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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtggatatgtactagtatgttctcatgtgacatctttttgcattttacttgaaaaactctactgagaatgcataatttcattttcctcttgtaatccagGTAGCAACCATTTCTGCAAACGGTGAAAAGGAAATTGGAGATCTAATATCAAAAGCCATGGAAAAAGTTGGAAAGGATGGAGTCATTACTATTGTT

Basic information

species Zea mays
transcript GRMZM2G074790_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074790_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g46290.1 (Oryza sativa), 3'ss of exon 4
--tgtggatatgtactagtatgttctcatgtgacatctttttgcattttacttgaaaaactctac---tgagaatgcataatttcattttcctcttgtaatccagGTAGCAACCATTTCTGCAAACGGTGAAAAGGAAATTGGAGATCTAATATCAAAAGCCATGGAAAAAGTTGGAAAGGATGGAGTCATTACTATTGTT
  |    |  |  |||  ||| ||        || |    | | | ||  |  | |    |  |    | |||||   | ||||||| || ||   |||| |||||||||||| ||||||||||| || ||||||||||| |||||| | |||||||| || |||||||| ||||||||||||||||| |||||||||  |
aataatcactttgactc-tatattactgca-aactttccatagtaattatcccgcattcttgcatgcttaagaatatgttatttcatatttct---gtaaaccagGTAGCAACTATTTCTGCAAATGGAGAAAAGGAAATAGGAGATTTGATATCAAAGGCGATGGAAAAGGTTGGAAAGGATGGAGTTATTACTATTACT
















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|18450792|gb|BM429070.1|BM429070
EST:     ACCTCAAAAGTAAAGCGTGGAAGATTAATTCTCCAGAAGAAATTAACCAG                         GTAGCAACCATTTCTGCAAACGGTGAAAAGGAAATTGGAGATCTAATATCA
genomic: ACCTCAAAAGTAAAGCGTGGAAGATTAATTCTCCAGAAGAAATTAACCAGgtgagatact ... tgtaatccagGTAGCAACCATTTCTGCAAACGGTGAAAAGGAAATTGGAGATCTAATATCA
EST: gi|149014572|gb|EE044215.2|EE044215
EST:     ACCTCAAAAGTAAAGCGTGGAAGATTAATTCTCCAGAAGAAATTAACCAG                         GTAGCAACCATTTCTGCAAACGGTGAAAAGGAAATTGGAGATCTAATATCA
genomic: ACCTCAAAAGTAAAGCGTGGAAGATTAATTCTCCAGAAGAAATTAACCAGgtgagatact ... tgtaatccagGTAGCAACCATTTCTGCAAACGGTGAAAAGGAAATTGGAGATCTAATATCA
EST: gi|71438972|gb|DR820022.1|DR820022
EST:     ACCTCAAAAGTAAAGCGTGGAAGATTAATTCTCCAGAAGAAATTAACCAG                         GTAGCAACCATTTCTGCAAACGGTGAAAAGGAAATTGGAGATCTAATATCA
genomic: ACCTCAAAAGTAAAGCGTGGAAGATTAATTCTCCAGAAGAAATTAACCAGgtgagatact ... tgtaatccagGTAGCAACCATTTCTGCAAACGGTGAAAAGGAAATTGGAGATCTAATATCA
EST: gi|18649393|gb|BM498212.1|BM498212
EST:     ACCTCAAAAGTAAAGCGTGGAAGATTAATTCTCCAGAAGAAATTAACCAG                         GTAGCAACCATTTCTGCAAACGGTGAAAAGGAAATTGGAGATCTAATATCA
genomic: ACCTCAAAAGTAAAGCGTGGAAGATTAATTCTCCAGAAGAAATTAACCAGgtgagatact ... tgtaatccagGTAGCAACCATTTCTGCAAACGGTGAAAAGGAAATTGGAGATCTAATATCA
EST: gi|149083932|gb|EE173310.2|EE173310
EST:     ACCTCAAAAGTAAAGCGTGGAAGATTAATTCTCCAGAAGAAATTAACCAG                         GTAGCAACCATTTCTGCAAACG
genomic: ACCTCAAAAGTAAAGCGTGGAAGATTAATTCTCCAGAAGAAATTAACCAGgtgagatact ... tgtaatccagGTAGCAACCATTTCTGCAAACG
EST: gi|149051769|gb|EE155894.2|EE155894
EST:     ACCTCAAAAGTAAAGCGTGGAAGATTAATTCTCCAGAAGAAATTAACCAG                         GTAGCAACCATTTCTGCAAACGGTGAAAAGGAAATTGGAGATCTAATATCA
genomic: ACCTCAAAAGTAAAGCGTGGAAGATTAATTCTCCAGAAGAAATTAACCAGgtgagatact ... tgtaatccagGTAGCAACCATTTCTGCAAACGGTGAAAAGGAAATTGGAGATCTAATATCA
EST: gi|148966460|gb|EE017469.2|EE017469
EST:     ACCTCAAAAGTAAAGCGTGGAAGATTAATTCTCCAGAAGAAATTAACCAG                         GTAGCAACCATTTCTGCAAACGGTGAAAAGGAAATTGGAGATCTAATATCA
genomic: ACCTCAAAAGTAAAGCGTGGAAGATTAATTCTCCAGAAGAAATTAACCAGgtgagatact ... tgtaatccagGTAGCAACCATTTCTGCAAACGGTGAAAAGGAAATTGGAGATCTAATATCA
EST: gi|78118616|gb|DV537000.1|DV537000
EST:     ACCTCAAAAGTAAAGCGTGGAAGATTAATTCTCCAGAAGAAATTAACCAG                         GTAGCAACCATTTCTGCAAACGGTGAAAAGGAAATCGGAGATCTAATATCA
genomic: ACCTCAAAAGTAAAGCGTGGAAGATTAATTCTCCAGAAGAAATTAACCAGgtgagatact ... tgtaatccagGTAGCAACCATTTCTGCAAACGGTGAAAAGGAAATTGGAGATCTAATATCA
EST: gi|18649617|gb|BM498436.1|BM498436
EST:     ACCTCAAAAGTAAAGCGTGGAAGATTAATTCTCCAGAAGAAATTAACCAG                         GTAGCAACCATTTCTGCAAACGGTGAAAAGGAAATTGGAGATCTAATATCA
genomic: ACCTCAAAAGTAAAGCGTGGAAGATTAATTCTCCAGAAGAAATTAACCAGgtgagatact ... tgtaatccagGTAGCAACCATTTCTGCAAACGGTGAAAAGGAAATTGGAGATCTAATATCA
EST: gi|148937683|gb|EC881881.2|EC881881
EST:     ACCTCAAAAGTAAAGCGTGGAAGATTAATTCTCCAGAAGAAATTAACCAG                         GTAGCAACCATTTCTGCAAACGGTGAAAAGGAAATTGGAGATCTAATATCA
genomic: ACCTCAAAAGTAAAGCGTGGAAGATTAATTCTCCAGAAGAAATTAACCAGgtgagatact ... tgtaatccagGTAGCAACCATTTCTGCAAACGGTGAAAAGGAAATTGGAGATCTAATATCA
EST: gi|31351656|gb|CD436013.1|CD436013
EST:     ACCTCAAAAGTAAAGCGTGGAAGATTAATTCTCCAGAAGAAATTAACCAG                         GTAGCAACCATTTCTGCAAACGGTGAAAAGGAAATTGGAGATCTAATATCA
genomic: ACCTCAAAAGTAAAGCGTGGAAGATTAATTCTCCAGAAGAAATTAACCAGgtgagatact ... tgtaatccagGTAGCAACCATTTCTGCAAACGGTGAAAAGGAAATTGGAGATCTAATATCA
EST: gi|31350305|gb|CD434662.1|CD434662
EST:     ACCTCAAAAGTAAAGCGTGGAAGATTAATTCTCCAGAAGAAATTAACCAG                         GTAGCAACCATTTCTGCAAACGGTGAAAAGGAAATTGGAGATCTAATATCA
genomic: ACCTCAAAAGTAAAGCGTGGAAGATTAATTCTCCAGAAGAAATTAACCAGgtgagatact ... tgtaatccagGTAGCAACCATTTCTGCAAACGGTGAAAAGGAAATTGGAGATCTAATATCA
EST: gi|6021191|gb|AW066119.1|AW066119
EST:     ACCTCAAAAGTAAAGCGTGGAAGATTAATTCTCCAGAAGAAATTAACCAG                         GTAGCAACCATTTCTGCAAACGGTGAAAAGGAAATTGGAGATCTAATATCA
genomic: ACCTCAAAAGTAAAGCGTGGAAGATTAATTCTCCAGAAGAAATTAACCAGgtgagatact ... tgtaatccagGTAGCAACCATTTCTGCAAACGGTGAAAAGGAAATTGGAGATCTAATATCA
EST: gi|211181732|gb|FL012623.1|FL012623
EST:     ACCTCAAAAGTAAAGCGTGGAAGATTAATTCTC-AGAAGAAATTACCCAG                         -TAGCAAC-ATTTCTGCAAACG-TGGAAAGG
genomic: ACCTCAAAAGTAAAGCGTGGAAGATTAATTCTCCAGAAGAAATTAACCAGgtgagatact ... tgtaatccagGTAGCAACCATTTCTGCAAACGGTGAAAAGG
EST: gi|18450399|gb|BM428677.1|BM428677
EST:     ACCTCAAAAGTAAAGCGTGGAAGATTAATTCTCCAGAAGAAATTAACCAG                         GTAGCAACCATTTCTGCAAACGGTGAAAAGGAAATTGGAGATCTAATATCA
genomic: ACCTCAAAAGTAAAGCGTGGAAGATTAATTCTCCAGAAGAAATTAACCAGgtgagatact ... tgtaatccagGTAGCAACCATTTCTGCAAACGGTGAAAAGGAAATTGGAGATCTAATATCA
EST: gi|18648745|gb|BM497564.1|BM497564
EST:     ACCTCAAAAGTAAAGCGTGGAAGATTAATTCTCCAGAAGAAATTAACCAG                         GTAGCAACCATTTCTGCAAACGGTGAAAAGGAAATTGGAGATCTAATATCA
genomic: ACCTCAAAAGTAAAGCGTGGAAGATTAATTCTCCAGAAGAAATTAACCAGgtgagatact ... tgtaatccagGTAGCAACCATTTCTGCAAACGGTGAAAAGGAAATTGGAGATCTAATATCA
EST: gi|18648744|gb|BM497563.1|BM497563
EST:     ACCTCAANAGTAAAGCGTGGAAGATTAATTCTCCAGAAGAAATTAACCAG                         GTAGCAACCATTTCTGCAAACGGTGAAAAGGAAATTGGAGATCTAATATCA
genomic: ACCTCAAAAGTAAAGCGTGGAAGATTAATTCTCCAGAAGAAATTAACCAGgtgagatact ... tgtaatccagGTAGCAACCATTTCTGCAAACGGTGAAAAGGAAATTGGAGATCTAATATCA
EST: gi|67015320|gb|CO444069.1|CO444069
EST:     ACCTCAAAAGTAAAGCGTGGAAGATTAATTCTCCAGAAGAAATTAACCAG                         GTAGCAACCATTTCTGCAAACGGTGAAAAGGAAATTGGAGATCTAATATCA
genomic: ACCTCAAAAGTAAAGCGTGGAAGATTAATTCTCCAGAAGAAATTAACCAGgtgagatact ... tgtaatccagGTAGCAACCATTTCTGCAAACGGTGAAAAGGAAATTGGAGATCTAATATCA
EST: gi|74242338|gb|DT650252.1|DT650252
EST:     ACCTCAAAAGTAAAGCGTGGAAGATTAATTCTCCAGAAGAAATTAACCAG                         GTAGCAACCATTTCTGCAAACGGTGAAAAGGAAATTGGAGATCTAATATCA
genomic: ACCTCAAAAGTAAAGCGTGGAAGATTAATTCTCCAGAAGAAATTAACCAGgtgagatact ... tgtaatccagGTAGCAACCATTTCTGCAAACGGTGAAAAGGAAATTGGAGATCTAATATCA
EST: gi|149010196|gb|EE042014.2|EE042014
EST:     ACCTCAAAAGTAAAGCGTGGAAGATTAATTCTCCAGAAGAAATTAACCAG                         GTAGCAACCATTTCTGCAAACGGTGAAAAGGAAATTGGAGATCTAATATCA
genomic: ACCTCAAAAGTAAAGCGTGGAAGATTAATTCTCCAGAAGAAATTAACCAGgtgagatact ... tgtaatccagGTAGCAACCATTTCTGCAAACGGTGAAAAGGAAATTGGAGATCTAATATCA
EST: gi|31664231|gb|CD572956.1|CD572956
EST:     ACCTCAAAAGTAAAGCGTGGAAGATTAATTCTCCAGAAGAAATTAACCAG                         GTAGCAACCATTTCTGCAAACGGTGAAAAGGAAATTGGAGATCTAATATCA
genomic: ACCTCAAAAGTAAAGCGTGGAAGATTAATTCTCCAGAAGAAATTAACCAGgtgagatact ... tgtaatccagGTAGCAACCATTTCTGCAAACGGTGAAAAGGAAATTGGAGATCTAATATCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacttgaaaaactctactgagaatgcataatttcattttcctcttgtaatccagGTAGCAACCATTTCTGCAAACGGTGAAAAGGAAATTGGAGATCTAATATCAAAAGCCATGGAAAAAGTTGGAAAGGATGGAGTCATTACTATTGTT
                               tttcattttcctcttg  CT-rich tract
                           ataatttcatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtggatatgtactagtatgttctcatgtgacatctttttgcattttacttgaaaaactctactgagaatgcataatttcattttcctcttgtaatccagGTAGCAACCATTTCTGCAAACGGTGAAAAGGAAATTGGAGATCTAATATCAAAAGCCATGGAAAAAGTTGGAAAGGATGGAGTCATTACTATTGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - -atatgta
- - - - - - - - - - - - catgtga
- - - - - - - - - - - - - - - - - - - ttgcatt
- - - - - - - - - - - - - - - - - - - - - - -ttacttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaatgca