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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gacaattttggtagatgtttgagagcatcacaagatccagttttagcaattgtttttcaatgtgggttgatgattttagcatgtcttgtgggtggtgcagGTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAGCTCAGGCCTTGATGAGGGACTATCTGCTAGCTGATCCACTAGTTCCGTA

Basic information

species Zea mays
transcript GRMZM2G016184_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G016184_T04 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g46410.1 (Oryza sativa), 3'ss of exon 1
--gacaattttggtagatgtt--tgagagcatcacaagatccagttttagcaat-tgtttttcaatgtgggttgat-gattttagcatgtcttg-tgggtggtgcagGTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAGCTCAGGCCTTGATGAGGGACTATCTGCTAGCTGATCCACTAGTTCCGTA
   | |  |||||||||||||  |||  |||  | | | |    | ||  |||| |||||   ||||||| | | | ||| |   ||| |  || ||   || |    |  |||   ||          |  ||||||||| |  |||||||| ||||||||||  |||||||| |||||  |||| ||||||||||| |       
ataaaatgtttggtagatgtttctgaaggcagaaaatggtttgatctttccaatctgtttcgaaatgtggctggtttgatctcgacatcttgtgatgcagGGCGTTTCTAGTGTCAAAAAGAGAGGAGGGATGGCGATGACGGGGTACAAGTACCAAGCTCAGGAGTTGATGAGAGACTACTTGCTGGCTGATCCACTGG-------
















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|211526418|gb|FL361966.1|FL361966
EST:     GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAG                         GTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG
genomic: GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAGgtaatatccc ... ggtggtgcagGTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG
EST: gi|211114299|gb|FL364736.1|FL364736
EST:     GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCAYCGCGAG                         GTGCTGTTTGAACCGTGAAGATGGCGGCGATSACTGCTTACAAGTATCAAG
genomic: GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAGgtaatatccc ... ggtggtgcagGTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG
EST: gi|211099206|gb|FL356886.1|FL356886
EST:     GCGCGK-ACCTCCCAGKCCCAACACGCCCGCAAGCTCCGCTCACCGCGAG                         GTGCTGTTTGAACCCGGTGAAGATGGCGGCGATGACTGCTTACAAGTATCA
genomic: GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAGgtaatatccc ... ggtggtgcagGTGCTGTTTGAACC-G-TGAAGATGGCGGCGATGACTGCTTACAAGTATCA
EST: gi|211446537|gb|FL323006.1|FL323006
EST:     GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAG                         GTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG
genomic: GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAGgtaatatccc ... ggtggtgcagGTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG
EST: gi|211179443|gb|FL364371.1|FL364371
EST:     GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAG                         GTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG
genomic: GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAGgtaatatccc ... ggtggtgcagGTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG
EST: gi|211370346|gb|FL342982.1|FL342982
EST:     GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAG                         GTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG
genomic: GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAGgtaatatccc ... ggtggtgcagGTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG
EST: gi|211367569|gb|FL335348.1|FL335348
EST:     GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAG                         GTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTWTCAAG
genomic: GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAGgtaatatccc ... ggtggtgcagGTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG
EST: gi|211430478|gb|FL350076.1|FL350076
EST:     GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAG                         GTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG
genomic: GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAGgtaatatccc ... ggtggtgcagGTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG
EST: gi|211224648|gb|FL333450.1|FL333450
EST:     GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAG                         GTGCTGTTTGAACCGTGAAG
genomic: GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAGgtaatatccc ... ggtggtgcagGTGCTGTTTGAACCGTGAAG
EST: gi|44681921|gb|CK786969.1|CK786969
EST:     GCGCGGCACCTCCCAGTCCCAACACCCCCGCAAGCTCCGCTCACCGCGAG                         GTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG
genomic: GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAGgtaatatccc ... ggtggtgcagGTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG
EST: gi|76293603|gb|DV033171.1|DV033171
EST:     GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAG                         GTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG
genomic: GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAGgtaatatccc ... ggtggtgcagGTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG
EST: gi|211134109|gb|FL315814.1|FL315814
EST:     GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAG                         GTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG
genomic: GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAGgtaatatccc ... ggtggtgcagGTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG
EST: gi|148947020|gb|EC892317.2|EC892317
EST:     GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAG                         GTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG
genomic: GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAGgtaatatccc ... ggtggtgcagGTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG
EST: gi|76286797|gb|DV026365.1|DV026365
EST:     GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAG                         GTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG
genomic: GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAGgtaatatccc ... ggtggtgcagGTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG
EST: gi|211200884|gb|FL351309.1|FL351309
EST:     GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAG                         GTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG
genomic: GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAGgtaatatccc ... ggtggtgcagGTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG
EST: gi|50322746|gb|CO517872.1|CO517872
EST:     GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAG                         GTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG
genomic: GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAGgtaatatccc ... ggtggtgcagGTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG
EST: gi|50338098|gb|CO533224.1|CO533224
EST:     GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAG                         GTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG
genomic: GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAGgtaatatccc ... ggtggtgcagGTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG
EST: gi|211235414|gb|FL352706.1|FL352706
EST:     GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAG                         GTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG
genomic: GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAGgtaatatccc ... ggtggtgcagGTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG
EST: gi|148953653|gb|EC899012.2|EC899012
EST:     GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAG                         GTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG
genomic: GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAGgtaatatccc ... ggtggtgcagGTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG
EST: gi|211176856|gb|FL323774.1|FL323774
EST:     GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAG                         GTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG
genomic: GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAGgtaatatccc ... ggtggtgcagGTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG
EST: gi|76280960|gb|DV020528.1|DV020528
EST:     GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAG                         GTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG
genomic: GCGCGGCACCTCCCAGTCCCAACACGCCCGCAAGCTCCGCTCACCGCGAGgtaatatccc ... ggtggtgcagGTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaattgtttttcaatgtgggttgatgattttagcatgtcttgtgggtggtgcagGTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAGCTCAGGCCTTGATGAGGGACTATCTGCTAGCTGATCCACTAGTTCCGTA
                   ggttgat  putative branch site (score: 5)
       tttttcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gacaattttggtagatgtttgagagcatcacaagatccagttttagcaattgtttttcaatgtgggttgatgattttagcatgtcttgtgggtggtgcagGTGCTGTTTGAACCGTGAAGATGGCGGCGATGACTGCTTACAAGTATCAAGCTCAGGCCTTGATGAGGGACTATCTGCTAGCTGATCCACTAGTTCCGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - -ttttggt
- - - - - - - atgtttg
- - - - - - - - - - - - gcatcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatgtc