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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCATGTCTATAAGACAATAGATGCTCTCCCAGTAGATGCACATCCTATGACACAGTTTACCACAGGAGTAATGGCTCTTCAGgtgattacatttctgtcatgctcttttctaaatataatatcataattgtgaaataaaatagcattttccttgtgatttatttgcactttttagaattgga...

Basic information

species Zea mays
transcript GRMZM2G063851_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063851_T04 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os11g33240.3 (Oryza sativa), 5'ss of exon 8
CTCATGTCTATAAGACAATAGATGCTCTCCCAGTAGATGCACATCCTATGACACAGTTTACCACAGGAGTAATGGCTCTTCAGgtgattacatttctgtcatgctcttttctaa---atataatatcataattgtgaaataaaatagcattttccttgtgatttatttgca--ctttttagaattgga
  ||||| |||||| |||| ||||||||||| |||  ||| ||||| |||||||||||||||||||| || ||||| ||||| || |  ||| ||||    | ||  ||| |||    ||  ||||||      ||||||||||    | | |  |||  ||||||||| |  | | ||  | |    
GCCATGTGTATAAGGCAATTGATGCTCTCCCTGTAACTGCTCATCCAATGACACAGTTTACCACAGGGGTGATGGCACTTCAAgtaa--acacttcttcttttcttgtttttaatttgtagcatatcactcccctgaaataaaaacatactctg-ttgccatttatttgaaagcatatttaattct--

upper sequence: GRMZM2G063851_T04 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 5'ss of exon 9
CTCATGTCTATAAGACAATAGATGCTCTCCCAGTAGATGCACATCCTATGACACAGTTTACCACAGGAGTAATGGCTCTTCAGgtga---ttaca-tttctgtcatgc-tcttttctaaatata-atatcataattgtgaaataaaatagcattttccttgtgatttatttgcactttttagaattgga
 |||||| ||| || |||| |||||||| || |||  ||| ||||| ||||| ||||||||||||||||| ||||| |||||||| |   ||  |   | | |||  | |||    |||||| | ||    |        | |  ||  | || ||  || ||       ||||  |   | |      
GTCATGTGTATGAGGCAATCGATGCTCTTCCTGTAACTGCTCATCCGATGACCCAGTTTACCACAGGAGTGATGGCACTTCAGgtaaaccttgtagcatatatcactcatctgaaataaatacatattctgttgccacttatttgaa-ggtatatttattttggagatggtgcatgtaaaaaag-----
















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|51592469|gb|CV071615.1|CV071615
EST:     TAGATGCACATCCTATGACACAGTTTACCACGGGAGTAATGGCTCTTCAG                         GTTGAGAGTGAATTTCAAAAGGCTTATGAC
genomic: TAGATGCACATCCTATGACACAGTTTACCACAGGAGTAATGGCTCTTCAGgtgattacat ... cccatttcagGTTGAGAGTGAATTTCAAAAGGCTTATGAC
EST: gi|211131287|gb|FL186946.1|FL186946
EST:     TAGATGCACATCCTATGACACAGTTTACCACGGGAGTAATGGCTCTTCAG                         GTTGAGAGTGAATTTCAAAAGGCTTATGACAATGGATTGCCAAAGTCAAA
genomic: TAGATGCACATCCTATGACACAGTTTACCACAGGAGTAATGGCTCTTCAGgtgattacat ... cccatttcagGTTGAGAGTGAATTTCAAAAGGCTTATGACAATGGATTGCCAAAGTCAAA
EST: gi|149084983|gb|EE174493.2|EE174493
EST:     TAGATGCACATCCTATGACACAGTTTACCACAGGAGTAATGGCTCTTCAG                         GTTGAGAGTGAATTTCAAAAGGCTTATGACAATGGATTGCCAAAGTCAAA
genomic: TAGATGCACATCCTATGACACAGTTTACCACAGGAGTAATGGCTCTTCAGgtgattacat ... cccatttcagGTTGAGAGTGAATTTCAAAAGGCTTATGACAATGGATTGCCAAAGTCAAA
EST: gi|21480820|gb|BQ577503.1|BQ577503
EST:     TAGATGCACATCCTATGACACAGTTTACCACAGGAGTAATGGCTCTTCAG                         GTTGAGAGTGAATTTCAAAAGGCTTATGACAATGGATTGCCAAAGTCAAA
genomic: TAGATGCACATCCTATGACACAGTTTACCACAGGAGTAATGGCTCTTCAGgtgattacat ... cccatttcagGTTGAGAGTGAATTTCAAAAGGCTTATGACAATGGATTGCCAAAGTCAAA
EST: gi|67013663|gb|CO442412.1|CO442412
EST:     TAGATGCACATNCTATGACACAGTTTACCACGGGAGTAATGGCTCTTCAG                         GTTGAGAGTGAATTTCAAAAGGCT-ATGTACA-TGGATTGCCAAAGTCAA-
genomic: TAGATGCACATCCTATGACACAGTTTACCACAGGAGTAATGGCTCTTCAGgtgattacat ... cccatttcagGTTGAGAGTGAATTTCAAAAGGCTTATG-ACAATGGATTGCCAAAGTCAAA
EST: gi|211131286|gb|FL186945.1|FL186945
EST:     TAGATGCACATCCTATGACACAGTTTACCACGGGAGTAATGGCTCTTCAG                         GTTGAGAGTGAATTTCAAAAGGCTTATGACAATGGATTGCCAAAGTCAAA
genomic: TAGATGCACATCCTATGACACAGTTTACCACAGGAGTAATGGCTCTTCAGgtgattacat ... cccatttcagGTTGAGAGTGAATTTCAAAAGGCTTATGACAATGGATTGCCAAAGTCAAA
EST: gi|149100799|gb|EE186893.2|EE186893
EST:     TAGATGCACATCCTATGACACAGTTTACCACAGGAGTAATGGCTCTTCAG                         GTTGAGAGTGAATTTCAAAAGGCTTATGACAATGGATTGCCAAAGTCAAA
genomic: TAGATGCACATCCTATGACACAGTTTACCACAGGAGTAATGGCTCTTCAGgtgattacat ... cccatttcagGTTGAGAGTGAATTTCAAAAGGCTTATGACAATGGATTGCCAAAGTCAAA
EST: gi|32868179|gb|CF007861.1|CF007861
EST:     TAGATGCACATCCTATGACACAGTTTACCACAGGAGTAATGGCTCTTCAG                         GTTGAGAGTGAATTTCAAAAGGCTTATGACAATGGATTGCCAAAGTCAAA
genomic: TAGATGCACATCCTATGACACAGTTTACCACAGGAGTAATGGCTCTTCAGgtgattacat ... cccatttcagGTTGAGAGTGAATTTCAAAAGGCTTATGACAATGGATTGCCAAAGTCAAA
EST: gi|149014218|gb|EE043773.2|EE043773
EST:     TAGATGCACATCCTATGACACAGTTTACCACAGGAGTAATGGCTCTTCAG                         GTTGAGAGTGAATTTCAAAAGGCTTATGACAATGGATTGCCAAAGTCAAA
genomic: TAGATGCACATCCTATGACACAGTTTACCACAGGAGTAATGGCTCTTCAGgtgattacat ... cccatttcagGTTGAGAGTGAATTTCAAAAGGCTTATGACAATGGATTGCCAAAGTCAAA
EST: gi|211510240|gb|FL228187.1|FL228187
EST:     TAGATGCACATCCTATGACACAGTTTACCACAGGAGTAATGGCTCTTCAN                         GTTGAGAGTGAATTTCAAA-GGCT
genomic: TAGATGCACATCCTATGACACAGTTTACCACAGGAGTAATGGCTCTTCAGgtgattacat ... cccatttcagGTTGAGAGTGAATTTCAAAAGGCT
EST: gi|149105261|gb|EE290752.2|EE290752
EST:     TAGATGCACATCCTATGACACAGTTTACCACAGGAGTAATGGCTCTTCAG                         GTTGAGAGTGAATTTCAAAAGGCTTATGACAATGGATTGCCAAAGTCAAA
genomic: TAGATGCACATCCTATGACACAGTTTACCACAGGAGTAATGGCTCTTCAGgtgattacat ... cccatttcagGTTGAGAGTGAATTTCAAAAGGCTTATGACAATGGATTGCCAAAGTCAAA
EST: gi|148991806|gb|EE033387.2|EE033387
EST:     TAGATGCACATCCTATGACACAGTTTACCACAGGAGTAATGGCTCTTCAG                         GTTGAGAGTGAATTTTCAAA-GGCTTATGACAATGGATTGCCAAAGTCAAA
genomic: TAGATGCACATCCTATGACACAGTTTACCACAGGAGTAATGGCTCTTCAGgtgattacat ... cccatttcagGTTGAGAGTGAATTT-CAAAAGGCTTATGACAATGGATTGCCAAAGTCAAA
EST: gi|148931316|gb|EC874179.2|EC874179
EST:     TAGATGCACATCCTATGACACAGTTTACCACAGGAGTAATGGCTCTTCAG                         GTTGAGAGTGAATTTCAAAAGGCTTATGACAATGGATTGCCAAAGTCAAA
genomic: TAGATGCACATCCTATGACACAGTTTACCACAGGAGTAATGGCTCTTCAGgtgattacat ... cccatttcagGTTGAGAGTGAATTTCAAAAGGCTTATGACAATGGATTGCCAAAGTCAAA
EST: gi|78087725|gb|DV516118.1|DV516118
EST:     TAGATGCACATCCTATGACACAGTTTACCACAGGAGTAATGGCTCTTCAG                         GTTGAGAGTGAATTTCAAAAGGCTTATGACAATGGATTGCCAAAGTCAAA
genomic: TAGATGCACATCCTATGACACAGTTTACCACAGGAGTAATGGCTCTTCAGgtgattacat ... cccatttcagGTTGAGAGTGAATTTCAAAAGGCTTATGACAATGGATTGCCAAAGTCAAA
EST: gi|148990704|gb|EE032108.2|EE032108
EST:     TAGATGCACATCCTATGACACAGTTTACCACAGGAGTAATGGCTCTTCAG                         GTTGAGAGTGAATTTCAAAAGGCTTATGACAATGGATTGCCCAAGTCAAAG
genomic: TAGATGCACATCCTATGACACAGTTTACCACAGGAGTAATGGCTCTTCAGgtgattacat ... cccatttcagGTTGAGAGTGAATTTCAAAAGGCTTATGACAATGGATTGCCAAAGTCAAAG
EST: gi|71771089|gb|DR969026.1|DR969026
EST:     TAGATGCACATCCTATGACACAGTTTACCACAGGAGTAATGGCTCTTCAG                         GTTGAGAGTGAATTTCAAAAGGCTTATGACAATGGATTGCCAAAGTCAAA
genomic: TAGATGCACATCCTATGACACAGTTTACCACAGGAGTAATGGCTCTTCAGgtgattacat ... cccatttcagGTTGAGAGTGAATTTCAAAAGGCTTATGACAATGGATTGCCAAAGTCAAA
EST: gi|67040702|gb|CO466957.1|CO466957
EST:     TAGATGCACATCCTATGACACAGTTTACCACGGGAGTAATGGCTCTTCAG                         GTTGAGAGTGAATTTCAAAAGGCTTATGACAATGGATTGCCAAAGTCAAA
genomic: TAGATGCACATCCTATGACACAGTTTACCACAGGAGTAATGGCTCTTCAGgtgattacat ... cccatttcagGTTGAGAGTGAATTTCAAAAGGCTTATGACAATGGATTGCCAAAGTCAAA
EST: gi|89758059|gb|DY687401.1|DY687401
EST:     TAGATGCACATCCTATGACACAGTTTACCACAGGAGTAATGGCTCTTCAG                         GTTGAGAGTGAATTTCAAAAGGCTTATGACAATGGATTGCCAAAGTCAAA
genomic: TAGATGCACATCCTATGACACAGTTTACCACAGGAGTAATGGCTCTTCAGgtgattacat ... cccatttcagGTTGAGAGTGAATTTCAAAAGGCTTATGACAATGGATTGCCAAAGTCAAA
EST: gi|149082974|gb|EE172211.2|EE172211
EST:     TAGATGCACATCCTATGACACAGTTTACCACAGGAGTAATGGCTCTTCAG                         GTTGAGAGTGAATTTCAAAAGGCTTATGACAATGGATTGCCAAAGTCAAA
genomic: TAGATGCACATCCTATGACACAGTTTACCACAGGAGTAATGGCTCTTCAGgtgattacat ... cccatttcagGTTGAGAGTGAATTTCAAAAGGCTTATGACAATGGATTGCCAAAGTCAAA

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), 45 (downstream exon)
Score: 103

CTCATGTCTATAAGACAATAGATGCTCTCCCAGTAGATGCACATCCTATGACACAGTTTACCACAGGAGTAATGGCTCTTCAGgtgattacat ... cccatttcagGTTGAGAGTGAATTTCAAAAGGCTTATGACAATGGATTGCCAAAGTCAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 453

CTCATGTCTATAAGACAATAGATGCTCTCCCAGTAGATGCACATCCTATGACACAGTTTACCACAGGAGTAATGGCTCTTCAGgtgattacat ... cccatttcagGTTGAGAGTGAATTTCAAAAGGCTTATGACAATGGATTGCCAAAGTCAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 440

CTCATGTCTATAAGACAATAGATGCTCTCCCAGTAGATGCACATCCTATGACACAGTTTACCACAGGAGTAATGGCTCTTCAGgtgattacat ... cccatttcagGTTGAGAGTGAATTTCAAAAGGCTTATGACAATGGATTGCCAAAGTCAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 385

CTCATGTCTATAAGACAATAGATGCTCTCCCAGTAGATGCACATCCTATGACACAGTTTACCACAGGAGTAATGGCTCTTCAGgtgattacat ... cccatttcagGTTGAGAGTGAATTTCAAAAGGCTTATGACAATGGATTGCCAAAGTCAAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCATGTCTATAAGACAATAGATGCTCTCCCAGTAGATGCACATCCTATGACACAGTTTACCACAGGAGTAATGGCTCTTCAGgtgattacatttctgtcatgctcttttctaaatataatatcataattgtgaaataaaatagcattttccttgtgatttatttgcactttttagaattgga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaataaaa