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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggaatataattctattccaggaggcaattaaatcaacaacttataaaagatctctttactaatgccccccccccctccctatccgatgtttgcagAAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCAAAGGTAGATATCTTGATCGTGACAGAGGAATTATTGCAACAAACAAGCA

Basic information

species Zea mays
transcript GRMZM2G088974_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G088974_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os12g08270.1 (Oryza sativa), 3'ss of exon 7
gtatggaatataattctattccaggaggcaattaaatcaac-aacttataaaagatctctttactaa---------tgccccccccccctccctatccgatgtttgcagAAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCAAAGGTAGATATCTTGATCGTGACAGAGGAATTATTGCAACAAACAAGCA
||||  ||||  | | ||||| |  |   ||| || ||||| ||  |||        |||  | |||         ||  |        |   | ||  ||||||||||||||||| ||  |||||||||||||  ||||||||||||||||||| | ||||||||||||||||||||||||    || |||||||||||||| ||  |
gtatataata--actatattc-acaaaaaaatgaattcaactaaagtatcgttctgttctcaaataaaataaacattgttcggtaagtttttttttctcatgtttgcagAAGCTGGAGGTTTGGTAAAAGATGCTTCAGGAAACGATTTGGATTTCTCCAAAGGTAGATATCTTGATCGTGATGCTGGCATTATTGCAACAAATAAATA
















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|37375807|gb|CF624370.1|CF624370
EST:     TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAG                         AAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
genomic: TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAGgtatggaata ... atgtttgcagAAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
EST: gi|71315045|gb|DR794147.1|DR794147
EST:     TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAG                         AAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
genomic: TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAGgtatggaata ... atgtttgcagAAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
EST: gi|50324664|gb|CO519790.1|CO519790
EST:     ACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAG                         AAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
genomic: ACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAGgtatggaata ... atgtttgcagAAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
EST: gi|32933227|gb|CF038039.1|CF038039
EST:     TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAG                         AAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
genomic: TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAGgtatggaata ... atgtttgcagAAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
EST: gi|60672399|gb|DN475149.1|DN475149
EST:     TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAG                         AAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
genomic: TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAGgtatggaata ... atgtttgcagAAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
EST: gi|32928793|gb|CF033605.1|CF033605
EST:     TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAG                         AAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
genomic: TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAGgtatggaata ... atgtttgcagAAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
EST: gi|113702970|gb|EE680474.1|EE680474
EST:     TTACATAGAAACAGTTTGGGATCATGCAGCTGGTTCAATTATTGTCACAG                         AAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
genomic: TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAGgtatggaata ... atgtttgcagAAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
EST: gi|101401650|gb|EB822490.1|EB822490
EST:     TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAG                         AAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
genomic: TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAGgtatggaata ... atgtttgcagAAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
EST: gi|5006217|gb|AI712279.1|AI712279
EST:     TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAG                         AAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
genomic: TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAGgtatggaata ... atgtttgcagAAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
EST: gi|71762698|gb|DR960635.1|DR960635
EST:     TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAG                         AAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
genomic: TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAGgtatggaata ... atgtttgcagAAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
EST: gi|88753523|gb|DY537664.1|DY537664
EST:     TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAG                         AAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
genomic: TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAGgtatggaata ... atgtttgcagAAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
EST: gi|50334940|gb|CO530066.1|CO530066
EST:     TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAG                         AAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
genomic: TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAGgtatggaata ... atgtttgcagAAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
EST: gi|9952566|gb|BE639254.1|BE639254
EST:     TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAG                         AAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
genomic: TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAGgtatggaata ... atgtttgcagAAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
EST: gi|6538959|gb|AW225098.1|AW225098
EST:     TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAG                         AAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
genomic: TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAGgtatggaata ... atgtttgcagAAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
EST: gi|32929425|gb|CF034237.1|CF034237
EST:     TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAG                         AAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
genomic: TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAGgtatggaata ... atgtttgcagAAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
EST: gi|89754586|gb|DY685314.1|DY685314
EST:     TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAG                         AAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
genomic: TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAGgtatggaata ... atgtttgcagAAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
EST: gi|86467594|gb|DY233964.1|DY233964
EST:     TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAG                         AAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
genomic: TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAGgtatggaata ... atgtttgcagAAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
EST: gi|6465587|gb|AW191182.1|AW191182
EST:     TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAG                         AAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
genomic: TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAGgtatggaata ... atgtttgcagAAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
EST: gi|211320348|gb|FL456168.1|FL456168
EST:     TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAG                         AAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
genomic: TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAGgtatggaata ... atgtttgcagAAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
EST: gi|93011705|gb|EB637225.1|EB637225
EST:     TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAG                         AAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
genomic: TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAGgtatggaata ... atgtttgcagAAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
EST: gi|9731309|gb|BE510061.1|BE510061
EST:     TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAG                         AAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
genomic: TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAGgtatggaata ... atgtttgcagAAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
EST: gi|71766942|gb|DR964879.1|DR964879
EST:     TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAG                         AAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
genomic: TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAGgtatggaata ... atgtttgcagAAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
EST: gi|40333919|gb|CK367989.1|CK367989
EST:     TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAG                         AAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
genomic: TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAGgtatggaata ... atgtttgcagAAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
EST: gi|44901269|gb|CK827814.1|CK827814
EST:     TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAG                         AAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
genomic: TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAGgtatggaata ... atgtttgcagAAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
EST: gi|149080860|gb|EE169940.2|EE169940
EST:     TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAG                         AAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
genomic: TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAGgtatggaata ... atgtttgcagAAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
EST: gi|76013308|gb|DT940478.1|DT940478
EST:     TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAG                         AAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
genomic: TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAGgtatggaata ... atgtttgcagAAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
EST: gi|60338966|gb|DN205939.1|DN205939
EST:     TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAG                         AAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
genomic: TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAGgtatggaata ... atgtttgcagAAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
EST: gi|32929156|gb|CF033968.1|CF033968
EST:     TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAG                         AAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
genomic: TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAGgtatggaata ... atgtttgcagAAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
EST: gi|50324663|gb|CO519789.1|CO519789
EST:     ACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAG                         AAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
genomic: ACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAGgtatggaata ... atgtttgcagAAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
EST: gi|78075089|gb|DV503523.1|DV503523
EST:     TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAG                         AAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA
genomic: TTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAGgtatggaata ... atgtttgcagAAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCA

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: 72

GCCCTAGCACGTGGTGATGGTGCCATTTTTCTGCGCATCCCGCACAAAAGTTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAGgtatggaata ... atgtttgcagAAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCAAAGGTAGATATCTTGATCGTGACAGAGGAATTATTGCAACAAACAAGCA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 21

GCCCTAGCACGTGGTGATGGTGCCATTTTTCTGCGCATCCCGCACAAAAGTTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAGgtatggaata ... atgtttgcagAAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCAAAGGTAGATATCTTGATCGTGACAGAGGAATTATTGCAACAAACAAGCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 28

GCCCTAGCACGTGGTGATGGTGCCATTTTTCTGCGCATCCCGCACAAAAGTTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAGgtatggaata ... atgtttgcagAAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCAAAGGTAGATATCTTGATCGTGACAGAGGAATTATTGCAACAAACAAGCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 42

GCCCTAGCACGTGGTGATGGTGCCATTTTTCTGCGCATCCCGCACAAAAGTTACATAGAAACAGTTTGGGATCATGCAGCTGGATCAATTATTGTCACAGgtatggaata ... atgtttgcagAAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCAAAGGTAGATATCTTGATCGTGACAGAGGAATTATTGCAACAAACAAGCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttataaaagatctctttactaatgccccccccccctccctatccgatgtttgcagAAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCAAAGGTAGATATCTTGATCGTGACAGAGGAATTATTGCAACAAACAAGCA
                tactaat  putative branch site (score: 42)
                        ccccccccccctccct  CT-rich tract
              tttactaat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggaatataattctattccaggaggcaattaaatcaacaacttataaaagatctctttactaatgccccccccccctccctatccgatgtttgcagAAGCTGGTGGCATGGTAAAAGATGCCGCAGGAAACGATTTGGATTTTTGCAAAGGTAGATATCTTGATCGTGACAGAGGAATTATTGCAACAAACAAGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA