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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaacagcgtcacacagagcaaatggaacacttctaaaagcattcttcttcccctaattgaactttaccttgtggctgaatagaaagcaatttagtgcagGCGTCCATGTTGATACTGTTGTCATGAATCCTCCCTTTGGTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAG

Basic information

species Zea mays
transcript GRMZM2G113640_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G113640_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g06730.1 (Oryza sativa), 3'ss of exon 5
gaaacagcgtcacacagagcaaatggaacacttctaaa----agcattcttcttcccctaattgaactttaccttgtggctgaatagaaagcaatttagtgcagGCGTCCATGTTGATACTGTTGTCATGAATCCTCCCTTTGGTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAG
     |  || |   | |  ||||   | | || || |    ||| |   |  |  |   ||||||      |   ||      |||  | |  || |  | |||| | | |||||| |||||||||||||||||||||||||| ||| | || || ||||| |||||||| ||| | ||||||| | || ||
--tgaatggttattgaaacaaaatcatatatttatacacataagcgtagatgctttcaacattgaaaagcttccc-tgatcttttagctacctgttgaa-gtagGCCTTCTTGTTGACACTGTTGTCATGAATCCTCCCTTTGGGACAAGCAGAAAAGGAGCTGACATGGAATTCATTTCTATGGGCATGAAG

upper sequence: GRMZM2G113640_T03 (Zea mays), 3'ss of exon 4
lower sequence: AT4G28830.1 (Arabidopsis thaliana), 3'ss of exon 5
gaaacagcgtcacacagagcaaatggaacacttctaaaagcattcttcttcccctaattgaactttaccttgtggctgaatagaaagcaatttagtgcagGCGTCCATGTTGATACTGTTGTCATGAATCCTCCCTTTGGTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAG
   |||      |    |    |    |  |  | ||||| |   |||| ||  |||    | |||    |||||||  ||  |       ||  |  |||| |   ||| ||||| ||||| ||||| ||||| ||||||||||| | ||| ||||| ||||||||||| ||||||  |||  || ||
-gtacaatcctcctttcatttcagttcattcaacgaaaag-aagattctaccggtaac---atttt----tgtggctccatgaa-------ttgttttagGCCTGATTGTGGATACGGTTGTAATGAACCCTCCATTTGGTACACGGAAGAAAGGAGCTGACATGGAGTTTCTCTCTGCGGCAATGAAG

upper sequence: GRMZM2G113640_T03 (Zea mays), 3'ss of exon 4
lower sequence: Vv11s0016g03520.t01 (Vitis vinifera), 3'ss of exon 5
gaaacagcgt-cacacagagcaaatgga-acacttctaaaagcattcttcttcccctaattgaactttaccttgtggctgaatagaaagcaatttagtgcagGCGTCCATGTTGATACTGTTGTCATGAATCCTCCCTTTGGTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAG
  ||  |  |  |          ||  |  | |||| | |   |||  |   |   |  || || ||||  |    |    |  ||       ||| || |||      ||||||||||||||| ||||||||||| ||||| ||||| | ||| || || |||||||| || ||| || |||| ||| ||
-taattgtatatatgttctctgtatacatgctcttcaacatatattactgcacttgtcttttaattttatgtccatgtaacaatgattatctctta-tgtagGTCAAATTGTTGATACTGTTGTAATGAATCCTCCATTTGGAACACGGAAGAAGGGGGCTGACATGGATTTTCTCGCTGTGGCTTTGAAG

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|211270654|gb|FL248444.1|FL248444
EST:     GCTGATCTGGAGCTGGACATCGATTTAGTTTGGTCTGACATAAAGAACTTAAATCTGAAAG
genomic: gCTGGACATCGATTAAATCTGAAAGgtattgttct ... tttagtgcagGCGTCCATGTT
EST: gi|71438832|gb|DR819882.1|DR819882
EST:     GCTGATCTGGAGCTGGACATCGATTTAGTTTGGTCTGACATAAAGAACTTAAATCTGAAAG
genomic: gCTGGACATCGATTAAATCTGAAAGgtattgttct ... tttagtgcagGCGTCCATGTT
EST: gi|211270652|gb|FL248442.1|FL248442
EST:     GCTGATCTGGAGCTGGACATCGATTTAGTTTGGTCTGACATAAAGAACTTAAATCTGAWAG
genomic: gCTGGACATCGATTAAATCTGAAAGgtattgttct ... tttagtgcagGCGTCCATGTT
EST: gi|213171204|gb|FM188301.1|FM188301
EST:     TAAATCTGAAAG                         GCGTCCATGTTGATACTGTTGTCATGAATCCTCCCTTTGGTACACGAAGGA
genomic: TAAATCTGAAAGgtattgttct ... tttagtgcagGCGTCCATGTTGATACTGTTGTCATGAATCCTCCCTTTGGTACACGAAGGA
EST: gi|211270656|gb|FL248446.1|FL248446
EST:     GCTGATCTGGAGCTGGACATCGATTTAGTTTGGTCTGACATAAAGAACTTAAATCTGAAAG
genomic: gCTGGACATCGATTAAATCTGAAAGgtattgttct ... tttagtgcagGCGTCCATGTT
EST: gi|76012002|gb|DT939172.1|DT939172
EST:     GCTGATCTGGAGCTGGACATCGATTTAGTTTGGTCTGACATAAAGAACTTAAATCTGAAAG
genomic: gCTGGACATCGATTAAATCTGAAAGgtattgttct ... tttagtgcagGCGTCCATGTT
EST: gi|211270651|gb|FL248441.1|FL248441
EST:     GCTGATCTGGAGCTGGACATCGATTTAGTTTGGTCTGACATAAAGAACTTAAATCTGAAAG
genomic: gCTGGACATCGATTAAATCTGAAAGgtattgttct ... tttagtgcagGCGTCCATGTT
EST: gi|6227108|gb|AW155812.1|AW155812
EST:     CTGGACATCGATTTAGTTTGGTCTGACATAAAGAACTTAAATCTGAAAG        
genomic: TGGTCTGACATAAAGAACTTAAATCTGAAAGgtattgttct ... tttagtgcagG
EST: gi|50327796|gb|CO522922.1|CO522922
EST:     GCTGATCTGGAGCTGGACATCGATTTAGTTTGGTCTGACATAAAGAACTTAAATCTGAAAG
genomic: gCTGGACATCGATTAAATCTGAAAGgtattgttct ... tttagtgcagGCGTCCATGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttcccctaattgaactttaccttgtggctgaatagaaagcaatttagtgcagGCGTCCATGTTGATACTGTTGTCATGAATCCTCCCTTTGGTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAG
      ccctaat  putative branch site (score: 3)
         taattgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaaacagcgtcacacagagcaaatggaacacttctaaaagcattcttcttcccctaattgaactttaccttgtggctgaatagaaagcaatttagtgcagGCGTCCATGTTGATACTGTTGTCATGAATCCTCCCTTTGGTACACGAAGGAATGGAGCAGACATGGAGTTCCTCTCTATGGCCTTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA