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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGGTTCGGTTCTTCTCGGCTGTGCCTTCCTGTATGATATCTTCTGGGTGTTTATCTCCAAGAGATGGTTTCATGAGAGCGTGATGATTGTGgtaagcgtgtgaaaggggattctgctatttggtggtatcctgaattttgctggttatagcatgttggtttcttctgcaaatag

Basic information

species Zea mays
transcript GRMZM2G165351_T02
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165351_T03 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os06g51430.1 (Oryza sativa), 5'ss of exon 10
GTGGGTTCGGTTCTTCTCGGCTGTGCCTTCCTGTATGATATCTTCTGGGTGTTTATCTCCAAGAGATGGTTTCATGAGAGCGTGATGATTGTGgtaagcgt-gtgaaag--------gggattctgctatttggtggtatcctgaattttgctggttatagcatgttggtttcttctgcaaatag
|||||||| ||||| ||| ||||||||||| | ||||| ||||||||||||||| |||||||||||||||||||||||||||||||||| ||||||||  | ||| ||          |  ||||| || |||||| | || |   ||  |||   |     ||| |||| |  |   ||||   
GTGGGTTCAGTTCTCCTCAGCTGTGCCTTCTTTTATGACATCTTCTGGGTGTTTGTCTCCAAGAGATGGTTTCATGAGAGCGTGATGATCGTGgtaagttttgtggaaatttattctagacttctggtaattggtgatctcattgtttaagctaagttggttatgctggtgtgcttctcaaag--

upper sequence: GRMZM2G165351_T03 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA07G07610.1 (Glycine max), 5'ss of exon 11
GTGGGTTCGGTTCTTCTCGGCTGTGCCTTCCTGTATGATATCTTCTGGGTGTTTATCTCCAAGAGATGGTTTCATGAGAGCGTGATGATTGTGgtaagcgtgtgaaagggga---------ttctgctatttggtg-gtatcctgaattttgctggttatagcatgttggtttcttctgcaaatag---------------
|| ||  | ||||||||| | ||||||||||| ||||| ||||||||||||||| |||| ||  | ||||| |||||||| |||||||| ||||| || || | ||||   |          ||| | |||        | | ||| ||| ||    || |  ||| || |||| | |  ||||                 
GTTGGAACTGTTCTTCTCAGTTGTGCCTTCCTATATGACATCTTCTGGGTGTTTGTCTCTAAACGGTGGTTCCATGAGAGTGTGATGATAGTGgtgagtgttttaaagaacaatcccccgtctctaccattcttcacaaagcttgattttggcctcatacatgatgctgttttcctgttaaaattattattctccatacag

upper sequence: GRMZM2G165351_T03 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA03G01100.2 (Glycine max), 5'ss of exon 10
GTGGGTTCGGTTCTTCTCGGCTGTGCCTTCCTGTATGATATCTTCTGGGTGTTTATCTCCAAGAGATGGTTTCATGAGAGCGTGATGATTGTGgtaagcgtgtgaaaggggattctgctatttggtggtatcctgaattttgctggttatagcatgttggtttcttctgcaaatag
|| ||  | ||||||||| | ||||||||||| ||||| || || ||||||||| |||| ||  | ||||| |||||||| |||||||| ||||| || || | ||||    |||| |  | |     | | |  ||  ||| |  |     |||    | | ||  |        
GTTGGAACTGTTCTTCTCAGTTGTGCCTTCCTATATGACATTTTTTGGGTGTTTGTCTCTAAACGGTGgttccatgagagtgtgatgatagtggtgagtgttttaaagaaagttct-ccctctaccattcttcccaaagttgattttggcctcatacatgatgctgttt-------

upper sequence: GRMZM2G165351_T03 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA18G46760.1 (Glycine max), 5'ss of exon 10
GTGGGTTCGGTTCTTCTCGGCTGTGCCTTCCTGTATGATATCTTCTGGGTGTTTATCTCCAAGAGATGGTTTCATGAGAGCGTGATGATTGTGgtaagcgtgtgaaaggggattctgctatttggtggtatcc-tgaattttgctggttat-------agcatgttggtttcttctgcaaatag-------------------------
|| ||  | ||||||||| | ||||||||||| || || ||||||||||||||| |||| ||  | ||||| |||||||| |||||||| ||||| || |  |   |||    ||| |  |    |  | | |   ||  ||| |  ||||       | |||| || |||  |    |||                            
GTCGGAACTGTTCTTCTCAGTTGTGCCTTCCTATACGACATCTTCTGGGTGTTTGTCTCTAAATGGTGGTTCCATGAGAGTGTGATGATAGTGgtgagtgatttcgaggaagatctcccttagactattcttcacaaagcttgttttttatctcataaaacatgatgcttttcttattaaactaatgcaacattttcacttctttgcag

upper sequence: GRMZM2G165351_T03 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA09G39500.1 (Glycine max), 5'ss of exon 10
GTGGGTTCGGTTCTTCTCGGCTGTGCCTTCCTGTATGATATCTTCTGGGTGTTTATCTCCAAGAGATGGTTTCATGAGAGCGTGATGATTGTGgtaagcgtgtgaaaggggattctgctatttggtggtatcctgaattttgctggttata-------gcatgttggtttcttctgcaaatag-----------------------------
|| ||  | ||||||||| | ||||||||||| || || ||||||||||||||| |||| ||  | ||||| |||||||| |||||||| ||||| || |  |    ||    ||| |  || |    ||||   ||  ||| |  | ||         |||| | | | ||| |   | ||                              
GTTGGAACTGTTCTTCTCAGTTGTGCCTTCCTATACGACATCTTCTGGGTGTTTGTCTCTAAATGGTGGTTCCATGAGAGTGTGATGATAGTGgtgagtgatttcttggaagatct-cccttcgacaatatcacaaagcttgtttttgatctcataatacatgattgatgcttttcttattaaactaatgcaacattttcacttctttgcag

upper sequence: GRMZM2G165351_T03 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA03G01100.1 (Glycine max), 5'ss of exon 10
GTGGGTTCGGTTCTTCTCGGCTGTGCCTTCCTGTATGATATCTTCTGGGTGTTTATCTCCAAGAGATGGTTTCATGAGAGCGTGATGATTGTGgtaagcgtgtgaaaggggattct------gctatttggtggtatcctgaattttgctggttatagcatgttggtttcttctgcaaatag---------------
|| ||  | ||||||||| | ||||||||||| ||||| || || ||||||||| |||| ||  | ||||| |||||||| |||||||| ||||| || || | ||||    ||||       | |||       |   ||| ||| ||    || |  ||| || |||| | |  ||||                 
GTTGGAACTGTTCTTCTCAGTTGTGCCTTCCTATATGACATTTTTTGGGTGTTTGTCTCTAAACGGTGGTTCCATGAGAGTGTGATGATAGTGgtgagtgttttaaagaaagttctccctctaccattcttcccaaagttgattttggcctcatacatgatgctgttttcctgttaaaattattattctccatacag

upper sequence: GRMZM2G165351_T03 (Zea mays), 5'ss of exon 8
lower sequence: AT1G63690.2 (Arabidopsis thaliana), 5'ss of exon 10
GTGGGTTCGGTTCTTCTCGGCTGTGCCTTCCTGTATGATATCTTCTGGGTGTTTATCTCCAAGAGATGGTTTCATGAGAGCGTGATGATTGTGgtaagcgtgtgaaaggggattctgctatttggtggtatcctgaattttgctggttatagcatgttggtttcttctgcaaatag-----------------------------------------------------------
|| ||  | ||||||||| ||||||||||| |||| |||||||||||||||||| |||||||||  | ||| || || ||||| |||||||| |||||      |      |  |  | |     | | ||     ||| |     |  |   |      | || | |  ||||                                                             
GTCGGGACAGTTCTTCTCAGCTGTGCCTTCTTGTACGATATCTTCTGGGTGTTTGTCTCCAAGAAGTTGTTCCACGAAAGCGTAATGATTGTCGTAAgtaaccaaccaatcagccatccaccattttgcataa-agattctaacaatgctcaaactcaaatctcctttagaaatcttcatcacgtctcatatgttcaagaaaatgcaacgttgcttctttcttctttgcaggtag

upper sequence: GRMZM2G165351_T03 (Zea mays), 5'ss of exon 8
lower sequence: AT1G63690.1 (Arabidopsis thaliana), 5'ss of exon 10
GTGGGTTCGGTTCTTCTCGGCTGTGCCTTCCTGTATGATATCTTCTGGGTGTTTATCTCCAAGAGATGGTTTCATGAGAGCGTGATGATTGTGgtaagcgtgtgaaaggggattctgctatttggtggtatcctgaattttgctggttatagcatgttggtttcttctgcaaatag-------------------------------------------------------
|| ||  | ||||||||| ||||||||||| |||| |||||||||||||||||| |||||||||  | ||| || || ||||| |||||||| |||||      |      |  |  | |     | | ||     ||| |     |  |   |      | || | |  ||||                                                         
GTCGGGACAGTTCTTCTCAGCTGTGCCTTCTTGTACGATATCTTCTGGGTGTTTGTCTCCAAGAAGTTGTTCCACGAAAGCGTAATGATTGTCgtaagtaaccaaccaatcagccatccaccattttgcataa-agattctaacaatgctcaaactcaaatctcctttagaaatcttcatcacgtctcatatgttcaagaaaatgcaacgttgcttctttcttctttgcag

upper sequence: GRMZM2G165351_T03 (Zea mays), 5'ss of exon 8
lower sequence: AT1G01650.1 (Arabidopsis thaliana), 5'ss of exon 10
GTGGGTTCGGTTCTTCTCGGCTGTGCCTTCCTGTATGATATCTTCTGGGTGTTTATCTCCAAGAGATGGTTTCATGAGAGCGTGATGATTGTGgtaagcgt----------------------gtgaaaggggattctgctatttggtggtatcctgaat--tttgctggttatagcatgttggtttcttctgcaaatag-----------------------------
|| || |  ||||||||| ||||||||||| ||||||| ||||||||||| ||| | || ||  | ||||| | ||| ||||||||||||||||||||  |                       || |||  || | || ||  |  |   |      ||  ||  |||  |    ||   || | |  || |  ||| |                             
GTCGGGTTTGTTCTTCTCAGCTGTGCCTTCATGTATGACATCTTCTGGGTTTTTGTTTCAAAATGGTGGTTCCGTGAAAGCGTGATGATTGTGgtaagtttttcttttttgctccagaccatcatgcaagaagactttgttagatattccaactacacatacttatctgtctgctccacactgatattatcggagaattgtacgtcttttcccattttcccacatatag

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|32843028|gb|CD982709.1|CD982709
EST:     TCTGGGTGTTTATCTCCAAGAGATGGTTTCATGAGAGCGTGATGATTGTG                         GTTGCGCGTGGCGACAAGACCGACGAGGATGGTGTGCCCATGCTGCTAAAA
genomic: TCTGGGTGTTTATCTCCAAGAGATGGTTTCATGAGAGCGTGATGATTGTGgtaagcgtgt ... ctgcaaatagGTTGCGCGTGGCGACAAGACCGACGAGGATGGTGTGCCCATGCTGCTAAAA
EST: gi|32848049|gb|CD987730.1|CD987730
EST:     TCTGGGTGTTTATCTCCAAGAGATGGTTTCATGAGAGCGTGATGATTGTG                         GTTGCGCGTGGCGACAAGACCGACGAGGATGGTGTGCCCATGCTGCTAAAA
genomic: TCTGGGTGTTTATCTCCAAGAGATGGTTTCATGAGAGCGTGATGATTGTGgtaagcgtgt ... ctgcaaatagGTTGCGCGTGGCGACAAGACCGACGAGGATGGTGTGCCCATGCTGCTAAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGGTTCGGTTCTTCTCGGCTGTGCCTTCCTGTATGATATCTTCTGGGTGTTTATCTCCAAGAGATGGTTTCATGAGAGCGTGATGATTGTGgtaagcgtgtgaaaggggattctgctatttggtggtatcctgaattttgctggttatagcatgttggtttcttctgcaaatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG