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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcctcgtgcttcattgctacaagcttagtcttattgcttccgagactattcttggtgtcaatgtttacatgttattaactttggaatttgggcttccagCTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGCGCACCGAATTGCCTGTGGGTCCATTCTGCATTTTGTACATCCACAGCAC

Basic information

species Zea mays
transcript GRMZM2G369652_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G369652_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g71980.2 (Oryza sativa), 3'ss of exon 1
atcctcgtgcttcattgctacaagcttagtcttattgcttccgagactattcttggtgtcaatgtttacatgttattaactttggaatttgggcttccagCTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGCGCACCGAATTGCCTGTGGGTCCATTCTGCATTTTGTACATCCACAGCAC
|   || ||    |   ||       || |  | |||  |  |   ||     |  | ||| |||  |||      |||| |  |  ||| |  |||||||||| || || | |||||| |||||||||||||||||  |  |||| ||||||||||||||||| | ||| ||||||||| |||||||||| ||||||||
actgtcatgaagtaaacctgatgctgtaatgctcttgtgttaggcccttactcttttctcattgtcaacactaacataacatctgcttttcgaattccagCTCCTGTCATAGGTGGTGATCGTCTGAAGAAGTATGTTCTTCACAAGCTGCGCACCGAATTGCCAGAGGGGCCATTCTGCCTTTTGTACATGCACAGCAC
















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|211524855|gb|FL078294.1|FL078294
EST:     GGATAGGGCAGGCCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGG                         CTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGC
genomic: GGATAGGGCAGGCCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGGgtgcgcgaat ... gggcttccagCTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGC
EST: gi|71316327|gb|DR794851.1|DR794851
EST:     GGATAGGGCAGGCCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGG                         CTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGC
genomic: GGATAGGGCAGGCCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGGgtgcgcgaat ... gggcttccagCTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGC
EST: gi|211527860|gb|FL078307.1|FL078307
EST:     GGATAGGGCAGGCCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGG                         CTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGC
genomic: GGATAGGGCAGGCCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGGgtgcgcgaat ... gggcttccagCTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGC
EST: gi|16925779|gb|BM078842.1|BM078842
EST:     GGATAGGGCAGGCCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGG                         CTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGC
genomic: GGATAGGGCAGGCCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGGgtgcgcgaat ... gggcttccagCTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGC
EST: gi|149073812|gb|EE162133.2|EE162133
EST:     CCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGG                         CTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGC
genomic: CCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGGgtgcgcgaat ... gggcttccagCTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGC
EST: gi|211524860|gb|FL078299.1|FL078299
EST:     GGATAGGGCAGGCCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGG                         CTCCAGTAATTGATGGTAAACGTCTGAAGAAGTATGTGTTCTACAAACTGC
genomic: GGATAGGGCAGGCCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGGgtgcgcgaat ... gggcttccagCTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGC
EST: gi|211527863|gb|FL078310.1|FL078310
EST:     GGATAGGGCAGGCCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGG                         CTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGC
genomic: GGATAGGGCAGGCCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGGgtgcgcgaat ... gggcttccagCTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGC
EST: gi|211524858|gb|FL078297.1|FL078297
EST:     GGATAGGGCAGGCCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGG                         CTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGC
genomic: GGATAGGGCAGGCCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGGgtgcgcgaat ... gggcttccagCTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGC
EST: gi|211527865|gb|FL078312.1|FL078312
EST:     GGATMGGGCAGGCCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGG                         CTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGC
genomic: GGATAGGGCAGGCCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGGgtgcgcgaat ... gggcttccagCTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGC
EST: gi|211524859|gb|FL078298.1|FL078298
EST:     GGATAGGGCAGGCCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGG                         CTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGC
genomic: GGATAGGGCAGGCCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGGgtgcgcgaat ... gggcttccagCTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGC
EST: gi|211401307|gb|FL085283.1|FL085283
EST:     GGATAGGGCAGGCCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGG                         CTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGC
genomic: GGATAGGGCAGGCCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGGgtgcgcgaat ... gggcttccagCTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGC
EST: gi|211524856|gb|FL078295.1|FL078295
EST:     GGATAGGGCAGGCCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGG                         CTCCAGTAATTGATGGTAAACGTCTGAAGAAGTATGTGTTCTACAAACTGC
genomic: GGATAGGGCAGGCCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGGgtgcgcgaat ... gggcttccagCTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGC
EST: gi|149073813|gb|EE162134.2|EE162134
EST:     GGATAGGGCAGGCCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGG                         CTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGC
genomic: GGATAGGGCAGGCCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGGgtgcgcgaat ... gggcttccagCTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGC
EST: gi|211524864|gb|FL078303.1|FL078303
EST:     GGATAGGGCAGGCCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGG                         CTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGC
genomic: GGATAGGGCAGGCCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGGgtgcgcgaat ... gggcttccagCTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGC
EST: gi|211524867|gb|FL078306.1|FL078306
EST:     GGATAGGGCAGGCCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGG                         CTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGC
genomic: GGATAGGGCAGGCCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGGgtgcgcgaat ... gggcttccagCTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGC
EST: gi|148964796|gb|EC906041.2|EC906041
EST:     GGATAGGGCAGGCCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGG                         CTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGC
genomic: GGATAGGGCAGGCCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGGgtgcgcgaat ... gggcttccagCTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGC
EST: gi|60355848|gb|DN222821.1|DN222821
EST:     GTTTTTCCCGG                         CTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGC
genomic: GTTTTTCCCGGgtgcgcgaat ... gggcttccagCTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGC
EST: gi|211527867|gb|FL078314.1|FL078314
EST:     GGATAGGGCAGGCCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGG                         CTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGC
genomic: GGATAGGGCAGGCCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGGgtgcgcgaat ... gggcttccagCTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGC
EST: gi|211524861|gb|FL078300.1|FL078300
EST:     GGATAGGGCAGGCCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGG                         CTCCAGTAATTGATGGTGAACGTCTGAAGATGTATGTGTTCTACAAACTGC
genomic: GGATAGGGCAGGCCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGGgtgcgcgaat ... gggcttccagCTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGC
EST: gi|67028677|gb|CO457426.1|CO457426
EST:     GGATAGGGCAGGCCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGG                         CTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGC
genomic: GGATAGGGCAGGCCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGGgtgcgcgaat ... gggcttccagCTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGC
EST: gi|211524863|gb|FL078302.1|FL078302
EST:     GGATAGGGCAGGCCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGG                         CTCCAGTAATTGATGGTGAACGTCTGAAGATGTATGTGTTCTACAAACTGC
genomic: GGATAGGGCAGGCCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGGgtgcgcgaat ... gggcttccagCTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGC
EST: gi|211524854|gb|FL078293.1|FL078293
EST:     GGATAGGGCAGGCCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGG                         CTCCAGTAATTGATGGTGAACGTCTGAAGATGTATGTGTTCTACAAACTGC
genomic: GGATAGGGCAGGCCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGGgtgcgcgaat ... gggcttccagCTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGC
EST: gi|211527866|gb|FL078313.1|FL078313
EST:     GGATAGGGCAGGCCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGG                         CTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGC
genomic: GGATAGGGCAGGCCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGGgtgcgcgaat ... gggcttccagCTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGC
EST: gi|211524865|gb|FL078304.1|FL078304
EST:     GGATAGGGCAGGCCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGG                         CTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGC
genomic: GGATAGGGCAGGCCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGGgtgcgcgaat ... gggcttccagCTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGC
EST: gi|211524857|gb|FL078296.1|FL078296
EST:     GGATAGGGCAGGCCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGG                         CTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGC
genomic: GGATAGGGCAGGCCGAACCATCGTCCGCGTCGTCGGCAAGTTTTTCCCGGgtgcgcgaat ... gggcttccagCTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actattcttggtgtcaatgtttacatgttattaactttggaatttgggcttccagCTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGCGCACCGAATTGCCTGTGGGTCCATTCTGCATTTTGTACATCCACAGCAC
                            tattaac  putative branch site (score: 1)
                                                cttcc  putative PPT
                   tttacatgttattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcctcgtgcttcattgctacaagcttagtcttattgcttccgagactattcttggtgtcaatgtttacatgttattaactttggaatttgggcttccagCTCCAGTAATTGATGGTGAACGTCTGAAGAAGTATGTGTTCTACAAACTGCGCACCGAATTGCCTGTGGGTCCATTCTGCATTTTGTACATCCACAGCAC

- - - gtgcttc
- - - - - - - -tgctaca
- - - - - - - - - - - - - - - - - -tgcttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtta