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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggattgaaaagaaaaactaccttgatgtatactgtaagtaaagatgtctgtttaacgtatatgttctcttgcaaaaagGATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATTGCAGAGGGTTCCAACTCTGCGGAGTTTGGAAAGAAGGTAGAAAGGACTG

Basic information

species Zea mays
transcript GRMZM2G017386_T03
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017386_T03 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g44110.1 (Oryza sativa), 3'ss of exon 8
gtaaggattgaaaagaaaaactaccttgatgtatactgtaagtaa--agatgtctgtttaacgtatatgttctcttgcaaaaagGATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATTGCAGAGGGTTCCAACTCTGCGGAGTTTGGAAAGAAGGTAGAAAGGACTG
|||| |||||||||   |||||    || ||||||||||||||||  | ||   || |||||  |||| |||   ||||||| ||||||||| || || || |||||||| |||||||||||||| ||||| ||||||||||| || || ||  | || |||| ||| ||||||||||| ||||
gtaatgattgaaaaaccaaact----tgttgtatactgtaagtaataaaattcttgcttaac--atatcttcatgtgcaaaa-gGATCGGAGGAACCGAAGGAGTCGCACAGGAAGCATGGATATCGAGTCGATTGCAGAGGGCTCAAATTCAACCGAATTTGCAAACAAGGTAGAAAGAACTG
















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|60398631|gb|DN231447.1|DN231447
EST:     TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAG                         GATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
genomic: TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAGgtaaggattg ... ttgcaaaaagGATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
EST: gi|148996026|gb|EE035279.2|EE035279
EST:     TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAG                         GATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
genomic: TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAGgtaaggattg ... ttgcaaaaagGATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
EST: gi|5919441|gb|AW054538.1|AW054538
EST:     TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAG                         GATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
genomic: TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAGgtaaggattg ... ttgcaaaaagGATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
EST: gi|211334248|gb|FL383115.1|FL383115
EST:     TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAG                         GATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
genomic: TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAGgtaaggattg ... ttgcaaaaagGATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
EST: gi|5932735|gb|AW057096.1|AW057096
EST:     TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAG                         GATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
genomic: TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAGgtaaggattg ... ttgcaaaaagGATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
EST: gi|32935226|gb|CF040038.1|CF040038
EST:     GGATGCTTGAGTCAGAAGAAGTACCATACCGGGAG                         GATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
genomic: GGATGCTTGAGTCAGAAGAAGTACCATACCGGGAGgtaaggattg ... ttgcaaaaagGATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
EST: gi|32935252|gb|CF040064.1|CF040064
EST:     GGATGCTTGAGTCAGAAGAA-NACCATACCGGGAG                         GATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
genomic: GGATGCTTGAGTCAGAAGAAGTACCATACCGGGAGgtaaggattg ... ttgcaaaaagGATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
EST: gi|149005056|gb|EE039581.2|EE039581
EST:     TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAG                         GATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
genomic: TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAGgtaaggattg ... ttgcaaaaagGATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
EST: gi|86467803|gb|DY234173.1|DY234173
EST:     TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAG                         GATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
genomic: TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAGgtaaggattg ... ttgcaaaaagGATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
EST: gi|5901151|gb|AW042251.1|AW042251
EST:     TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAG                         GATCGGAGAAATCGTAGAAGTCGC
genomic: TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAGgtaaggattg ... ttgcaaaaagGATCGGAGAAATCGTAGAAGTCGC
EST: gi|83279062|gb|DV943070.1|DV943070
EST:     TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAG                         GATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
genomic: TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAGgtaaggattg ... ttgcaaaaagGATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
EST: gi|5650293|gb|AI920653.1|AI920653
EST:     TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAANAAGTNCCATNCCGGGAG                         GATCGGAGAAATCGTAGAAGTCGCNCTGGAAGCATGGATATTGAGTCCATT
genomic: TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAGgtaaggattg ... ttgcaaaaagGATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
EST: gi|4646617|gb|AI491437.2|AI491437
EST:     TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAG                         GATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
genomic: TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAGgtaaggattg ... ttgcaaaaagGATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
EST: gi|211277723|gb|FL440066.1|FL440066
EST:     TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAARAAGTACCATACCGGGAG                         GATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
genomic: TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAGgtaaggattg ... ttgcaaaaagGATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
EST: gi|93011783|gb|EB637303.1|EB637303
EST:     TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAG                         GATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT
genomic: TGGGCCAGGTTGTTAGGATGCTTGAGTCAGAAGAAGTACCATACCGGGAGgtaaggattg ... ttgcaaaaagGATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgtatactgtaagtaaagatgtctgtttaacgtatatgttctcttgcaaaaagGATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATTGCAGAGGGTTCCAACTCTGCGGAGTTTGGAAAGAAGGTAGAAAGGACTG
                          gtttaac  putative branch site (score: 3)
                                      tgttctctt  putative PPT
           taagtaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggattgaaaagaaaaactaccttgatgtatactgtaagtaaagatgtctgtttaacgtatatgttctcttgcaaaaagGATCGGAGAAATCGTAGAAGTCGCACTGGAAGCATGGATATTGAGTCCATTGCAGAGGGTTCCAACTCTGCGGAGTTTGGAAAGAAGGTAGAAAGGACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG