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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttgtagaaacctttttctcttaggttctgaagtagtttatctagtataaagtttgtttttttctaattatgtccatgttttttctctgatcttattagTTTTTCAAGTGGCGGTGAAGATGGTTATGTAAGGCTGCATCATTTTGATTCCGACTACTTCAGCATCAAGATGTAGATAAAGAACACCAGACTAACCCGA

Basic information

species Zea mays
transcript GRMZM2G028834_T03
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G028834_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os08g21660.1 (Oryza sativa), 3'ss of exon 6
-ctttgtagaaacctttttctcttaggttctgaagtagtttatctagtataaagtttgtttttttctaattatgtccatgttttttctctgatcttat-tagTTTTTCAAGTGGCGGTGAAGATGGTTATGTAAGGCTGCATCATTTTGATTCCGACTACTTCAGCATCAAGATGTAGATAAAGAACACCAGACTAACCCGA-
  | | |  || | | ||| | ||   |  ||   | ||| ||  |  |     |||| |||   ||     | | ||| | | |  |  ||| |||   || ||||| ||||| ||||||||||| |||||||||||||| ||||||||||| |||||||||| ||||||||| || |   ||||   | ||  |  | || 
gttctcttcaagcatgttttttttctctcatgtgatggttaattaa--agtgtttttgctttgagcttcagttattcatatctatgatgcgatgttaaacagCTTTTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTCTGACTACTTCAACATCAAGATTTAAACCTAGAAGTTCTGAA-ACTCTGAG

upper sequence: GRMZM2G028834_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os05g16660.1 (Oryza sativa), 3'ss of exon 6
ctttgtagaaacctttttctcttaggttctgaagtagtttatctagtataaagtttgtttttttctaa---ttatgtccatgttttttctctgatcttattagTTTTTCAAGTGGCGGTGAAGATGGTTATGTAAGGCTGCATCATTTTGATTCCGACTACTTCAGCATCAAGATGTAGATAAAGAACACCAGACTAACCCGA-
  |  |  |     |||||||  | ||  ||   || ||||| | ||  | |   ||||||  | | |   | |  ||    | | |  |  | | |||  || || || ||||| ||||||||||| |||||||||||||| ||||||||||| |||||||||| ||||||||| || |  |||||     ||  |  | || 
--tcttcaagcatattttctcacatgtcatggt-taatttatgttgttcagaaagtgttttgctttgagcttcagttcttcatgtataatacggtgttaacagCTTCTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGATTCTGACTACTTCAACATCAAGATTTAAAGCAAGAAGTTGTGAA-ACTCTGAG

upper sequence: GRMZM2G028834_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os05g16660.3 (Oryza sativa), 3'ss of exon 6
-------------------------------------------------ctttgtagaaacct-ttttctcttaggttctgaagtagtttatctagtataaagtttgtttttttctaa---ttatgtccatgttttttctctgatcttattagTTTTTCAAGTGGCGGTGAAGATGGTTATGTAAGGCTGCATCATTTTGATTCCGACTACTTCAGCATCAAGATGTAGATAAAGAACACCAGACTAACCCGA
                                                   || |  || | | |||||||  | ||  ||   || ||||| | ||  | |   ||||||  | | |   | |  ||    | | |  |  | | |||  || || || ||||| ||||||||||| |||||||||||||| ||||||||                                                    
tggtgaaaaagaaaatttatgagagctgctttatgtgatagctagtttatattcttcaagcatattttctcacatgtcatggt-taatttatgttgttcagAAAGTGTTTTGCTTTGAGCTTCAGTTCTTCATGTATAATACGGTGTTAACAGCTTCTCGAGTGGTGGTGAAGATGGATATGTAAGGCTGCACCATTTTGA----------------------------------------------------

upper sequence: GRMZM2G028834_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA01G03610.2 (Glycine max), 3'ss of exon 7
---ctttgtagaaacctttttctcttaggttctgaagtagtttatctagtataaagtttgtttttttctaattatgtccatgttttttctctgatcttattagTTTTTCAAGTGGCGGTGAAGATGGTTATGTAAGGCTGCATCATTTTGATTCCGACTACTTCAGCATCAAGATGTAGA--TAAAGAACACCAGACTAACCCGA
   |||    || ||   ||||| | | | |||    || |  | ||   | |  |||| ||||  |   ||  ||  |     | ||||      |   ||||||||||||||| |||||||||||||||||| || |||| || |||||  | || || |||| |||||| || |||      |        |  || |    
gcacttcagtgatacagctttct-taatggtctcgtttaat--aactgtcagactgtttcttttacttctatactggtctctcatattcttcttcttgtgtagTTTTTCAAGTGGAGGTGAAGATGGTTATGTACGGTTGCACCACTTTGACCCAGATTATTTCAACATCAAAATATAGTGCCGGATGGTTTGTGGTTAGCAT--

upper sequence: GRMZM2G028834_T03 (Zea mays), 3'ss of exon 6
lower sequence: AT2G46290.1 (Arabidopsis thaliana), 3'ss of exon 8
-ctttgtagaaacctttttctcttaggttctgaagtagtttatctagtataaagtttgtttttttctaattatgtccatgttttttctctgatct--tattagTTTTTCAAGTGGCGGTGAAGATGGTTATGTAAGGCTGCATCATTTTGATTCCGACTACTTCAGCATCAAGATGTAGATAAAGAACACCAGACTAACCCGA
      ||  ||  |||   | | |     |||   | |   ||   |    ||  ||||||||     || |  |   || |||| |   || |  | | ||||| || ||||| |||||||| || || || || |||||||||||||| ||| | ||||||| ||||||||| |||||       ||  | ||  ||   
gtaaactaacaaaatttgattttgattgattgatacaatcc-tcagttgatgagagtgttttttaggctttgttgctgagtgttttttggaatgtattttcagTTTCTCTAGTGGAGGTGAAGACGGCTACGTGAGACTGCATCATTTTGACTCCAATTACTTCAACATCAAGATTTAGATTCTTTGAACATGTCTTTCCATT

upper sequence: GRMZM2G028834_T03 (Zea mays), 3'ss of exon 6
lower sequence: AT2G46280.3 (Arabidopsis thaliana), 3'ss of exon 6
ctttgtagaaacctttttctcttaggtt--ctgaagtagtttatctagtataaagttt---gttttt-ttctaattatgtccatg--ttttttctctgatcttattagTTTTTCAAGTGGCGGTGAAGATGGTTATGTAAGGCTGCATCATTTTGATTCCGACTACTTCAGCATCAAGATGTAGATAAAGAACACCAGA---CTAACCCGA
 |   |  | | | |||    || | ||   |||   | |      |  || | ||||   || | | || |   | | ||  ||  ||| |    ||    | | ||||| || ||||| |||||||| ||||| || ||||||||||||||||| ||||||||||||| ||||||||| |||||   ||  ||  ||     ||||   
gtaaattaacaacatttggattttgattgattgacacaatcctcacatgatgaggttttgagtgtgtgttttggctctctcactgagtttgtggaatgtatatttcagTTTCTCTAGTGGAGGTGAAGACGGTTACGTGAGGCTGCATCATTTTGACTCCGACTACTTCAACATCAAGATTTAGATTCCGACTACTTGAACGTCAACC---

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|113693247|gb|DW845432.1|DW845432
EST:     GGACATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAG                         TTTTTCAAGTGGCGGTG
genomic: GGACATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAGgtaataattt ... atcttattagTTTTTCAAGTGGCGGTG
EST: gi|113655803|gb|DW809491.1|DW809491
EST:     TTTGGCATTTAATCCTGATGGGCGGAG                         TTTTTCAAGTGGCGGTGAAGATGGTTATGTAAGGCTGTCATCATTTTGATT
genomic: TTTGGCATTTAATCCTGATGGGCGGAGgtaataattt ... atcttattagTTTTTCAAGTGGCGGTGAAGATGGTTATGTAAGGCTG-CATCATTTTGATT
EST: gi|166671097|gb|EG308237.1|EG308237
EST:     GGACATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAG                         TTTTTCAAGTGGTGGTG
genomic: GGACATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAGgtaataattt ... atcttattagTTTTTCAAGTGGCGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtataaagtttgtttttttctaattatgtccatgttttttctctgatcttattagTTTTTCAAGTGGCGGTGAAGATGGTTATGTAAGGCTGCATCATTTTGATTCCGACTACTTCAGCATCAAGATGTAGATAAAGAACACCAGACTAACCCGA
                                  ttttttctctgatctt  CT-rich tract
     aagtttgtttttttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttgtagaaacctttttctcttaggttctgaagtagtttatctagtataaagtttgtttttttctaattatgtccatgttttttctctgatcttattagTTTTTCAAGTGGCGGTGAAGATGGTTATGTAAGGCTGCATCATTTTGATTCCGACTACTTCAGCATCAAGATGTAGATAAAGAACACCAGACTAACCCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC