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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagcctttttgtaaactgttggatcggcaatctttgtggttccttggatgtttaagcagtctgccatggttttgtagGCTTCACAGGATCTGTCTTCGCTCAAGGACATAGCAGGGGAGACTGGAAAGAAGCTGACATCTCTGGCCTCCAATTTCATCAGCGACCTGGACAGGATCC

Basic information

species Zea mays
transcript GRMZM2G176612_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G176612_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g63710.2 (Oryza sativa), 3'ss of exon 5
---------------------------------------------------------------------------------------gtagcctttttgtaaactgttggat-cggcaatc--tttgtggttc-cttggatgtttaagcagtctgccatggttttgtagGCTTCACAGGATCTGTCTTCGCTCAAGGACATAGCAGGGGAGACTGGAAAGAAGCTGACATCTCTGGCCTCCAATTTCATCAGCGACCTGGACAGGATCC
                                                                                        |    |  |  | || | ||   | |    ||   |   ||   | |    || | | | | | |||  || ||| || |||| || || ||||||||||| |||||| | || || || || ||||||||||||||||||||| | ||||||||||| ||||||||||| ||||| ||||
gtagttattctgtaaataattgccagccttttgtcacctcttgcatatttagtttttaagcaaccgagcatgcaaatcattactacactgagttactactgaattattcagtacaaagattgatccttgaaacgcacaaatatcttacctg-ctgggattgttgtgcagGCATCTCAAGATCTGTCTTCCCTCAAGAATATGGCTGGAGAAACTGGAAAGAAGCTGACATCTATAGCCTCCAATTTTATCAGCGACCTCGACAGAATCC

upper sequence: GRMZM2G176612_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA01G12340.2 (Glycine max), 3'ss of exon 7
----------------------------------------------------------------------gtagcctttttgtaaactgttggatcggcaatctttgtggttccttggatgtttaagcagtctgccatggttttgtagGCTTCACAGGATCTGTCTTCGCTCAAGGACATAGCAGGGGAGACTGGAAAGAAGCTGACATCTCTGGCCTCCAATTTCATCAGCGACCTGGACAGGATCC--
                                                                       ||      ||    ||  | |  || | | || |  ||| |   | | |||            ||   || ||| ||||   ||||||||| ||||| || ||| |||| ||||| ||||||||||||||||| |  || ||||||||||  || || |  || ||   ||||| |   
gtattctttaccttttactggatttgggaatttcattattcatgtcatttgtcatctgaacaacaaaatgataattgaattagtgacattagtttctgtattcatgttggatgggttgctgtacgcctccctcccctctgtgttgcagGCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAGAAGCTCAGCTCACTGGCCTCCACATTGATGACAGATCT--TCAGGACCGAA

upper sequence: GRMZM2G176612_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA08G36700.2 (Glycine max), 3'ss of exon 6
--------------------------------------------------------------gtagcctttttgt-aaactgttggatcggcaatctttgtggttcc-ttggatgtttaagcagtctgccatggttttgtagGCTTCACAGGATCTGTCTTCGCTCAAGGACATAGCAGGGGAGACTGGAAAGAAGCTGACATCTCTGGCCTCCAATTTCATCAGCGACCTGGACAGGATCC--
                                                               |    |  |  | ||| |  |||  |   | |   |||  |    ||||||||  |         ||   |||||| ||||   ||||||||| ||||| || ||| |||| ||||| |||||||||||||||||||  ||  |||||||||  || || |  || ||   ||||| |   
gtattccttaccttgtactggatttggaaatttcattattcatgttatttgtcattcgaacaatgaaatgataatcaaattagtgg--cattagttcctgtattgatgttggatgtacacctccctcccctctgttttgcagGCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAGAAGCTGAGCTCATTGGCCTCCACATTGATGACAGATCT--TCAGGACCGAA

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|50325052|gb|CO520178.1|CO520178
EST:     CTAACCTGGACCTAAGCGCTGCTGATCTCATCAACAGAATATCTTTCCAG                         GCTTCACAGGATCTGTCTTCGCTCAAGGACATAGCAGGGGAGACTGGAAAG
genomic: CTAACCTGGACCTAAGCGCTGCTGATCTCATCAACAGAATATCTTTCCAGgtagcctttt ... ggttttgtagGCTTCACAGGATCTGTCTTCGCTCAAGGACATAGCAGGGGAGACTGGAAAG
EST: gi|211185000|gb|FL061794.1|FL061794
EST:     TCATCAACAGAATATCTTTCCAG                         GCTTCACAGGATCTGTCTTCGCTCAAGGACATAGCAGGGGAGACTGGAAAG
genomic: TCATCAACAGAATATCTTTCCAGgtagcctttt ... ggttttgtagGCTTCACAGGATCTGTCTTCGCTCAAGGACATAGCAGGGGAGACTGGAAAG
EST: gi|93015028|gb|EB640548.1|EB640548
EST:     CTAACCTGGACCTAAGCGCTGCTGATCTCATCAACAGAATATCTTTCCAG                         GCTTCACAGGATCTGTCTTCGCTCAAGGACATAGCAGGGGAGACTGGAAAG
genomic: CTAACCTGGACCTAAGCGCTGCTGATCTCATCAACAGAATATCTTTCCAGgtagcctttt ... ggttttgtagGCTTCACAGGATCTGTCTTCGCTCAAGGACATAGCAGGGGAGACTGGAAAG
EST: gi|20507926|gb|BQ279824.1|BQ279824
EST:     CTAACCTGGACCTAAGCGCTGCTGATCTCATCAACAGAATATCTTTCCAG                         GCTTCACAGGATCTGTCTTCGCTCAAGGACATAGCAGGGGAGACTGGAAAG
genomic: CTAACCTGGACCTAAGCGCTGCTGATCTCATCAACAGAATATCTTTCCAGgtagcctttt ... ggttttgtagGCTTCACAGGATCTGTCTTCGCTCAAGGACATAGCAGGGGAGACTGGAAAG
EST: gi|78027094|gb|DV495481.1|DV495481
EST:     CTAACCTGGACCTAAGCGCTGCTGATCTCATCAACAGAATATCTTTCCAG                         GCTTCACAGGATCTGTCTTCGCTCAAGGACATAGCAGGGGAGACTGGAAAG
genomic: CTAACCTGGACCTAAGCGCTGCTGATCTCATCAACAGAATATCTTTCCAGgtagcctttt ... ggttttgtagGCTTCACAGGATCTGTCTTCGCTCAAGGACATAGCAGGGGAGACTGGAAAG
EST: gi|50324069|gb|CO519195.1|CO519195
EST:     CTAACCTGGACCTAAGCGCTGCTGATCTCATCAACAGAATATCTTTCCAG                         GCTTCACAGGATCTGTCTTCGCTCAAGGACATAGCAGGGGAGACTGGAAAG
genomic: CTAACCTGGACCTAAGCGCTGCTGATCTCATCAACAGAATATCTTTCCAGgtagcctttt ... ggttttgtagGCTTCACAGGATCTGTCTTCGCTCAAGGACATAGCAGGGGAGACTGGAAAG
EST: gi|5108137|gb|AI739850.1|AI739850
EST:     CTAACCTGGACCTAAGCGCTGCTGATCTCATCAACAGAATATCTTTCCAG                         GCTTCACAGGATCTGTCTTCGCTCAAGGACATAGCAGGGGAGACTGGAAAG
genomic: CTAACCTGGACCTAAGCGCTGCTGATCTCATCAACAGAATATCTTTCCAGgtagcctttt ... ggttttgtagGCTTCACAGGATCTGTCTTCGCTCAAGGACATAGCAGGGGAGACTGGAAAG
EST: gi|4296089|gb|AI438706.1|AI438706
EST:     CTAACCTGGACCTAAGCGCTGCTGATCTCATCAACAGAATATCTTTNCAG                         GCTTCACAGGATCTGTCTTCGCTCAAGGACATAGCAGGGGAGACTGGAAAG
genomic: CTAACCTGGACCTAAGCGCTGCTGATCTCATCAACAGAATATCTTTCCAGgtagcctttt ... ggttttgtagGCTTCACAGGATCTGTCTTCGCTCAAGGACATAGCAGGGGAGACTGGAAAG
EST: gi|60339034|gb|DN206007.1|DN206007
EST:     CTAACCTGGACCTAAGCGCTGCTGATCTCATCAACAGAATATCTTTCCAG                         GCTTCACAGGATCTGTCTTCGCTCAAGGACATAGCAGGGGAGACTGGAAAG
genomic: CTAACCTGGACCTAAGCGCTGCTGATCTCATCAACAGAATATCTTTCCAGgtagcctttt ... ggttttgtagGCTTCACAGGATCTGTCTTCGCTCAAGGACATAGCAGGGGAGACTGGAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcggcaatctttgtggttccttggatgtttaagcagtctgccatggttttgtagGCTTCACAGGATCTGTCTTCGCTCAAGGACATAGCAGGGGAGACTGGAAAGAAGCTGACATCTCTGGCCTCCAATTTCATCAGCGACCTGGACAGGATCC
                         atgtttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagcctttttgtaaactgttggatcggcaatctttgtggttccttggatgtttaagcagtctgccatggttttgtagGCTTCACAGGATCTGTCTTCGCTCAAGGACATAGCAGGGGAGACTGGAAAGAAGCTGACATCTCTGGCCTCCAATTTCATCAGCGACCTGGACAGGATCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA