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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtagttccttttgctaattggtgcctttgtgcactgagcttctatgtaatatctactctaacttgttttgaaattttaaatctctttcagGCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCTAACAAGCAAGACATGGTATGTTCAGCCACATTTTCTCTGGAGCATTTAT

Basic information

species Zea mays
transcript GRMZM2G011518_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011518_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os10g42940.1 (Oryza sativa), 3'ss of exon 4
--------------gtttgtagttccttttgc--taattggtgcct--ttgtgcactgagcttctatgtaatatctactctaacttgttttgaaattttaaatctctttcagGCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCTAACAAGCAAGACATGGTATGTTCAGCCACATTTTCTCTGGAGCATTTAT
               |   || ||  || ||    |    |||  |  || ||||||||  ||   ||   | | | |||||||||  | ||   |  |   | |||||||||| || || |||||||||||||||||||| |||||  |||||||||||||||||||||||||||||                                  
gtttacatatatgtataaataatttattatgaggcagcaagtgtttgcttctgcactgacatttgttgccttgt-tgctctaacttactgtgtggtaatc--tgtctttcagGCCATTATTAATGACCCTTTTATGCTTAATAGTGTTCTATTGGTGTTTGCTAACAAGCAAGACATG----------------------------------
















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|211535182|gb|FL238609.1|FL238609
EST:     TTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAG                         GCTATAATCAATGACCCTTTTATGCTTAACAGTGTGT
genomic: TTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAGgtttgtagtt ... tctctttcagGCTATAATCAATGACCCTTTTATGCTTAACAGTGTGT
EST: gi|21330796|gb|BQ486177.1|BQ486177
EST:     TTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAG                         GCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCT
genomic: TTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAGgtttgtagtt ... tctctttcagGCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCT
EST: gi|60399000|gb|DN231816.1|DN231816
EST:     TTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAG                         GCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCT
genomic: TTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAGgtttgtagtt ... tctctttcagGCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCT
EST: gi|211532193|gb|FL238605.1|FL238605
EST:     TTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAG                         GCTATAATCAATGAACCTTTTATGCTTAACAGTGTGTT
genomic: TTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAGgtttgtagtt ... tctctttcagGCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTT
EST: gi|211532190|gb|FL238602.1|FL238602
EST:     TTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAG                         GCTATAATCAATGACCCTTTTATGCT
genomic: TTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAGgtttgtagtt ... tctctttcagGCTATAATCAATGACCCTTTTATGCT
EST: gi|211535183|gb|FL238610.1|FL238610
EST:     TGATTCACTGGATAGAGAGAGAATCGGGGAGAGCCAGGGCGTAGTTTCAG                         GCTATAATCAATGACCCTTTTATGCTTAACAGTGTG
genomic: TGATTCACTGGATAGAGAGAGAATCGGG-AGAGCCAGGGCGGAGTTTCAGgtttgtagtt ... tctctttcagGCTATAATCAATGACCCTTTTATGCTTAACAGTGTG
EST: gi|76016402|gb|DT943572.1|DT943572
EST:     TTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAG                         GCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCT
genomic: TTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAGgtttgtagtt ... tctctttcagGCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCT
EST: gi|32802499|gb|CD954735.1|CD954735
EST:     TTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAG                         GCTATAATCAATGACCCTTTTATGCTTA
genomic: TTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAGgtttgtagtt ... tctctttcagGCTATAATCAATGACCCTTTTATGCTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagcttctatgtaatatctactctaacttgttttgaaattttaaatctctttcagGCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCTAACAAGCAAGACATGGTATGTTCAGCCACATTTTCTCTGGAGCATTTAT
                    ctctaac  putative branch site (score: 2)
                                             tctctttc  putative PPT
                       taacttgttttgaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtagttccttttgctaattggtgcctttgtgcactgagcttctatgtaatatctactctaacttgttttgaaattttaaatctctttcagGCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCTAACAAGCAAGACATGGTATGTTCAGCCACATTTTCTCTGGAGCATTTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA