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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCTTACCTTATGGAAGCTCAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGAgtaagctgcataagcacagatccaacaattctttattatatttatttgctgatcacatacatatttagaattttaagttatgagctctagagaaattttatggtactatgacatttgtacag

Basic information

species Zea mays
transcript GRMZM2G113742_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G113742_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os08g25799.1 (Oryza sativa), 5'ss of exon 4
CTTCTTACCTTATGGAAGCTCAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGAgtaagctgcataagc-acagatccaaca------------attct---ttattatatttatttgctgatcacatacatatttagaat-------tttaagttatgagctctagagaaattttatggtac-tatgacatttgtacag--------------
|||||||  || ||| ||||||||||||||||| | | ||||||| || | | ||||||||| ||||||||||||||   | ||| ||| ||  | ||            |||||   | ||| | |  | ||   |     |||  ||| | | ||       | | |  | || | | | ||      | ||  ||| ||  |||  ||||||               
CTTCTTATATTTTGGGAGCTCAAAGTGGAACAAATCTATCTCCTACAGTTCCAACTCCAGATTTGAAAGAgtaagctttgtcagctacatatgtagcatgactgtccaaaattctgtctcattgtgtccacttctagtcaggatatttatgttgcatcattgcatgtgacatgtgtgatttggactgtactgatattacatagtacaaatgtacaataacttcttcgtag
















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|78087009|gb|DV515402.1|DV515402
EST:     CAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGA                         GAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
genomic: CAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGAgtaagctgca ... atttgtacagGAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
EST: gi|211108289|gb|FL269572.1|FL269572
EST:     AAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAAGA                         GAGTCA-GAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAA
genomic: AAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAA-GAgtaagctgca ... atttgtacagGAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAA
EST: gi|24773354|gb|CA408608.1|CA408608
EST:     CAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGA                         GAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
genomic: CAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGAgtaagctgca ... atttgtacagGAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
EST: gi|211222683|gb|FL110211.1|FL110211
EST:     CAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGA                         GAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
genomic: CAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGAgtaagctgca ... atttgtacagGAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
EST: gi|24961617|gb|CA483617.1|CA483617
EST:     CAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGA                         GAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
genomic: CAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGAgtaagctgca ... atttgtacagGAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
EST: gi|101389911|gb|EB816886.1|EB816886
EST:     CAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGA                         GAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
genomic: CAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGAgtaagctgca ... atttgtacagGAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
EST: gi|76909193|gb|DV163265.1|DV163265
EST:     CAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGA                         GAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
genomic: CAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGAgtaagctgca ... atttgtacagGAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
EST: gi|88757895|gb|DY542036.1|DY542036
EST:     CAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGA                         GAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
genomic: CAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGAgtaagctgca ... atttgtacagGAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
EST: gi|78073924|gb|DV502358.1|DV502358
EST:     CAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGA                         GAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
genomic: CAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGAgtaagctgca ... atttgtacagGAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
EST: gi|71426738|gb|DR807788.1|DR807788
EST:     CAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGA                         GAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
genomic: CAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGAgtaagctgca ... atttgtacagGAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
EST: gi|30087487|gb|CB885693.1|CB885693
EST:     AGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGA                         GAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
genomic: AGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGAgtaagctgca ... atttgtacagGAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
EST: gi|149007848|gb|EE040277.2|EE040277
EST:     CAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGA                         GAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
genomic: CAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGAgtaagctgca ... atttgtacagGAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
EST: gi|60341005|gb|DN207978.1|DN207978
EST:     CAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGA                         GAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
genomic: CAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGAgtaagctgca ... atttgtacagGAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
EST: gi|76932640|gb|DV173098.1|DV173098
EST:     CAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGA                         GAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
genomic: CAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGAgtaagctgca ... atttgtacagGAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
EST: gi|211222687|gb|FL110215.1|FL110215
EST:     CAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGA                         GAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
genomic: CAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGAgtaagctgca ... atttgtacagGAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
EST: gi|211222685|gb|FL110213.1|FL110213
EST:     CAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGA                         GAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
genomic: CAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGAgtaagctgca ... atttgtacagGAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
EST: gi|74240765|gb|DT648679.1|DT648679
EST:     CAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGA                         GAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
genomic: CAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGAgtaagctgca ... atttgtacagGAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
EST: gi|101386138|gb|EB815112.1|EB815112
EST:     CAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGA                         GAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
genomic: CAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGAgtaagctgca ... atttgtacagGAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
EST: gi|71318298|gb|DR795913.1|DR795913
EST:     CAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGA                         GAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
genomic: CAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGAgtaagctgca ... atttgtacagGAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
EST: gi|67026619|gb|CO455368.1|CO455368
EST:     CAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGA                         GAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
genomic: CAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGAgtaagctgca ... atttgtacagGAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
EST: gi|101389909|gb|EB816885.1|EB816885
EST:     CAAAGTGGAACAACTTTGTCTCTTAGAGGTTCTACTCCAGATGTGAAAGA                         GAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
genomic: CAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGAgtaagctgca ... atttgtacagGAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
EST: gi|78120958|gb|DV539342.1|DV539342
EST:     CAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGA                         GAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
genomic: CAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGAgtaagctgca ... atttgtacagGAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
EST: gi|60341894|gb|DN208867.1|DN208867
EST:     CAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGA                         GAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
genomic: CAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGAgtaagctgca ... atttgtacagGAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
EST: gi|30087488|gb|CB885694.1|CB885694
EST:     CAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGA                         GAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
genomic: CAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGAgtaagctgca ... atttgtacagGAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
EST: gi|60400474|gb|DN233281.1|DN233281
EST:     CAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGA                         GAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
genomic: CAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGAgtaagctgca ... atttgtacagGAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
EST: gi|76916798|gb|DV166558.1|DV166558
EST:     CAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGA                         GAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
genomic: CAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGAgtaagctgca ... atttgtacagGAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
EST: gi|149007847|gb|EE040276.2|EE040276
EST:     ACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGA                         GAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG
genomic: ACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGAgtaagctgca ... atttgtacagGAGTCAAGAAGTTAAAGAAGCACTCAGAGCACAAATGGAAGTGCAACGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTCTTACCTTATGGAAGCTCAAAGTGGAACAACTTTGTCTCCTAGAGGTTCTACTCCAGATGTGAAAGAgtaagctgcataagcacagatccaacaattctttattatatttatttgctgatcacatacatatttagaattttaagttatgagctctagagaaattttatggtactatgacatttgtacag

- - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG