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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagccatccaaaatccagagataacaactttgaataaataagaaaacttacaattaattttcatggcagGATGGAGATATCATCAATATTGATGTTACTGTCTACCTCAAT

Basic information

species Zea mays
transcript GRMZM2G101438_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G101438_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv07s0031g00820.t01 (Vitis vinifera), 3'ss of exon 4
----------------------------gtaagccatccaaaatccagagataacaactttgaataaataagaaaacttacaattaattttcatg-gcagGATGGAGATATCATCAATATTGATGTTACTGTCTACCTCAAT
                             | |||||       |  ||  ||      ||| | ||  | | |  ||||| |   |||| ||||  ||||||||| ||||| ||||||||||||||||| || || || |||
gtctattttacttaaggacttagatttcttgagccagt-gtggttaagtcattgtgtttttaagtag-tcaaatcacttatacaaaattgtcatttgcagGATGGCGATATAATCAATATTGATGTTACCGTTTATCTAAAT
















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|148995508|gb|EE034697.2|EE034697
EST:     CAGTGAATGAATGCATCTGTCATGGGATTCCGGATTCTCGTCCCCTTGAG                         GATGGAGATATCATCAATATTGATGTTACTGTCTACCTCAAT
genomic: CAGTGAATGAATGCATCTGTCATGGGATTCCGGATTCTCGTCCCCTTGAGgtaagccatc ... ttcatggcagGATGGAGATATCATCAATATTGATGTTACTGTCTACCTCAAT
EST: gi|76912468|gb|DV164746.1|DV164746
EST:     CAGTGAATGAATGCATCTGTCATGGGATTCCGGATTCTCGTCCCCTTGAG                         GATGGAGATATCATCAATATTGATGTTACTGTCTACCTCAAT
genomic: CAGTGAATGAATGCATCTGTCATGGGATTCCGGATTCTCGTCCCCTTGAGgtaagccatc ... ttcatggcagGATGGAGATATCATCAATATTGATGTTACTGTCTACCTCAAT
EST: gi|78075681|gb|DV504115.1|DV504115
EST:     CAGTGAATGAATGCATCTGTCATGGGATTCCGGATTCTCGTCCCCTTGAG                         GATGGAGATATCATCAATATTGATGTTACTGTCTACCTCAAT
genomic: CAGTGAATGAATGCATCTGTCATGGGATTCCGGATTCTCGTCCCCTTGAGgtaagccatc ... ttcatggcagGATGGAGATATCATCAATATTGATGTTACTGTCTACCTCAAT
EST: gi|101399011|gb|EB821378.1|EB821378
EST:     CAGTGAATGAATGCATCTGTCATGGGATTCCGGATTCTCGTCCCCTTGAG                         GATGGAGATATCATCAATATTGATGTTACTGTCTACCTCAAT
genomic: CAGTGAATGAATGCATCTGTCATGGGATTCCGGATTCTCGTCCCCTTGAGgtaagccatc ... ttcatggcagGATGGAGATATCATCAATATTGATGTTACTGTCTACCTCAAT
EST: gi|71436246|gb|DR817296.1|DR817296
EST:     CAGTGAATGAATGCATCTGTCATGGGATTCCGGATTCTCGTCCCCTTGAG                         GATGGAGATATCATCAATATTGATGTTACTGTCTACCTCAAT
genomic: CAGTGAATGAATGCATCTGTCATGGGATTCCGGATTCTCGTCCCCTTGAGgtaagccatc ... ttcatggcagGATGGAGATATCATCAATATTGATGTTACTGTCTACCTCAAT
EST: gi|116819988|gb|EC863161.1|EC863161
EST:     CAGTGAATGAATGCATCTGTCATGGCATTCCGGATTCTCGTCCCCTTGAG                         GATGAAGATATCATCAATATTGATGTTACTGTCTACCTCAAT
genomic: CAGTGAATGAATGCATCTGTCATGGGATTCCGGATTCTCGTCCCCTTGAGgtaagccatc ... ttcatggcagGATGGAGATATCATCAATATTGATGTTACTGTCTACCTCAAT
EST: gi|76289409|gb|DV028977.1|DV028977
EST:     CAGTGAATGAATGCATCTGTCATGGGATTCCGGATTCTCGTCCCCTTGAG                         GATGGAGATATCATCAATATTGATGTTACTGTCTACCTCAAT
genomic: CAGTGAATGAATGCATCTGTCATGGGATTCCGGATTCTCGTCCCCTTGAGgtaagccatc ... ttcatggcagGATGGAGATATCATCAATATTGATGTTACTGTCTACCTCAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccagagataacaactttgaataaataagaaaacttacaattaattttcatggcagGATGGAGATATCATCAATATTGATGTTACTGTCTACCTCAAT
                                           ttttcat  CT-rich tract
           aactttgaataaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagccatccaaaatccagagataacaactttgaataaataagaaaacttacaattaattttcatggcagGATGGAGATATCATCAATATTGATGTTACTGTCTACCTCAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT