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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caatgttctgcattgacttaactgttccctataccttcatgtttgtccatcccattgttttgagaaaaacacctctataatcccttttcttgtttttcagCATGTCCTGCAATATGGGAAACCAGAAGAGCGTTCTACTATAATTGCACAACTCGCTGGACAGATAGTGAAGATGAGCCAGCAGAAATTTGCATCCAATG

Basic information

species Zea mays
transcript GRMZM2G123537_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G123537_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os02g57390.1 (Oryza sativa), 3'ss of exon 8
--caatgttctgcattgact-taactgttccctataccttcatgtttgtccatcccattgttttgagaaaaacacctctataatcccttttcttgt-ttttcagCATGTCCTGCAATATGGGAAACCAGAAGAGCGTTCTACTATAATTGCACAACTCGCTGGACAGATAGTGAAGATGAGCCAGCAGAAATTTGCATCCAATG
| |||| || | | || | | | |||||| | || | | | || || | | | | | || || | ||| |||||||| ||||| | ||||||||||| || |||||| |||| ||| ||||| ||||| ||||| |||||||||||||| ||||||||||| |||||||
ctccatgtgatgtactttctcttgttttcgtttataccattggagtt----actttacttttgtgtcccatttattcaaagagcttccttgtttatatttgtagCATGTCTTGCAACACGGGAAACCAGATGAACGTTCTGCTATTATTAAGCAACTGGCTGGGCAGATTGTGAAGATGAGCCAACAGAAATTTGCTTCCAATG
















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|47961753|gb|CN844462.1|CN844462
EST:     AGTCCGTGGTTACTTTAACGGAGGACCAGTATGGTAATTATGTAATCCAG                         CATGTCCTGCAATATGGGAAACCAGAAGAGCGTTCTACTATAATTGCACAA
genomic: AGTCCGTGGTTACTTTAACGGAGGACCAGTATGGTAATTATGTAATCCAGgtaactggtt ... tgtttttcagCATGTCCTGCAATATGGGAAACCAGAAGAGCGTTCTACTATAATTGCACAA
EST: gi|211232325|gb|FK959922.1|FK959922
EST:     CCGTGGTTACTTTAACGGAGGACCAGTATGGTAATTATGTAATCCAG                         CATGTCCTGCAATATGGGAAACCAGAAGAGCGTTCTACTATAATTGCACAA
genomic: CCGTGGTTACTTTAACGGAGGACCAGTATGGTAATTATGTAATCCAGgtaactggtt ... tgtttttcagCATGTCCTGCAATATGGGAAACCAGAAGAGCGTTCTACTATAATTGCACAA
EST: gi|60394394|gb|DN227264.1|DN227264
EST:     AGTCCGTGGTTACTTTAACGGAGGACCAGTATGGTAATTATGTAATCCAG                         CATGTCCTGCAATATGGGAAACCAGAAGAGCGTTCTACTATAATTGCACAA
genomic: AGTCCGTGGTTACTTTAACGGAGGACCAGTATGGTAATTATGTAATCCAGgtaactggtt ... tgtttttcagCATGTCCTGCAATATGGGAAACCAGAAGAGCGTTCTACTATAATTGCACAA
EST: gi|60355644|gb|DN222617.1|DN222617
EST:     AGTCCGTGGTTACTTTAACGGAGGACCAGTATGGTAATTATGTAATCCAG                         CATGTCCTGCAATATGGGAAACCAGAAGAGCGTTCTACTATAATTGCACAA
genomic: AGTCCGTGGTTACTTTAACGGAGGACCAGTATGGTAATTATGTAATCCAGgtaactggtt ... tgtttttcagCATGTCCTGCAATATGGGAAACCAGAAGAGCGTTCTACTATAATTGCACAA
EST: gi|60355743|gb|DN222716.1|DN222716
EST:     AGTCCGTGGTTACTTTAACGGAGGACCAGTATGGTAATTATGTAATCCAG                         CATGTCCTGCAATATGGGAAACCAGAAGAGCGTTCTACTATAATTGCACAA
genomic: AGTCCGTGGTTACTTTAACGGAGGACCAGTATGGTAATTATGTAATCCAGgtaactggtt ... tgtttttcagCATGTCCTGCAATATGGGAAACCAGAAGAGCGTTCTACTATAATTGCACAA
EST: gi|60398356|gb|DN231172.1|DN231172
EST:     AGTCCGTGGTTACTTTAACGGAGGACCAGTATGGTAATTATGTAATCCAG                         CATGTCCTGCAATATGGGAAACCAGAAGAGCGTTCTACTATAATTGCACAA
genomic: AGTCCGTGGTTACTTTAACGGAGGACCAGTATGGTAATTATGTAATCCAGgtaactggtt ... tgtttttcagCATGTCCTGCAATATGGGAAACCAGAAGAGCGTTCTACTATAATTGCACAA
EST: gi|60399207|gb|DN232021.1|DN232021
EST:     AGTCCGTGGTTACTTTAACGGAGGACCAGTATGGTAATTATGTAATCCAG                         CATGTCCTGCAATATGGGAAACCAGAAGAGCGTTCTACTATAATTGCACAA
genomic: AGTCCGTGGTTACTTTAACGGAGGACCAGTATGGTAATTATGTAATCCAGgtaactggtt ... tgtttttcagCATGTCCTGCAATATGGGAAACCAGAAGAGCGTTCTACTATAATTGCACAA
EST: gi|32867179|gb|CF006861.1|CF006861
EST:     AGTCCGTGGTTACTTTAACGGAGGACCAGTATGGTAATTATGTAATCCAG                         CATGTCCTGCAATATGGGAAACCAGAAGAGCGTTCTACTATAATTGCACAA
genomic: AGTCCGTGGTTACTTTAACGGAGGACCAGTATGGTAATTATGTAATCCAGgtaactggtt ... tgtttttcagCATGTCCTGCAATATGGGAAACCAGAAGAGCGTTCTACTATAATTGCACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccatcccattgttttgagaaaaacacctctataatcccttttcttgtttttcagCATGTCCTGCAATATGGGAAACCAGAAGAGCGTTCTACTATAATTGCACAACTCGCTGGACAGATAGTGAAGATGAGCCAGCAGAAATTTGCATCCAATG
                          cctctataatcccttt  CT-rich tract
 attgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caatgttctgcattgacttaactgttccctataccttcatgtttgtccatcccattgttttgagaaaaacacctctataatcccttttcttgtttttcagCATGTCCTGCAATATGGGAAACCAGAAGAGCGTTCTACTATAATTGCACAACTCGCTGGACAGATAGTGAAGATGAGCCAGCAGAAATTTGCATCCAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG