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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgcactggtgatcgtttcagtttgtagtatgtagctgtgttgttccaaattctgaaacaattgcccctggtacgtttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACTGGAGATACGATACCACCGATGATATATCTGAAGAGGTGCTGCGGGCATC

Basic information

species Zea mays
transcript GRMZM2G151268_T04
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G151268_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os12g01170.1 (Oryza sativa), 3'ss of exon 6
gtttgtgcactggtgatcgtttcagtttgtagtatgta-gctgtgttgttccaaattctgaaacaattgcccctggtacgtttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACTGGAGATACGATACCACCGATGATATATCTGAAGAGGTGCTGCGGGCATC---
   |      |  |  |  | || ||||||    | || |||    || |||    ||| || | |  ||    |  |        |||||| || |||||||||||||| | ||||||  ||||||| ||||| |||||||||||||| ||| |    |||||||| |||||||| ||| |||| |||||   
--gtaaattataatttttttctcggtttgtttattttatgctagagtgctcc----tctaaagctagcgctttggaca--------ttcagACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACTGGAGATATGATGCT---GATGATATCTCTGAAGAAGTGTTGCGAGCATCAAG
















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|60400202|gb|DN233009.1|DN233009
EST:     ACCTATCTCTTCTTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
genomic: ACCTATCTCTTCTTCGCAGCAGGCATCAGgtttgtgcac ... ttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|45847355|gb|CN071298.1|CN071298
EST:     ACCTATCTCTTCTTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
genomic: ACCTATCTCTTCTTCGCAGCAGGCATCAGgtttgtgcac ... ttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|4647161|gb|AI622236.1|AI622236
EST:     ACCTATCTCTTCTTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
genomic: ACCTATCTCTTCTTCGCAGCAGGCATCAGgtttgtgcac ... ttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|78122445|gb|DV540829.1|DV540829
EST:     ACCTATCNNNNNNNCGCAGCAGGCATCAG                         ATCGCAGAGGGGGGTCTTCAGTTTCCAACCCAAGGAAAGATGAGTACAACT
genomic: ACCTATCTCTTCTTCGCAGCAGGCATCAGgtttgtgcac ... ttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|21432449|gb|BQ547939.1|BQ547939
EST:     ACCTATCTCTTCTTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
genomic: ACCTATCTCTTCTTCGCAGCAGGCATCAGgtttgtgcac ... ttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|91049337|gb|EB159755.1|EB159755
EST:     ACCTATCTCTTCTTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
genomic: ACCTATCTCTTCTTCGCAGCAGGCATCAGgtttgtgcac ... ttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|60359679|gb|DN226652.1|DN226652
EST:     ACCTATCTCTTCTTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
genomic: ACCTATCTCTTCTTCGCAGCAGGCATCAGgtttgtgcac ... ttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|32909956|gb|CF014768.1|CF014768
EST:     ACCTATCTCTTCTTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
genomic: ACCTATCTCTTCTTCGCAGCAGGCATCAGgtttgtgcac ... ttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|23357627|gb|BU645276.1|BU645276
EST:     ACCTATCTCTTCTTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
genomic: ACCTATCTCTTCTTCGCAGCAGGCATCAGgtttgtgcac ... ttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|60399944|gb|DN232751.1|DN232751
EST:     ACCTATCTCTTCTTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGGTC
genomic: ACCTATCTCTTCTTCGCAGCAGGCATCAGgtttgtgcac ... ttactttcagATCGCAGAGGGGGGTC
EST: gi|47961828|gb|CN844537.1|CN844537
EST:     ACCTATTTCTTCTTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
genomic: ACCTATCTCTTCTTCGCAGCAGGCATCAGgtttgtgcac ... ttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|26557650|gb|CA829885.1|CA829885
EST:     ACCTATCTCTTTTTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
genomic: ACCTATCTCTTCTTCGCAGCAGGCATCAGgtttgtgcac ... ttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|94478768|gb|EB707726.1|EB707726
EST:     ACCTATCTCTTCTTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGGTCTTCCGTTTCCAACACAAGGAAAGATGAGTACAACT
genomic: ACCTATCTCTTCTTCGCAGCAGGCATCAGgtttgtgcac ... ttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|60399998|gb|DN232805.1|DN232805
EST:     ACCTATCTCTTCTTTGCAGCAGGCATCAG                         ATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
genomic: ACCTATCTCTTCTTCGCAGCAGGCATCAGgtttgtgcac ... ttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|113701244|gb|EE678748.1|EE678748
EST:     ACCTATCTCTTCTTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
genomic: ACCTATCTCTTCTTCGCAGCAGGCATCAGgtttgtgcac ... ttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|12971760|gb|BG267644.1|BG267644
EST:     ACCTATCTCTTCTTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
genomic: ACCTATCTCTTCTTCGCAGCAGGCATCAGgtttgtgcac ... ttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|15323531|gb|BI478753.1|BI478753
EST:     ACCTATCTCTTCTTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
genomic: ACCTATCTCTTCTTCGCAGCAGGCATCAGgtttgtgcac ... ttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|21809549|gb|BQ667867.1|BQ667867
EST:     ACCTATCTCTTCTTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
genomic: ACCTATCTCTTCTTCGCAGCAGGCATCAGgtttgtgcac ... ttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|211191649|gb|FL029190.1|FL029190
EST:     ACCTATCTCTTCTTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
genomic: ACCTATCTCTTCTTCGCAGCAGGCATCAGgtttgtgcac ... ttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|211194039|gb|FL029192.1|FL029192
EST:     ACCTATCTCTTCTTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
genomic: ACCTATCTCTTCTTCGCAGCAGGCATCAGgtttgtgcac ... ttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|89106102|gb|DY576319.1|DY576319
EST:     ACCTATCTCTTCTTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
genomic: ACCTATCTCTTCTTCGCAGCAGGCATCAGgtttgtgcac ... ttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|60348471|gb|DN215444.1|DN215444
EST:     ACCTATCTCTTCTTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
genomic: ACCTATCTCTTCTTCGCAGCAGGCATCAGgtttgtgcac ... ttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|67042990|gb|CO469245.1|CO469245
EST:     ACCTATCTCTTCTTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGGTCTTCAGTTTCCAACACAGGGAAAGATGAGTACAACT
genomic: ACCTATCTCTTCTTCGCAGCAGGCATCAGgtttgtgcac ... ttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|29945211|gb|CB815526.1|CB815526
EST:     ACCTATCTCTTCTTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
genomic: ACCTATCTCTTCTTCGCAGCAGGCATCAGgtttgtgcac ... ttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|211191650|gb|FL029191.1|FL029191
EST:     ACCTATCTCTTCTTCGCAGCAGGCATCAG                         ATCGCANAAGGGGGTCTTCAGTTTCCAACACAANGARAGATGAGTACAACT
genomic: ACCTATCTCTTCTTCGCAGCAGGCATCAGgtttgtgcac ... ttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|26557724|gb|CA829959.1|CA829959
EST:     ACCTATCTCTTCTTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
genomic: ACCTATCTCTTCTTCGCAGCAGGCATCAGgtttgtgcac ... ttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtagctgtgttgttccaaattctgaaacaattgcccctggtacgtttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACTGGAGATACGATACCACCGATGATATATCTGAAGAGGTGCTGCGGGCATC
                                            tttactttc  CT-rich tract
                        aaacaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtgcactggtgatcgtttcagtttgtagtatgtagctgtgttgttccaaattctgaaacaattgcccctggtacgtttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACTGGAGATACGATACCACCGATGATATATCTGAAGAGGTGCTGCGGGCATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC