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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCGTGCTCAGCGTCGGCAACCTCTCCACCCAGTACGCTTGGGCCTATGTGGGCCTCTCCGTCACTGAGGTCATCAGCTCCAGCATGGTGGTGGTCATAGgtaggttcgcatcatcgttagtaataatcatcacatgagagggaagggaaagggagggacctcaatgatcatgcacatttgcttcttctcccattaaaaa...

Basic information

species Zea mays
transcript GRMZM2G025528_T04
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G025528_T04 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os12g31850.3 (Oryza sativa), 5'ss of exon 3
GTCGTGCTCAGCGTCGGCAACCTCTCCACCCAGTACGCTTGGGCCTATGTGGGCCTCTCCGTCACTGAGGTCATCAGCTCCAGCATGGTGGTGGTCATAGgtaggttcgcatcatcgttagtaataat-catcacatgagagggaagggaaagggagggacctcaatga--tcatgcacatttgcttcttctcccattaaaaa
|| ||||||||  | || |||||||| || ||||| || ||||| ||||| || ||||| || ||||||||||||||||| || ||||| || || ||||||||||     |  || ||   || | | || || ||   |  |   |           |    |   |  | | | | | ||  |  ||||     | | | 
GTTGTGCTCAGTATAGGGAACCTCTCTACTCAGTATGCATGGGCATATGTAGGTCTCTCAGTGACTGAGGTCATCAGCTCAAGTATGGTTGTTGTAATAGgtaggtaaaacttctcttttacaacactgcaacatatattattgtttgatttttttttaagtaaagaaaattgagggaaaattattgattctt--ggtgata-
















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|148994757|gb|EE034229.2|EE034229
EST:     GGGCCTCTCCGTCACTGAGGTCATCAGCTCCAGCATGGTGGTGGTCATAG                         GCACCACGCTGAACTACTTCCTGGACAACCGCATCAACAGGGCAGAGATTC
genomic: GGGCCTCTCCGTCACTGAGGTCATCAGCTCCAGCATGGTGGTGGTCATAGgtaggttcgc ... tgttcttcagGCACCACGCTGAACTACTTCCTGGACAACCGCATCAACAGGGCAGAGATTC
EST: gi|148970951|gb|EE021758.2|EE021758
EST:     GGGCCTCTCCGTCACTGAGGTCATCAGCTCCAGCATGGTGGTGGTCATAG                         GCACCACGCTGAACTACTTCCTGGACAACCGCATCAACAGGGCAGAGATTC
genomic: GGGCCTCTCCGTCACTGAGGTCATCAGCTCCAGCATGGTGGTGGTCATAGgtaggttcgc ... tgttcttcagGCACCACGCTGAACTACTTCCTGGACAACCGCATCAACAGGGCAGAGATTC
EST: gi|148936313|gb|EC880396.2|EC880396
EST:     GGGCCTCTCCGTCACTGAGGTCATCAGCTCCAGCATGGTGGTGGTCATAG                         GCACCACGCTGAACTACTTCCTGGACAACCGCATCAACAGGGCAGAGATTC
genomic: GGGCCTCTCCGTCACTGAGGTCATCAGCTCCAGCATGGTGGTGGTCATAGgtaggttcgc ... tgttcttcagGCACCACGCTGAACTACTTCCTGGACAACCGCATCAACAGGGCAGAGATTC
EST: gi|71313732|gb|DR793456.1|DR793456
EST:     GGGCCTCTCCGTCACTGAGGTCATCAGCTCCAGCATGGTGGTGGTCATAG                         GCACCACGCTGAACTACTTCCTGGACAACCGCCTCAACAGGGCAGAGATTC
genomic: GGGCCTCTCCGTCACTGAGGTCATCAGCTCCAGCATGGTGGTGGTCATAGgtaggttcgc ... tgttcttcagGCACCACGCTGAACTACTTCCTGGACAACCGCATCAACAGGGCAGAGATTC
EST: gi|148957676|gb|EC903790.2|EC903790
EST:     GGGCCTCTCCGTCACTGAGGTCATCAGCTCCAGCATGGTGGTGGTCATAG                         GCACCACGCTGAACTACTTCCTGGACAACCGCATCAACAGGGCAGAGATTC
genomic: GGGCCTCTCCGTCACTGAGGTCATCAGCTCCAGCATGGTGGTGGTCATAGgtaggttcgc ... tgttcttcagGCACCACGCTGAACTACTTCCTGGACAACCGCATCAACAGGGCAGAGATTC
EST: gi|149086713|gb|EE176255.2|EE176255
EST:     GGGCCTCTCCGTCACTGAGGTCATCAGCTCCAGCATGGTGGTGGTCATAG                         GCACCACGCTGAACTACTTCCTGGACAACCGCATCAACAGGGCAGAGATTC
genomic: GGGCCTCTCCGTCACTGAGGTCATCAGCTCCAGCATGGTGGTGGTCATAGgtaggttcgc ... tgttcttcagGCACCACGCTGAACTACTTCCTGGACAACCGCATCAACAGGGCAGAGATTC
EST: gi|148953239|gb|EE152723.2|EE152723
EST:     GGGCCTCTCCGTCACTGAGGTCATCAGCTCCAGCATGGTGGTGGTCATAG                         GCACCACGCTGAACTACTTCCTGGACAACCGCATCAACAGGGCAGAGATTC
genomic: GGGCCTCTCCGTCACTGAGGTCATCAGCTCCAGCATGGTGGTGGTCATAGgtaggttcgc ... tgttcttcagGCACCACGCTGAACTACTTCCTGGACAACCGCATCAACAGGGCAGAGATTC
EST: gi|211063921|gb|FK969107.1|FK969107
EST:     GGGCCTCTCCGTCACTGAGGTCATCAGCTCCAGCATGGTGGTGGTCATAG                         GCACCACGCTGAACTACTTCCTGGACAACCGCATCAACAGGGCAGAGATTC
genomic: GGGCCTCTCCGTCACTGAGGTCATCAGCTCCAGCATGGTGGTGGTCATAGgtaggttcgc ... tgttcttcagGCACCACGCTGAACTACTTCCTGGACAACCGCATCAACAGGGCAGAGATTC
EST: gi|149083933|gb|EE173311.2|EE173311
EST:     GGGCCTCTCCGTCACTGAGGTCATCAGCTCCAGCATGGTGGTGGTCATAG                         GCACCACGCTGAACTACTTCCTGGACAACCGCATCAACAGGGCAGAGATTC
genomic: GGGCCTCTCCGTCACTGAGGTCATCAGCTCCAGCATGGTGGTGGTCATAGgtaggttcgc ... tgttcttcagGCACCACGCTGAACTACTTCCTGGACAACCGCATCAACAGGGCAGAGATTC
EST: gi|50339614|gb|CO534740.1|CO534740
EST:     GGGCCTCTCCGTCACTGAGGTCATCAGCTCCAGCATGGTGGTGGTCATAG                         GCACCACGCTGAACTACTTCCTGGACAACCGCATCAACAGGGCAGAGATTC
genomic: GGGCCTCTCCGTCACTGAGGTCATCAGCTCCAGCATGGTGGTGGTCATAGgtaggttcgc ... tgttcttcagGCACCACGCTGAACTACTTCCTGGACAACCGCATCAACAGGGCAGAGATTC
EST: gi|71330461|gb|DR801989.1|DR801989
EST:     GGGCCTCTCCGTCACTGAGGTCATCAGCTCCAGCATGGTGGTGGTCATAG                         GCACCACGCTGAACTACTTCCTGGACAACCGCATCAACAGGGCAGAGATTC
genomic: GGGCCTCTCCGTCACTGAGGTCATCAGCTCCAGCATGGTGGTGGTCATAGgtaggttcgc ... tgttcttcagGCACCACGCTGAACTACTTCCTGGACAACCGCATCAACAGGGCAGAGATTC
EST: gi|149072804|gb|EE161051.2|EE161051
EST:     GGGCCTCTCCGTCACTGAGGTCATCAGCTCCAGCATGGTGGTGGTCATAG                         GCACCACGCTGAACTACTTCCTGGACAACCGCATCAACAGGGCAGAGATTC
genomic: GGGCCTCTCCGTCACTGAGGTCATCAGCTCCAGCATGGTGGTGGTCATAGgtaggttcgc ... tgttcttcagGCACCACGCTGAACTACTTCCTGGACAACCGCATCAACAGGGCAGAGATTC
EST: gi|93014257|gb|EB639777.1|EB639777
EST:     GGGCCTCTCCGTCACTGAGGTCATCAGCTCCCGCATGGTGGTGGTCATAG                         GCACCACGCTGAACTACTTCCTGGACAACCGCATCAACAGG
genomic: GGGCCTCTCCGTCACTGAGGTCATCAGCTCCAGCATGGTGGTGGTCATAGgtaggttcgc ... tgttcttcagGCACCACGCTGAACTACTTCCTGGACAACCGCATCAACAGG
EST: gi|148995735|gb|EE034963.2|EE034963
EST:     GGGCCTCTCCGTCACTGAGGTCATCAGCTCCAGCATGGTGGTGGTCATAG                         GCACCACGCTGAACTACTTCCTGGACAACCGCATCAACAGGGCAGAGATTC
genomic: GGGCCTCTCCGTCACTGAGGTCATCAGCTCCAGCATGGTGGTGGTCATAGgtaggttcgc ... tgttcttcagGCACCACGCTGAACTACTTCCTGGACAACCGCATCAACAGGGCAGAGATTC
EST: gi|148982279|gb|EE028228.2|EE028228
EST:     GGGCCTCTCCGTCACTGAGGTCATCAGCTCCAGCATGGTGGTGGTCATAG                         GCACCACGCTGAACTACTTCCTGGACAACCGCATCAACAGGGCAGAGATTC
genomic: GGGCCTCTCCGTCACTGAGGTCATCAGCTCCAGCATGGTGGTGGTCATAGgtaggttcgc ... tgttcttcagGCACCACGCTGAACTACTTCCTGGACAACCGCATCAACAGGGCAGAGATTC
EST: gi|71446963|gb|DR828013.1|DR828013
EST:     GGGCCTCTCCGTCACTGAGGTCATCAGCTCCAGCATGGTGGTGGTCATAG                         GCACCACGCTGAACTACTTCCTGGACAACCGCATCAACAGGGCAGAGATTC
genomic: GGGCCTCTCCGTCACTGAGGTCATCAGCTCCAGCATGGTGGTGGTCATAGgtaggttcgc ... tgttcttcagGCACCACGCTGAACTACTTCCTGGACAACCGCATCAACAGGGCAGAGATTC
EST: gi|32923995|gb|CF028807.1|CF028807
EST:     GGGCCTCTCCGTCACTGAGGTCATCAGCTCCAGCATGGTGGTGGTCATAG                         GCACCACGCTGAACTACTTCCTGGACAACCGCATCAACAGGGCAGAGATTC
genomic: GGGCCTCTCCGTCACTGAGGTCATCAGCTCCAGCATGGTGGTGGTCATAGgtaggttcgc ... tgttcttcagGCACCACGCTGAACTACTTCCTGGACAACCGCATCAACAGGGCAGAGATTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCGTGCTCAGCGTCGGCAACCTCTCCACCCAGTACGCTTGGGCCTATGTGGGCCTCTCCGTCACTGAGGTCATCAGCTCCAGCATGGTGGTGGTCATAGgtaggttcgcatcatcgttagtaataatcatcacatgagagggaagggaaagggagggacctcaatgatcatgcacatttgcttcttctcccattaaaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG