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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAGgtaaacaattgtttccttcagctactactctaaatatatcaaaatggaaattaatgcatgcactgttttgtaatttcttgtataataagacttaaagatt...

Basic information

species Zea mays
transcript GRMZM2G156734_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G156734_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g36740.3 (Oryza sativa), 5'ss of exon 2
TATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAGgtaaacaattgtttccttcagctactactctaaatatatcaaaatggaaattaatgcatgcactgttttgtaatttcttgtataataagacttaaag-att-
|| ||||| ||||||||||||||| ||||||||||||||||||| || | |||||||||||||||||| | |||||  |||| || | | |      | ||      |||      |     |  || ||   || |   || |  |    | ||  ||| | ||     | | 
TACGCTCATAGAGAATGTGTGCAAAGATGGTGCAATGAGAAAGGAGACATAATCTGTGAAATCTGCCACGTGgtaagtaattcttgcatgctttagttccttgtggcataatttgttcct--tctattcaacaacaggggtgaatatgggggcatcctaatagttggctcactc

upper sequence: GRMZM2G156734_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT5G62460.1 (Arabidopsis thaliana), 5'ss of exon 3
TATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAGgtaaacaattgtttccttcagctactactctaaatatatcaaaatggaaattaatgcatgcactgttttgtaatttcttgtataataagacttaaagatt
||||||||  |  | ||||| ||||| ||||| ||||||||||| || |||| ||||||||| |||||  |||||   |||    ||  | |   |  | | |   ||||      |||  |  |  | |||||   || | ||| |  || |        |   ||| |  
TATGCTCATCGTAAGTGTGTTCAACGTTGGTGTAATGAGAAAGGCGACACAACCTGTGAAATATGCCACAAGgta--taatcaaatcactaa--caacatttttggtataatcttttggttac-accgaatgcaagtttatataactgttttttcttccttatggaaacag-

upper sequence: GRMZM2G156734_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv17s0000g06230.t01 (Vitis vinifera), 5'ss of exon 3
TATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAGgtaaacaattgtttcct-----tcagctacta-ctctaaatatatcaaaatggaaatta-atgcatgcactgttttgtaatttcttgtataataagacttaaagatt
| |||||| ||  ||||||| ||||||||||||||||||||||| |||  ||  || || ||||| ||| |||||   | ||| ||| |       |||   || ||| || || |||  | | | | ||  ||  |||      ||||  |||| |  |  |||| |   || |    
TTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAGgtatg-atttgcttcttaattcctagccgttatctccaagtacatctcatttgtagttgcataaatgtttatatttgagatttatatt--aataggtaataca----

upper sequence: GRMZM2G156734_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv01s0026g02470.t01 (Vitis vinifera), 5'ss of exon 5
TATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAGgtaaaca-attgtttccttcagctactactctaaatatatcaaaatggaaattaatgcatgcactgttttgtaatttcttgtataa--taagacttaaagatt
|||||||| ||  | ||||| ||||||||||||||||||||||| || | ||| ||||| ||||||||| ||||| ||   || |||  ||    | | ||| |   | |    |   ||      |||       |   |   | || |||  ||      | || |  |  | 
TATGCTCATAGGAAGTGTGTTCAACGATGGTGCAATGAGAAAGGAGACATAATTTGTGAGATCTGCCATCAGgtatactcgttattttttttcctttccactttc--tgtcctcaggaggctgcatatgtgctttttaaatcacatttcctttgatgggcccaaacctgcaagt-

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|76909618|gb|DV163452.1|DV163452
EST:     AACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAG                         TTGTACAAGCCTGGTTACACTGCCCCAACCCAGGTGCATCATGATGAAACT
genomic: AACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAGgtaaacaatt ... tgtttatcagTTGTACAAGCCTGGTTACACTGCCCCAACCCAGGTGCATCATGATGAAACT
EST: gi|31558678|gb|CD527890.1|CD527890
EST:     AACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAG                         TTGTACAAGCCTGGTTACACTGCCCCAACCCAGGTGCATCATGATGAAACT
genomic: AACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAGgtaaacaatt ... tgtttatcagTTGTACAAGCCTGGTTACACTGCCCCAACCCAGGTGCATCATGATGAAACT
EST: gi|71332393|gb|DR803153.1|DR803153
EST:     AACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAG                         TTGTACAAGCCTGGTTACACTGCCCCAACCCAGGTGCATCATGATGAAACT
genomic: AACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAGgtaaacaatt ... tgtttatcagTTGTACAAGCCTGGTTACACTGCCCCAACCCAGGTGCATCATGATGAAACT
EST: gi|29130457|gb|CB381161.1|CB381161
EST:     AACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAG                         TTGTACAAGCCTGGTTACACTGCCCCAACCCAGGTGCATCATGATGAAACT
genomic: AACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAGgtaaacaatt ... tgtttatcagTTGTACAAGCCTGGTTACACTGCCCCAACCCAGGTGCATCATGATGAAACT
EST: gi|31406064|gb|CD484796.1|CD484796
EST:     AACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAG                         TTGTACAAGCCTGGTTACACTGCCCCAACCCAGGTGCATCATGATGAAACT
genomic: AACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAGgtaaacaatt ... tgtttatcagTTGTACAAGCCTGGTTACACTGCCCCAACCCAGGTGCATCATGATGAAACT
EST: gi|28390336|gb|CB250165.1|CB250165
EST:     AACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAG                         TTGTACAAGCCTGGTTACACTGCCCCAACCCAGGTGCATCATGATGAAACT
genomic: AACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAGgtaaacaatt ... tgtttatcagTTGTACAAGCCTGGTTACACTGCCCCAACCCAGGTGCATCATGATGAAACT
EST: gi|29130571|gb|CB381275.1|CB381275
EST:     AACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAG                         TTGTACAAGCCTGGTTACACTGCCCCAACCCAGGTGCATCATGATGAAACT
genomic: AACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAGgtaaacaatt ... tgtttatcagTTGTACAAGCCTGGTTACACTGCCCCAACCCAGGTGCATCATGATGAAACT
EST: gi|28873794|gb|CB329735.1|CB329735
EST:     AACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAG                         TTGTACAAGCCTGGTTACACTGCCCCAACCCAGGTGCATCATGATGAAACT
genomic: AACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAGgtaaacaatt ... tgtttatcagTTGTACAAGCCTGGTTACACTGCCCCAACCCAGGTGCATCATGATGAAACT
EST: gi|211448719|gb|FL094703.1|FL094703
EST:     AACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAG                         TTGTACAAGCCTGGTTACACTGCCCCAACCCAGGTGCATCATGATGAAACT
genomic: AACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAGgtaaacaatt ... tgtttatcagTTGTACAAGCCTGGTTACACTGCCCCAACCCAGGTGCATCATGATGAAACT
EST: gi|28361582|gb|CB239938.1|CB239938
EST:     TACAATCTGTGAAATCTGCCATGAAG                         TTGTACAAGCCCTGGTTACACTGCCCCAACCCAGGTGCATCATGATGAAA
genomic: TACAATCTGTGAAATCTGCCATG-AGgtaaacaatt ... tgtttatcagTTGTACAAG-CCTGGTTACACTGCCCCAACCCAGGTGCATCATGATGAAA
EST: gi|211010477|gb|FL237651.1|FL237651
EST:     AACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAG                         TTGTACAAGCCTGGTTACACTGCCCCAACCCAGGTGCATCATGATGAAACT
genomic: AACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAGgtaaacaatt ... tgtttatcagTTGTACAAGCCTGGTTACACTGCCCCAACCCAGGTGCATCATGATGAAACT
EST: gi|76013718|gb|DT940888.1|DT940888
EST:     AACGATGGTGCAATGAGAAAGGAGATACAATCTGTGAAATCTGCCATGAG                         TTGTACAAGCCTGGTTACACTGCCCCAACCCAGGTGCATCATGATGAAACT
genomic: AACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAGgtaaacaatt ... tgtttatcagTTGTACAAGCCTGGTTACACTGCCCCAACCCAGGTGCATCATGATGAAACT
EST: gi|22818791|gb|BU498881.1|BU498881
EST:     AACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAG                         TTGTACAAGCCTGGTTACACTGCCCCAACCCAGGTGCATCATGATGAAACT
genomic: AACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAGgtaaacaatt ... tgtttatcagTTGTACAAGCCTGGTTACACTGCCCCAACCCAGGTGCATCATGATGAAACT
EST: gi|101402591|gb|EB822839.1|EB822839
EST:     AACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAG                         TTGTACAAGCCTGGTTACACTGCCCCAACCCAGGTGCATCATGATGAAACT
genomic: AACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAGgtaaacaatt ... tgtttatcagTTGTACAAGCCTGGTTACACTGCCCCAACCCAGGTGCATCATGATGAAACT
EST: gi|29947111|gb|CB816487.1|CB816487
EST:     AACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAG                         TTGTACAAGCCTGGTTACACTGCCCCAACCCAGGTGCATCATGATGAAACT
genomic: AACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAGgtaaacaatt ... tgtttatcagTTGTACAAGCCTGGTTACACTGCCCCAACCCAGGTGCATCATGATGAAACT
EST: gi|30307008|gb|CD001681.1|CD001681
EST:     AACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAG                         TTGTACAAGCCTGGTTACACTGCCCCAACCCAGGTGCATCATGATGAAACT
genomic: AACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAGgtaaacaatt ... tgtttatcagTTGTACAAGCCTGGTTACACTGCCCCAACCCAGGTGCATCATGATGAAACT
EST: gi|211010485|gb|FL237659.1|FL237659
EST:     AACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAG                         TTGTACAAGCCTGGTTACACTGCCCCAACCCAGGTGCATCATGATGAAACT
genomic: AACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAGgtaaacaatt ... tgtttatcagTTGTACAAGCCTGGTTACACTGCCCCAACCCAGGTGCATCATGATGAAACT
EST: gi|76936722|gb|DV174850.1|DV174850
EST:     AACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAG                         TTGTACAAGCCTGGTTACACTGCCCCAACCCAGGTGCATCATGATGAAACT
genomic: AACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAGgtaaacaatt ... tgtttatcagTTGTACAAGCCTGGTTACACTGCCCCAACCCAGGTGCATCATGATGAAACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAGgtaaacaattgtttccttcagctactactctaaatatatcaaaatggaaattaatgcatgcactgttttgtaatttcttgtataataagacttaaagatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatggaaa