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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAAGTATCCATTGATGAAATTAAATTAACACCTCTAGAGCTTTCTGAACTGATAGCATCAATTAAGAATGGAACTATAAGTGGGAAGATCGGCAAGGAGgtaacattgctaaactgggtttccccccttgttactgtttttcagctctatgttctgagttttgacagtctatagggtctacacatttctaggctttgcaccctgattgatgacaaagcctctctaaatctgtccttgcag

Basic information

species Zea mays
transcript GRMZM2G091560_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G091560_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os11g34210.1 (Oryza sativa), 5'ss of exon 6
AAAAGTATCCATTGATGAAATTAAATTAACACCTCTAGAGCTTTCTGAACTGATAGCATCAATTAAGAATGGAACTATAAGTGGGAAGATCGGCAAGGAGgtaacattgctaaactgggtttccccccttgttactgtttttcagctctatgttctgagttttgacagtctatagggtctacacatttctaggctttgcaccctgattgatgacaaagcctctctaaatctgtccttgcag
|||| | ||||||||||||||||||||||||||||| |||||||||||| |||| ||||| || | |||||||||||| ||||||||||| || |||||||||   ||||    ||   ||||  |  |   |  ||||| |   ||  || |  || |    ||| |  | | |  | | |  |||  |    | || |    |                                    
AAAACTTTCCATTGATGAAATTAAATTAACACCTCTGGAGCTTTCTGAATTGATTGCATCTATAAGGAATGGAACTATCAGTGGGAAGATTGGAAAGGAGgtagatttgc----ctctatttcttc--tgactgttgtttctgtactgaatatgatg-gccaggactgagttttgactgttcttattatttctatctggagataggc----------------------------------
















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|211515148|gb|FL351622.1|FL351622
EST:     TGATAGCATCAATTAAGAATGGAACTATAAGTGGGAAGATCGGCAAGGAT                         ATACTGGCCGAGCTCATTGCCAAAGGCGGAACAGTTAAGGCTGTGATAGAA
genomic: TGATAGCATCAATTAAGAATGGAACTATAAGTGGGAAGATCGGCAAGGAGgtaacattgc ... gtccttgcagATACTGGCCGAGCTCATTGCCAAAGGCGGAACAGTTAAGGCTGTGATAGAA
EST: gi|78022483|gb|DV490870.1|DV490870
EST:     TGATAGCATCAATTAAGAATGGAACTATAAGTGGGAAGATCGGCAAGGAG                         ATACTGGCCGAGCTCATTGCCAAAGGCGGAACAGTTAAGGCTGTGATAGAA
genomic: TGATAGCATCAATTAAGAATGGAACTATAAGTGGGAAGATCGGCAAGGAGgtaacattgc ... gtccttgcagATACTGGCCGAGCTCATTGCCAAAGGCGGAACAGTTAAGGCTGTGATAGAA
EST: gi|12968520|gb|BG265466.1|BG265466
EST:     AGTGGGAAGATCGGCAAGGAG                         ATACTGGCCGAGCTCATTGCCAAAGGCGGAACAGTTAAGGCTGTGATAGAA
genomic: AGTGGGAAGATCGGCAAGGAGgtaacattgc ... gtccttgcagATACTGGCCGAGCTCATTGCCAAAGGCGGAACAGTTAAGGCTGTGATAGAA
EST: gi|211486172|gb|FL326647.1|FL326647
EST:     TGATAGCATCAATTAAGAATGGAACTATAAGTGGGAAGATCGGCAAGGAT                         ATACTGGCCGAGCTCATTGCCAAAGGCGGAACAGTTAAGGCTGTGATAGAA
genomic: TGATAGCATCAATTAAGAATGGAACTATAAGTGGGAAGATCGGCAAGGAGgtaacattgc ... gtccttgcagATACTGGCCGAGCTCATTGCCAAAGGCGGAACAGTTAAGGCTGTGATAGAA
EST: gi|4647395|gb|AI622470.1|AI622470
EST:     TGATAGCATCAATTAAGAATGGAACTATAAGTGGGAAGATCGGCAAGGAG                         ATACTGGCCGAGCTCATTGCCAAAGGCGGAACAGTTAAGGCTGTGATAGAA
genomic: TGATAGCATCAATTAAGAATGGAACTATAAGTGGGAAGATCGGCAAGGAGgtaacattgc ... gtccttgcagATACTGGCCGAGCTCATTGCCAAAGGCGGAACAGTTAAGGCTGTGATAGAA
EST: gi|5915470|gb|AW053111.1|AW053111
EST:     TGATAGCATCAATTAAGAATGGAACTATAAGTGGGAAGATCGGCAAGGAG                         ATACTGGCCGAGCTCATTGCCAAAGGCGGAACAGTTAAGGCTGTGATAGAA
genomic: TGATAGCATCAATTAAGAATGGAACTATAAGTGGGAAGATCGGCAAGGAGgtaacattgc ... gtccttgcagATACTGGCCGAGCTCATTGCCAAAGGCGGAACAGTTAAGGCTGTGATAGAA
EST: gi|5713973|gb|AI943958.1|AI943958
EST:     TGATAGCATCAATTAAGAATGGAACTATAAGTGGGAAGATCGGCAAGGAG                         ATACTGGCCGAGCTCATTGCCAAAGGCGGAACAGTTAAGGCTGTGATAGAA
genomic: TGATAGCATCAATTAAGAATGGAACTATAAGTGGGAAGATCGGCAAGGAGgtaacattgc ... gtccttgcagATACTGGCCGAGCTCATTGCCAAAGGCGGAACAGTTAAGGCTGTGATAGAA
EST: gi|211183316|gb|FL321581.1|FL321581
EST:     TGATAGCATCAATTAAGAATGGAACTATAAGTGGGAAGATCGGCAAGGAT                         ATACTGGCCGAGCTCATTGCCAAAGGCGGAACAGTTAAGGCTGTGATAGAA
genomic: TGATAGCATCAATTAAGAATGGAACTATAAGTGGGAAGATCGGCAAGGAGgtaacattgc ... gtccttgcagATACTGGCCGAGCTCATTGCCAAAGGCGGAACAGTTAAGGCTGTGATAGAA
EST: gi|211362610|gb|FL353331.1|FL353331
EST:     TGATAGCATCAATTAAGAATGGAACTATAAGTGGGAAGATCGGCAAGGAT                         ATACTGGCCGAGCTCATTGCCAAAGGCGGAACAGTTAAGGCTGTGATAGAA
genomic: TGATAGCATCAATTAAGAATGGAACTATAAGTGGGAAGATCGGCAAGGAGgtaacattgc ... gtccttgcagATACTGGCCGAGCTCATTGCCAAAGGCGGAACAGTTAAGGCTGTGATAGAA
EST: gi|5929050|gb|AW056342.1|AW056342
EST:     TGATAGCATCAATTAAGAATGGAACTATAAGTGGGAAGATCGGCAAGGAG                         ATACTGGCCGAGCTCATTGCCAAAGGCGGAACAGTTAAGGCTGTGATAGAA
genomic: TGATAGCATCAATTAAGAATGGAACTATAAGTGGGAAGATCGGCAAGGAGgtaacattgc ... gtccttgcagATACTGGCCGAGCTCATTGCCAAAGGCGGAACAGTTAAGGCTGTGATAGAA
EST: gi|211158667|gb|FL318097.1|FL318097
EST:     TGATAGCATCAATTAAGAATGGAACTATAAGTGGGAAGATCGGCAAGGAG                         ATACTGGCCGAGCTCATTGCCAAAGGCGGAACAGTTAAGGCTGTGATAGAA
genomic: TGATAGCATCAATTAAGAATGGAACTATAAGTGGGAAGATCGGCAAGGAGgtaacattgc ... gtccttgcagATACTGGCCGAGCTCATTGCCAAAGGCGGAACAGTTAAGGCTGTGATAGAA
EST: gi|211031236|gb|FL345766.1|FL345766
EST:     TGATAGCATCAATTAAGAATGGAACTATAAGTGGGAAGATCGGCAAGGAT                         ATACTGGCCGAGCTCATTGCCAAAGGCGGAACAGTTAAGGCTGTGATAGAA
genomic: TGATAGCATCAATTAAGAATGGAACTATAAGTGGGAAGATCGGCAAGGAGgtaacattgc ... gtccttgcagATACTGGCCGAGCTCATTGCCAAAGGCGGAACAGTTAAGGCTGTGATAGAA
EST: gi|211274217|gb|FL334363.1|FL334363
EST:     TGATAGCATCAATTAAGAATGGAACTATAAGTGGGAAGATCGGCAAGGAT                         ATACTGGCCGAGCTCATTGCCAAAGGCGGAACAGTTAAGGCTGTGATAGAA
genomic: TGATAGCATCAATTAAGAATGGAACTATAAGTGGGAAGATCGGCAAGGAGgtaacattgc ... gtccttgcagATACTGGCCGAGCTCATTGCCAAAGGCGGAACAGTTAAGGCTGTGATAGAA
EST: gi|33096769|gb|CF056739.1|CF056739
EST:     TGATAGCATCAATTAAGAATGGAACTATAAGTGGGAAGATCGGCAAGGAG                         ATACTGGCCGAGGCTCATTGCCAAAGGCGGAACAGTTAAGGCTGTGATAGA
genomic: TGATAGCATCAATTAAGAATGGAACTATAAGTGGGAAGATCGGCAAGGAGgtaacattgc ... gtccttgcagATACTGGCCGAG-CTCATTGCCAAAGGCGGAACAGTTAAGGCTGTGATAGA
EST: gi|94478769|gb|EB707727.1|EB707727
EST:     TGATAGCATCAATTAAGAATGGAACTATAAGTGGGAAGATCGGCAAGGAG                         ATACTGGCCGAGCTCATTGCCAAAGGCGGAACAGTTAAGGCTGTGATAGAA
genomic: TGATAGCATCAATTAAGAATGGAACTATAAGTGGGAAGATCGGCAAGGAGgtaacattgc ... gtccttgcagATACTGGCCGAGCTCATTGCCAAAGGCGGAACAGTTAAGGCTGTGATAGAA

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), 39 (downstream exon)
Score: 45

AAAAGTATCCATTGATGAAATTAAATTAACACCTCTAGAGCTTTCTGAACTGATAGCATCAATTAAGAATGGAACTATAAGTGGGAAGATCGGCAAGGAGgtaacattgc ... gtccttgcagATACTGGCCGAGCTCATTGCCAAAGGCGGAACAGTTAAGGCTGTGATAGAAGAGAAAGATTTGGTTCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 81

AAAAGTATCCATTGATGAAATTAAATTAACACCTCTAGAGCTTTCTGAACTGATAGCATCAATTAAGAATGGAACTATAAGTGGGAAGATCGGCAAGGAGgtaacattgc ... gtccttgcagATACTGGCCGAGCTCATTGCCAAAGGCGGAACAGTTAAGGCTGTGATAGAAGAGAAAGATTTGGTTCAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 40

AAAAGTATCCATTGATGAAATTAAATTAACACCTCTAGAGCTTTCTGAACTGATAGCATCAATTAAGAATGGAACTATAAGTGGGAAGATCGGCAAGGAGgtaacattgc ... gtccttgcagATACTGGCCGAGCTCATTGCCAAAGGCGGAACAGTTAAGGCTGTGATAGAAGAGAAAGATTTGGTTCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 65

AAAAGTATCCATTGATGAAATTAAATTAACACCTCTAGAGCTTTCTGAACTGATAGCATCAATTAAGAATGGAACTATAAGTGGGAAGATCGGCAAGGAGgtaacattgc ... gtccttgcagATACTGGCCGAGCTCATTGCCAAAGGCGGAACAGTTAAGGCTGTGATAGAAGAGAAAGATTTGGTTCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAAGTATCCATTGATGAAATTAAATTAACACCTCTAGAGCTTTCTGAACTGATAGCATCAATTAAGAATGGAACTATAAGTGGGAAGATCGGCAAGGAGgtaacattgctaaactgggtttccccccttgttactgtttttcagctctatgttctgagttttgacagtctatagggtctacacatttctaggctttgcaccctgattgatgacaaagcctctctaaatctgtccttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG