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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgccgcgtttctgccatcatccgaggagctagctccttgacgacacagtagacactctcctcttccccccgtgctcacgtcacgatctccacgattcctgcagGGTGGCAGCTGCAGCGGCCGCCGCGGCGCTGATGCTGGGCGGCGACGACGCGCACAAGTTCATTGGGCGGCCGCGGCTGGACCGCGCCGACTTGGCGAGC

Basic information

species Zea mays
transcript GRMZM2G311665_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G311665_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g48410.1 (Oryza sativa), 3'ss of exon 1
gtgccgcgtttctgccatcatccgaggagctagctccttgacgacacagtagacactctcctcttccccccgtgctcacgtcacgatctccacgattcctgcagGGTGGCAGCTGCAGCGGCCGCCGCGGCGCTGATGCTGGGCGGCGACGACGCGCACAAGTTCATTGGGCGGCCGCGGCTGGACCGCGCCGACTTGGCGAGC---------
                          | || | ||  ||     |||    ||    |||||      || ||   |   | ||  |  |  ||||||| |  |  | ||||  || ||||| || |||||||||||||| ||||||||||| |||||||||||||| ||||||||||||||||| ||||||||||| ||||||         
--------------------------gtgccaactttttc----cacctccgagctcctcctggagtaccagtatccctttaact-tagctccgattcc-gtcgatttgcagG-GCGGCGGCAGCGGCGGCGCTGATGCTAGGCGGCGACGAGGCGCACAAGTTCATGGGGCGGCCGCGGCTGGAGCGCGCCGACTTCGCGAGCATGATGAAC
















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|78090432|gb|DV518806.1|DV518806
EST:     TGCCTGAGCTTGCTCTTGCACCAGCAGCAGCAGCAGAACGAGAACCAGAG                         GGTGGCAGCTGCA
genomic: TGCCTGAGCTTGCTCTTGCACCAGCAGCAGCAGCAGAACGAGAACCAGAGgtgccgcgtt ... attcctgcagGGTGGCAGCTGCA
EST: gi|78082000|gb|DV510412.1|DV510412
EST:     TGCCTGAGCTTGCTCTTGCACCAGCAGCAGCAGCAGAACGAGAACCAGAG                         GGTGGCAGCTGCA
genomic: TGCCTGAGCTTGCTCTTGCACCAGCAGCAGCAGCAGAACGAGAACCAGAGgtgccgcgtt ... attcctgcagGGTGGCAGCTGCA
EST: gi|91049191|gb|EB159609.1|EB159609
EST:     TGCCTGAGCTTGCTCTTGCACCAGCAGCAGCAGCAGAACGAGAACCAGAG                         GGTGGCAGCTGCA
genomic: TGCCTGAGCTTGCTCTTGCACCAGCAGCAGCAGCAGAACGAGAACCAGAGgtgccgcgtt ... attcctgcagGGTGGCAGCTGCA
EST: gi|37417171|gb|CF646238.1|CF646238
EST:     TGCCTGAGCTTGCTCTTGCACCAGCAGCAGCAGCAGAACGAGAACCAGAG                         GGTGGCAGCTGCA
genomic: TGCCTGAGCTTGCTCTTGCACCAGCAGCAGCAGCAGAACGAGAACCAGAGgtgccgcgtt ... attcctgcagGGTGGCAGCTGCA
EST: gi|88753378|gb|DY537519.1|DY537519
EST:     TGCCTGAGCTTGCTCTTGCACCAGCAGCAGCAGCAGAACGAGAACCAGAG                         GGTGGCAGCTGCA
genomic: TGCCTGAGCTTGCTCTTGCACCAGCAGCAGCAGCAGAACGAGAACCAGAGgtgccgcgtt ... attcctgcagGGTGGCAGCTGCA
EST: gi|88754729|gb|DY538870.1|DY538870
EST:     TGCCTGAGCTTGCTCTTGCACCAGCAGCAGCAGCAGAACGAGAACCAGAG                         GGTGGCAGCTGCA
genomic: TGCCTGAGCTTGCTCTTGCACCAGCAGCAGCAGCAGAACGAGAACCAGAGgtgccgcgtt ... attcctgcagGGTGGCAGCTGCA
EST: gi|87157568|gb|DY402357.1|DY402357
EST:     TGCCTGAGCTTGCTCTTGCACCAGCAGCAGCAGCAGAACGAGAACCAGAG                         GGTGGCAGCTGCAGCGGCCGCCGCGGCGCTGATGCTGGGCGGCGACGACGC
genomic: TGCCTGAGCTTGCTCTTGCACCAGCAGCAGCAGCAGAACGAGAACCAGAGgtgccgcgtt ... attcctgcagGGTGGCAGCTGCAGCGGCCGCCGCGGCGCTGATGCTGGGCGGCGACGACGC
EST: gi|71759765|gb|DR957702.1|DR957702
EST:     TGCCTGAGCTTGCTCTTGCACCAGCAGCAGCAGCAGAACGAGAACCAGAG                         GGTGGCAGCTGCA
genomic: TGCCTGAGCTTGCTCTTGCACCAGCAGCAGCAGCAGAACGAGAACCAGAGgtgccgcgtt ... attcctgcagGGTGGCAGCTGCA
EST: gi|148991060|gb|EE032507.2|EE032507
EST:     TGCCTGAGCTTGCTCTTGCACCAGCAGCAGCAGCAGAACGAGAACCAGAG                         GGTGGCAGCTGCA
genomic: TGCCTGAGCTTGCTCTTGCACCAGCAGCAGCAGCAGAACGAGAACCAGAGgtgccgcgtt ... attcctgcagGGTGGCAGCTGCA
EST: gi|101383060|gb|EB813582.1|EB813582
EST:     TGCCTGAGCTTGCTCTTGCACCAGCAGCAGCAGCAGAACGAGAACCAGAG                         GGTGGCAGCTGCA
genomic: TGCCTGAGCTTGCTCTTGCACCAGCAGCAGCAGCAGAACGAGAACCAGAGgtgccgcgtt ... attcctgcagGGTGGCAGCTGCA
EST: gi|37426220|gb|CF650861.1|CF650861
EST:     TGCCTGAGCTTGCTCTTGCACCAGCAGCAGCAGCAGAACGAGAACCAGAG                         GGTGGCAGCTGCA
genomic: TGCCTGAGCTTGCTCTTGCACCAGCAGCAGCAGCAGAACGAGAACCAGAGgtgccgcgtt ... attcctgcagGGTGGCAGCTGCA
EST: gi|22520971|gb|BU079782.1|BU079782
EST:     TGCCTGAGCTTGCTCTTGCACCAGCAGCAGCAGCAGAACGAGAACCAGAG                         GGTGGCAGCTGCAGCGGCCGCCGCGGCGCTGATGCTGGGCGGCGACGACGC
genomic: TGCCTGAGCTTGCTCTTGCACCAGCAGCAGCAGCAGAACGAGAACCAGAGgtgccgcgtt ... attcctgcagGGTGGCAGCTGCAGCGGCCGCCGCGGCGCTGATGCTGGGCGGCGACGACGC
EST: gi|78114497|gb|DV532886.1|DV532886
EST:     TGCCTGAGCTTGCTCTTGCACCAGCAGCAGCAGCAGAACGAGAACCAGAG                         GGTGGCAGCTGCA
genomic: TGCCTGAGCTTGCTCTTGCACCAGCAGCAGCAGCAGAACGAGAACCAGAGgtgccgcgtt ... attcctgcagGGTGGCAGCTGCA
EST: gi|71302970|gb|DR787596.1|DR787596
EST:     TGCCTGAGCTTGCTCTTGCACCAGCAGCAGCAGCAGAACGAGAACCAGAG                         GGTGGCAGCTGCA
genomic: TGCCTGAGCTTGCTCTTGCACCAGCAGCAGCAGCAGAACGAGAACCAGAGgtgccgcgtt ... attcctgcagGGTGGCAGCTGCA
EST: gi|37425506|gb|CF650496.1|CF650496
EST:     TGCCTGAGCTTGCTCTTGCACCAGCAGCAGCAGCAGAACGAGAACCAGAG                         GGTGGCAGCTGCA
genomic: TGCCTGAGCTTGCTCTTGCACCAGCAGCAGCAGCAGAACGAGAACCAGAGgtgccgcgtt ... attcctgcagGGTGGCAGCTGCA
EST: gi|37419766|gb|CF647568.1|CF647568
EST:     TGCCTGAGCTTGCTCTTGCACCAGCAGCAGCAGCAGAACGAGAACCAGAG                         GGTGGCAGCTGCA
genomic: TGCCTGAGCTTGCTCTTGCACCAGCAGCAGCAGCAGAACGAGAACCAGAGgtgccgcgtt ... attcctgcagGGTGGCAGCTGCA
EST: gi|91049371|gb|EB159789.1|EB159789
EST:     TGCCTGAGCTTGCTCTTGCACCAGCAGCAGCAGCAGAACGAGAACCAGAG                         GGTGGCAGCTGCA
genomic: TGCCTGAGCTTGCTCTTGCACCAGCAGCAGCAGCAGAACGAGAACCAGAGgtgccgcgtt ... attcctgcagGGTGGCAGCTGCA
EST: gi|37425151|gb|CF650312.1|CF650312
EST:     TGCCTGAGCTTGCTCTTGCACCAGCAGCAGCAGCAGAACGAGAACCAGAG                         GGTGGCAGCTGCA
genomic: TGCCTGAGCTTGCTCTTGCACCAGCAGCAGCAGCAGAACGAGAACCAGAGgtgccgcgtt ... attcctgcagGGTGGCAGCTGCA
EST: gi|91867750|gb|EB399781.1|EB399781
EST:     TGCCTGAGCTTGCTCTTGCACCAGCAGCAGCAGCAGAACGAGAACCAGAG                         GGTGGCAGCTGCA
genomic: TGCCTGAGCTTGCTCTTGCACCAGCAGCAGCAGCAGAACGAGAACCAGAGgtgccgcgtt ... attcctgcagGGTGGCAGCTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagacactctcctcttccccccgtgctcacgtcacgatctccacgattcctgcagGGTGGCAGCTGCAGCGGCCGCCGCGGCGCTGATGCTGGGCGGCGACGACGCGCACAAGTTCATTGGGCGGCCGCGGCTGGACCGCGCCGACTTGGCGAGC
                       tgctcac  putative branch site (score: 2)
                                              ttcctgc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgccgcgtttctgccatcatccgaggagctagctccttgacgacacagtagacactctcctcttccccccgtgctcacgtcacgatctccacgattcctgcagGGTGGCAGCTGCAGCGGCCGCCGCGGCGCTGATGCTGGGCGGCGACGACGCGCACAAGTTCATTGGGCGGCCGCGGCTGGACCGCGCCGACTTGGCGAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA