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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtcccggttactttgttctaaatcattggtatgcccattgctccgcttgatttttgttgatctcgtgttctcggcatcggcggcagTGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCTGACATCATCGAGCACGAGAAGGCCCGCCAATGGAAG

Basic information

species Zea mays
transcript GRMZM2G135283_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G135283_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g52840.1 (Oryza sativa), 3'ss of exon 2
---------------------gtatgtcccggttactttgttc-taaatcattggtat-----gcccattgctccgcttgatttttgttgatctcgtgttctcggcatcggcggcagTGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCTGACATCATCGAGCACGAGAAGGCCCGCCAATGGAAG
                      | | ||  |  ||  |  | | |   || ||||| |     |    ||  | || ||  ||||| ||  | |  ||||   |   | ||  ||||||| | |||||| |||||||||||||||| ||||| || |||||||| || ||||||||||||||||||||||||||||||||||||
gtacgtgctctctctctctctctctctcttgactatgtgttccgttgctcgttggtgtctgtggtttgttcattcgttttttttttattattattttgtttgtg-tgttggatgcagTGGCCGAAGCAGCTGAACGCGCCGCTGGAGGAGGTGGATCCCGAGATCGCCGACATCATCGAGCACGAGAAGGCCCGCCAATGGAAG
















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|211286152|gb|FL173733.1|FL173733
EST:     GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACC                         TGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
genomic: GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACCgtatgtcccg ... tcggcggcagTGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
EST: gi|148946029|gb|EC891328.2|EC891328
EST:     GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACC                         TGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
genomic: GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACCgtatgtcccg ... tcggcggcagTGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
EST: gi|211286141|gb|FL173722.1|FL173722
EST:     GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACC                         TGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
genomic: GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACCgtatgtcccg ... tcggcggcagTGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
EST: gi|211379736|gb|FL173736.1|FL173736
EST:     GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACC                         TGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
genomic: GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACCgtatgtcccg ... tcggcggcagTGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
EST: gi|211379741|gb|FL173741.1|FL173741
EST:     GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACC                         TGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
genomic: GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACCgtatgtcccg ... tcggcggcagTGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
EST: gi|21987802|gb|BQ779330.1|BQ779330
EST:     GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACC                         TGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
genomic: GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACCgtatgtcccg ... tcggcggcagTGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
EST: gi|211284346|gb|FL173719.1|FL173719
EST:     GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACC                         TGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
genomic: GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACCgtatgtcccg ... tcggcggcagTGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
EST: gi|149078907|gb|EE167727.2|EE167727
EST:     GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACC                         TGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
genomic: GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACCgtatgtcccg ... tcggcggcagTGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
EST: gi|211382375|gb|FL173752.1|FL173752
EST:     GCGTCCMTTCMGGCGAC-GAGGAGAGATCCGGAATCACC                         TGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
genomic: GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACCgtatgtcccg ... tcggcggcagTGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
EST: gi|211379738|gb|FL173738.1|FL173738
EST:     GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACC                         TGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
genomic: GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACCgtatgtcccg ... tcggcggcagTGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
EST: gi|211379739|gb|FL173739.1|FL173739
EST:     GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACC                         TGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
genomic: GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACCgtatgtcccg ... tcggcggcagTGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
EST: gi|211286153|gb|FL173734.1|FL173734
EST:     GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACC                         TGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
genomic: GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACCgtatgtcccg ... tcggcggcagTGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
EST: gi|211379748|gb|FL173748.1|FL173748
EST:     GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACC                         TGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
genomic: GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACCgtatgtcccg ... tcggcggcagTGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
EST: gi|211286143|gb|FL173724.1|FL173724
EST:     GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACC                         TGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
genomic: GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACCgtatgtcccg ... tcggcggcagTGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
EST: gi|149012532|gb|EE042603.2|EE042603
EST:     GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACC                         TGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
genomic: GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACCgtatgtcccg ... tcggcggcagTGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
EST: gi|211379742|gb|FL173742.1|FL173742
EST:     GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACC                         TGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
genomic: GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACCgtatgtcccg ... tcggcggcagTGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
EST: gi|89761747|gb|DY689638.1|DY689638
EST:     GCGTCCCTTCCGGCGACGGAGGAAAGATCCGGAATCACC                         TGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
genomic: GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACCgtatgtcccg ... tcggcggcagTGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
EST: gi|211379749|gb|FL173749.1|FL173749
EST:     GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACC                         TGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
genomic: GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACCgtatgtcccg ... tcggcggcagTGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
EST: gi|211286154|gb|FL173735.1|FL173735
EST:     GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACC                         TGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
genomic: GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACCgtatgtcccg ... tcggcggcagTGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
EST: gi|211379740|gb|FL173740.1|FL173740
EST:     GCGTCTCTTCCGGCGACGGAGGAGAGATCCGGAATCACC                         TGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
genomic: GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACCgtatgtcccg ... tcggcggcagTGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
EST: gi|211379747|gb|FL173747.1|FL173747
EST:     GCGTCCCTTCCGGCGAC-GAGGAGAGATCCGGAATCACC                         TGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
genomic: GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACCgtatgtcccg ... tcggcggcagTGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
EST: gi|211379745|gb|FL173745.1|FL173745
EST:     GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACC                         TGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
genomic: GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACCgtatgtcccg ... tcggcggcagTGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
EST: gi|211379746|gb|FL173746.1|FL173746
EST:     GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACC                         TGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
genomic: GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACCgtatgtcccg ... tcggcggcagTGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
EST: gi|211286148|gb|FL173729.1|FL173729
EST:     GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACC                         TGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
genomic: GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACCgtatgtcccg ... tcggcggcagTGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
EST: gi|148969981|gb|EE020895.2|EE020895
EST:     GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACC                         TGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
genomic: GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACCgtatgtcccg ... tcggcggcagTGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
EST: gi|71299012|gb|DR785498.1|DR785498
EST:     GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACC                         TGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
genomic: GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACCgtatgtcccg ... tcggcggcagTGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
EST: gi|211379743|gb|FL173743.1|FL173743
EST:     GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACC                         TGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
genomic: GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACCgtatgtcccg ... tcggcggcagTGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
EST: gi|211286151|gb|FL173732.1|FL173732
EST:     GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACC                         TGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
genomic: GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACCgtatgtcccg ... tcggcggcagTGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
EST: gi|211284347|gb|FL173720.1|FL173720
EST:     GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACC                         TGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
genomic: GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACCgtatgtcccg ... tcggcggcagTGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
EST: gi|211286145|gb|FL173726.1|FL173726
EST:     GCGTCCCTTCCGGCGAC-GAGGAGAGATCCGGAATCACC                         TGGACTAAGCAGTCGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
genomic: GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACCgtatgtcccg ... tcggcggcagTGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
EST: gi|148947246|gb|EC892606.2|EC892606
EST:     GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACC                         TGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
genomic: GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACCgtatgtcccg ... tcggcggcagTGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
EST: gi|211382374|gb|FL173751.1|FL173751
EST:     GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACC                         TGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
genomic: GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACCgtatgtcccg ... tcggcggcagTGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
EST: gi|149081312|gb|EE170425.2|EE170425
EST:     GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACC                         TGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
genomic: GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACCgtatgtcccg ... tcggcggcagTGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
EST: gi|211379744|gb|FL173744.1|FL173744
EST:     GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACC                         TGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
genomic: GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACCgtatgtcccg ... tcggcggcagTGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
EST: gi|211379750|gb|FL173750.1|FL173750
EST:     GCGTCCCTTCCGGCGAC-GAGGAGAGATCCGGAATCACC                         TGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
genomic: GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACCgtatgtcccg ... tcggcggcagTGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
EST: gi|148945831|gb|EC891120.2|EC891120
EST:     GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACC                         TGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
genomic: GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACCgtatgtcccg ... tcggcggcagTGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
EST: gi|148973319|gb|EE024404.2|EE024404
EST:     GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACC                         TGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
genomic: GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACCgtatgtcccg ... tcggcggcagTGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
EST: gi|211379737|gb|FL173737.1|FL173737
EST:     GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACC                         TGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
genomic: GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACCgtatgtcccg ... tcggcggcagTGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
EST: gi|149089957|gb|EE179246.2|EE179246
EST:     GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACC                         TGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
genomic: GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACCgtatgtcccg ... tcggcggcagTGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
EST: gi|211286140|gb|FL173721.1|FL173721
EST:     GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACC                         TGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT
genomic: GCGTCCCTTCCGGCGACGGAGGAGAGATCCGGAATCACCgtatgtcccg ... tcggcggcagTGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcccattgctccgcttgatttttgttgatctcgtgttctcggcatcggcggcagTGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCTGACATCATCGAGCACGAGAAGGCCCGCCAATGGAAG
                       tgttgat  putative branch site (score: 4)
               ttgattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtcccggttactttgttctaaatcattggtatgcccattgctccgcttgatttttgttgatctcgtgttctcggcatcggcggcagTGGACTAAGCAGTTGAACGCGCCGCTGGAAGAGGTCGACCCCGAGATTGCTGACATCATCGAGCACGAGAAGGCCCGCCAATGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG