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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCCGCACCGCCTCCTAATGGAGCTTCAAGTTCTGATCAACCTGAAAGATGATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAGgtatatcttaagttaatgaaacaaattggaactttattttaaatttcttgccatgtttgtatagagcatttataacgtattgatgcagtttagaagtttg...

Basic information

species Zea mays
transcript GRMZM2G550865_T02
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G550865_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os03g14980.1 (Oryza sativa), 5'ss of exon 26
GTCCGCACCGCCTCCTAATGGAGCTTCAAGTTCTGATCAACCTGAAAGATGAT--TGAGAAGATGGAACTGGTAGATTTTTCGT--------GGCATGAGT---CTAACCAAGgtatatcttaagttaatgaaacaaattggaactttattttaaatttcttgccatgtttgtatagagcatttataacgtattgatgcagtttagaagtttg--
             ||||||||||| ||||||||||||||||| ||||||| ||  |||| || | ||| || || |||||| ||        || |  | |   |||||||||||||   |      | | ||   |   ||  | || ||  ||| ||      |       |     ||| |     |   || ||     |   |  | |  
-------------CCTAATGGAGCATCAAGTTCTGATCAACCAGAAAGATAATGATGAGGAGTTTGAAGTGTTACATTTTTTGTACTTGCACGGTACAAATTCACTAACCAAGgtatccttcttacaagttaattcaccggg--ccttcttacaaagttaacaaaagcaacaaaagtcacatattcgctgctctgttgagacatgatatatagaa
















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|166578693|gb|EG113196.1|EG113196
EST:     ATGAGTCTAACCAAG                         ATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
genomic: ATGAGTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
EST: gi|33095993|gb|CF055987.1|CF055987
EST:     GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAG                         ATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
genomic: GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
EST: gi|166642915|gb|EG224379.1|EG224379
EST:     GTCTAACCAAG                         ATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
genomic: GTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
EST: gi|8665781|gb|BE186597.1|BE186597
EST:     GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAG                         ATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
genomic: GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
EST: gi|8318797|gb|BE025437.1|BE025437
EST:     GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAG                         ATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
genomic: GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
EST: gi|113646681|gb|DW803477.1|DW803477
EST:     CATGAGTCTAACCAAG                         ATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAAGGG
genomic: CATGAGTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAA-GGG
EST: gi|78083754|gb|DV512147.1|DV512147
EST:     GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAG                         ATGGGCTTCAAAAGGTGGGGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
genomic: GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
EST: gi|7304567|gb|AW600506.1|AW600506
EST:     GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAG                         ATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
genomic: GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
EST: gi|4388094|gb|AI491266.1|AI491266
EST:     GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAG                         ATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
genomic: GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
EST: gi|40485947|gb|CK394819.1|CK394819
EST:     TTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAG                         ATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
genomic: TTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
EST: gi|8318798|gb|BE025438.1|BE025438
EST:     GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAG                         ATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
genomic: GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
EST: gi|211400405|gb|FL382672.1|FL382672
EST:     GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAG                         ATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
genomic: GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
EST: gi|19057574|gb|BM736241.1|BM736241
EST:     GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAG                         ATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
genomic: GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
EST: gi|116819483|gb|EC862618.1|EC862618
EST:     GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAG                         ATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
genomic: GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
EST: gi|19351198|gb|BM895730.1|BM895730
EST:     GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAG                         ATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
genomic: GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
EST: gi|87152457|gb|DY397246.1|DY397246
EST:     GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAG                         ATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
genomic: GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
EST: gi|6964703|gb|AW433396.1|AW433396
EST:     GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAG                         ATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
genomic: GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
EST: gi|60349715|gb|DN216688.1|DN216688
EST:     GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAG                         ATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
genomic: GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
EST: gi|28188075|gb|CB179685.1|CB179685
EST:     GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAG                         ATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
genomic: GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCCGCACCGCCTCCTAATGGAGCTTCAAGTTCTGATCAACCTGAAAGATGATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAGgtatatcttaagttaatgaaacaaattggaactttattttaaatttcttgccatgtttgtatagagcatttataacgtattgatgcagtttagaagtttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA