactgtagGAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 645

TTTGGAAATAGAGGCCACCCAGACAGCAGCCCTCAAGGTTGATGCCTCGCCACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAGgtgaggcagt ... cctactgtagGAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 534

TTTGGAAATAGAGGCCACCCAGACAGCAGCCCTCAAGGTTGATGCCTCGCCACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAGgtgaggcagt ... cctactgtagGAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 263

TTTGGAAATAGAGGCCACCCAGACAGCAGCCCTCAAGGTTGATGCCTCGCCACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAGgtgaggcagt ... cctactgtagGAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTGGAAATAGAGGCCACCCAGACAGCAGCCCTCAAGGTTGATGCCTCGCCACAGCTTGCCCGGAAGATCCCTGAAACACTGTTTGGGATATTTTTTGAGgtgaggcagtagtttatcggtagatgctagttcctatgttttaccacatataatcagaaagaataatccaaatatactgcatggcctactgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA