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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtgttttttttctcaacaatgtttagaaaggagaacatttccttattcacaacagctgaaaggattgcactgctgcagAGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAAAGGAACCAATAGAACATCAAGGCTTCAAATAACAACGAACAAAAAAGGA

Basic information

species Zea mays
transcript GRMZM2G006130_T05
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006130_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os11g03730.2 (Oryza sativa), 3'ss of exon 5
gttagtgttttttttctcaacaatg---tttagaaaggagaacatttccttattcacaacagct--gaaaggattgcactgctgcagAGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAAAGGAACCAATAGAACATCAAGGCTTCAAATAACAACGAACAAAAAAGGA
|||||||  |||| |||||| | ||         ||  || |  ||| |  |||| ||  || |  |||||||||  | || ||||| ||||||||  |||| |||||||||||| ||||||||||| |||||||| ||||||| |||||||| |||||||||||||||||||| ||||| || |||
gttagtgccttttctctcaatactgggacaggagaacaaggatgtttgcccattcccattagttttgaaaggattatattgttgcagGGTTTCTGGTGCATCGAATTGGACAAAACTGGAGCAGAAGTTGGTTGCTCAAGGAACAAATAGAACCTCAAGGCTTCAAATAACAACTAACAAGAAGGGA

upper sequence: GRMZM2G006130_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 5
gttagtgttttttttctcaacaatg---tttagaaaggagaacatttccttattcacaacagctgaaaggattgcactgctgcagAGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAAAGGAACCAATAGAACATCAAGGCTTCAAATAACAACGAACAAAAAAGGA
|| ||||  |||  |||||| | ||         ||  || |  | | |  |||| ||  || |||||| |||  | || ||||| ||||||||  | || |||||||||||| ||||||||||| |||||||||||||||| |||||||| |||||||||||||||||||| | ||| || |||
gtcagtgcctttgctctcaatactgggacaggagaacaaggatgtctgcccattcccattagttgaaagaattatattgttgcagGGTTTCTGGTGCGTCGAATTGGACAAAACTGGAGCAGAAGTTGGTTGCTAAAGGAACAAATAGAACCTCAAGGCTTCAAATAACAACTACCAAGAAGGGA
















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|211353134|gb|FL044611.1|FL044611
EST:     TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAAC                         AGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
genomic: TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAACgttagtgttt ... actgctgcagAGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
EST: gi|211350735|gb|FL044608.1|FL044608
EST:     TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAAC                         AGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
genomic: TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAACgttagtgttt ... actgctgcagAGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
EST: gi|211350729|gb|FL044602.1|FL044602
EST:     TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAAC                         AGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
genomic: TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAACgttagtgttt ... actgctgcagAGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
EST: gi|8367215|gb|BE050160.1|BE050160
EST:     TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAAC                         AGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
genomic: TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAACgttagtgttt ... actgctgcagAGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
EST: gi|60399112|gb|DN231926.1|DN231926
EST:     TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAAC                         AGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
genomic: TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAACgttagtgttt ... actgctgcagAGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
EST: gi|32924412|gb|CF029224.1|CF029224
EST:     TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAAC                         AGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
genomic: TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAACgttagtgttt ... actgctgcagAGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
EST: gi|32924555|gb|CF029367.1|CF029367
EST:     TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAAC                         AGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
genomic: TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAACgttagtgttt ... actgctgcagAGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
EST: gi|32924548|gb|CF029360.1|CF029360
EST:     TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAAC                         AGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
genomic: TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAACgttagtgttt ... actgctgcagAGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
EST: gi|211350733|gb|FL044606.1|FL044606
EST:     TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAAC                         AGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
genomic: TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAACgttagtgttt ... actgctgcagAGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
EST: gi|211350724|gb|FL044597.1|FL044597
EST:     TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAAC                         AGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
genomic: TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAACgttagtgttt ... actgctgcagAGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
EST: gi|211350722|gb|FL044595.1|FL044595
EST:     TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAAC                         AGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
genomic: TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAACgttagtgttt ... actgctgcagAGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
EST: gi|211350723|gb|FL044596.1|FL044596
EST:     TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAAC                         AGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
genomic: TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAACgttagtgttt ... actgctgcagAGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
EST: gi|211353135|gb|FL044612.1|FL044612
EST:     TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAAC                         AGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
genomic: TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAACgttagtgttt ... actgctgcagAGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
EST: gi|32924263|gb|CF029075.1|CF029075
EST:     TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAAC                         AGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
genomic: TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAACgttagtgttt ... actgctgcagAGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
EST: gi|8367922|gb|BE050867.1|BE050867
EST:     TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAAC                         AGTTTCTGGCGACATTATATTGTACAAAAGTGGAGCAGAAGCTGGTTGCTA
genomic: TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAACgttagtgttt ... actgctgcagAGTTTCTGGC-ACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTA
EST: gi|211350730|gb|FL044603.1|FL044603
EST:     TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAAC                         AGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
genomic: TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAACgttagtgttt ... actgctgcagAGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
EST: gi|211353132|gb|FL044609.1|FL044609
EST:     TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAAC                         AGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
genomic: TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAACgttagtgttt ... actgctgcagAGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
EST: gi|211350725|gb|FL044598.1|FL044598
EST:     TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAAC                         AGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
genomic: TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAACgttagtgttt ... actgctgcagAGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
EST: gi|211350728|gb|FL044601.1|FL044601
EST:     TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAAC                         AGTTTCTGGNACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
genomic: TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAACgttagtgttt ... actgctgcagAGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
EST: gi|88755664|gb|DY539805.1|DY539805
EST:     CATTAACAAGCTCTGATGGGTTGCAAAACTTGGGCT-CAGCTACAATAAC                         AGTTTCTGGCACATCAAATTGGACAAA
genomic: CATTAACAAGCTCTGATGGGTTGCAAAACTTGG-CTTCAGCTACAATAACgttagtgttt ... actgctgcagAGTTTCTGGCACATCAAATTGGACAAA
EST: gi|211350726|gb|FL044599.1|FL044599
EST:     CATTAACAANGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAAC                         AGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
genomic: CATTAACAA-GCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAACgttagtgttt ... actgctgcagAGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
EST: gi|211350734|gb|FL044607.1|FL044607
EST:     TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAAC                         AGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
genomic: TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAACgttagtgttt ... actgctgcagAGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
EST: gi|91051534|gb|EB161952.1|EB161952
EST:     TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAAC                         AGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
genomic: TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAACgttagtgttt ... actgctgcagAGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
EST: gi|211350732|gb|FL044605.1|FL044605
EST:     TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAAC                         AGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
genomic: TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAACgttagtgttt ... actgctgcagAGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
EST: gi|211350727|gb|FL044600.1|FL044600
EST:     TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAAC                         AGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
genomic: TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAACgttagtgttt ... actgctgcagAGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
EST: gi|211350731|gb|FL044604.1|FL044604
EST:     TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAAC                         AGTTTCTGGCACATCAAATTGGACAAAAGTGAAGCAGAAGCTGGTTGCTAA
genomic: TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAACgttagtgttt ... actgctgcagAGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
EST: gi|211353136|gb|FL044613.1|FL044613
EST:     TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAAC                         AGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
genomic: TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAACgttagtgttt ... actgctgcagAGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
EST: gi|32924256|gb|CF029068.1|CF029068
EST:     TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAAC                         AGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA
genomic: TCATTAACAAGCTCTGATGGGTTGCAAAACTTGGCTTCAGCTACAATAACgttagtgttt ... actgctgcagAGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagaaaggagaacatttccttattcacaacagctgaaaggattgcactgctgcagAGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAAAGGAACCAATAGAACATCAAGGCTTCAAATAACAACGAACAAAAAAGGA
          aacattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtgttttttttctcaacaatgtttagaaaggagaacatttccttattcacaacagctgaaaggattgcactgctgcagAGTTTCTGGCACATCAAATTGGACAAAAGTGGAGCAGAAGCTGGTTGCTAAAGGAACCAATAGAACATCAAGGCTTCAAATAACAACGAACAAAAAAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA