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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGCTAAGGAACTTGTAAGATCAAGACGTGCTGTTAATCGTCTTTATGAGAACAAGGCTCAACTAAATTCAGTATCAATGCACCTTGGAGAAATTGTCGgtatggcttttttatgatttttttttgttggtttggtgtctgacgttgtccaagagaatgtccttttaatttctggaagagtgattctgttagttaatat...

Basic information

species Zea mays
transcript GRMZM2G165195_T05
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165195_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os07g29630.1 (Oryza sativa), 5'ss of exon 3
CTTGCTAAGGAACTTGTAAGATCAAGACGTGCTGTTAATCGTCTTTATGAGAACAAGGCTCAACTAAATTCAGTATCAATGCACCTTGGAGAAATTGTCGgtatggcttttttatgatttttttttgttggtttggtgtctgacgttgtccaagagaatgtccttttaatttctggaagagtgattctgttagttaatat-
|||||||||||||| || || ||||||||||||||||||||||| ||||| |||||||||||||||||||||||||||||||| |||||||||||||| ||||||   ||||| |  || |    || | |   ||  |     |   | ||    ||  | | |   ||      |  |||   | ||   |  | ||  
CTTGCTAAGGAACTAGTGAGGTCAAGACGTGCTGTTAATCGTCTCTATGAAAACAAGGCTCAACTAAATTCAGTATCAATGCATCTTGGAGAAATTGTTGgtatgttctttttctttttatgagctgatagagaggatttattagcaattcagcctaaccttcatcgtatcagcccacaagttcct-tgcaggcaattaca

upper sequence: GRMZM2G165195_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA06G23570.2 (Glycine max), 5'ss of exon 4
CTTGCTAAGGAACTTGTAAGATCAAGACGTGCTGTTAATCGTCTTTATGAGAACAAGGCTCAACTAAATTCAGTATCAATGCACCTTGGAGAAATTGTCGgtatggcttttttatgatttttttttgttggtttggtgtctgacgttgtccaagagaatgtccttttaatttctggaagagtgattc-tgttagttaatat--
||||| ||||||||||| ||||| || |   |||| || || |||||||| ||||| || ||| | |||||| ||||||||||||||||||| | ||| |||| || ||||| ||| ||| ||    ||   ||  | | |  | || |   | | || |    | ||| ||    |   ||| ||  |   || |  |    
CTTGCCAAGGAACTTGTGAGATCTAGGCAAACTGTGAACCGCCTTTATGAAAACAAAGCACAAATGAATTCAATATCAATGCACCTTGGAGAGAGTGTTGgta-ggttttttcatgttttattagccttaacttaattttt--ccttatagcaaataaggattgtctaagttagttacttgtgtttaataccaggttcttgat

upper sequence: GRMZM2G165195_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA11G19930.1 (Glycine max), 5'ss of exon 4
CTTGCTAAGGAACTTGTAAGATCAAGACGTGCTGTTAATCGTCTTTATGAGAACAAGGCTCAACTAAATTCAGTATCAATGCACCTTGGAGAAATTGTCGgtatggcttttttatgatttttttttgttggtttggtgtctgacgttgtccaagagaatgtccttttaatttctggaagagtgattc-tgttagttaatat-
||| ||||||||||||| ||||| ||     | || || ||||||||||| || || || ||| | |||||| ||||||||||||||||||| | ||| |||| || ||||  ||| ||| ||    ||    |  | | || | |  |   | | || | |  | ||| ||    |   ||| ||  |   || |  |   
CTTACTAAGGAACTTGTGAGATCTAGGAAAACGGTGAACCGTCTTTATGAAAATAAAGCACAAATGAATTCAATATCAATGCACCTTGGAGAGAGTGTTGgta-ggtttttccatgttttattagccttaagataat-tttgccttgttaacaaataaggactctctaagttagttacctgtgcttgataccaggtttttga

upper sequence: GRMZM2G165195_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA12G08510.1 (Glycine max), 5'ss of exon 3
CTTGCTAAGGAACTTGTAAGATCAAGACGTGCTGTTAATCGTCTTTATGAGAACAAGGCTCAACTAAATTCAGTATCAATGCACCTTGGAGAAATTGTCGgtatggcttttttatgatttttttttgttg-gtttggtgtctgacgttgtccaagagaatgtccttttaatttctggaagagtgattctgttagttaatat
||||||||||||||||| ||||| ||     | || || ||||||||||| || || || ||| | |||||| ||||||||||||||||||| | ||| |||| || ||||  |||  ||    |  ||  |  | ||  |  |    | |      | |    |     |   ||  |    | ||  | || ||| |  
CTTGCTAAGGAACTTGTGAGATCTAGGAAAACGGTGAACCGTCTTTATGAAAATAAAGCACAAATGAATTCAATATCAATGCACCTTGGAGAGAGTGTTGgta-ggtttttccatgccttaagataattttgccttgtaacaaataaggactctctaagttagttacctgtacttgataccaggttttagataattattcc

upper sequence: GRMZM2G165195_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA04G21900.1 (Glycine max), 5'ss of exon 3
CTTGCTAAGGAACTTGTAAGATCAAGACGTGCTGTTAATCGTCTTTATGAGAACAAGGCTCAACTAAATTCAGTATCAATGCACCTTGGAGAAATTGTCGgtatggcttttttatgatttttttttgttggtttggtgtctgacgttgtccaagagaatgtccttttaatttctggaagagtgattc-tgttagttaatat--
||||||||||||||||| ||||| ||     |||| || ||||||||||| || || || ||| | |||||| ||||||||||||||||||| | ||| |||| || ||||  ||| ||| ||    ||   ||  | | |||| || |   | | || |    | ||| ||    |   ||| ||  |   || |  |    
CTTGCTAAGGAACTTGTGAGATCTAGGAAAACTGTGAACCGTCTTTATGAAAATAAAGCACAAATGAATTCAATATCAATGCACCTTGGAGAGAGTGTTGgta-ggtttttccatgttttgttagccttaacttaat-tttgac-ttatagcaaataaggattgtctaaattagttatttgtgtttagtaccaggttcttgat

upper sequence: GRMZM2G165195_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv06s0061g00540.t01 (Vitis vinifera), 5'ss of exon 4
CTTGCTAAGGAACTTGTAAGATCAAGACGTGCTGTTAATCGTCTTTATGAGAACAAGGCTCAACTAAATTCAGTATCAATGCACCTTGGAGAAATTGTCGgtatggcttttttatgatttttttttgttggtttggtgtctgacgttgtccaagag---aatgtccttttaatt----tctggaagagtgattctgttagttaatat
||||||| |||| |||| ||||| ||| |  | || || |||||| |||| |||||||||||| | |||||  |||||||||||||||| |||| ||| |||| |      |    |    | | | |   | | |    ||    | || || |    ||  |||| | || |     |  | ||||   | |   | ||      
CTTGCTATGGAAATTGTGAGATCTAGAAGAACAGTGAACCGTCTTCATGAAAACAAGGCTCAATTGAATTCTATATCAATGCACCTTGGGGAAAGTGTTGgtaagataacatatctaaacatgtgtatcc-tgttgcacatgttactatctaaaactgcaacttcctctaaaatacatccctgcagagcagtgcctgttgt------

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|211495219|gb|FL000399.1|FL000399
EST:     GAACAAGGCTCAACTAAATTCAGTATCAATGCACCTTGGAGAAATTGTCG                         CAACTGCAAGAACAGTGGGTCATCTGTCCAAAAGCACTGAAGTGATGAAAA
genomic: GAACAAGGCTCAACTAAATTCAGTATCAATGCACCTTGGAGAAATTGTCGgtatggcttt ... caattttcagCAACTGCAAGAACAGTGGGTCATCTGTCCAAAAGCACTGAAGTGATGAAAA
EST: gi|76010550|gb|DT937720.1|DT937720
EST:     GAACAAGGCTCAACTAAATTCAGTATCAATGCACCTTGGAGAAATTGTCG                         CAACTGCAAGAACAGTGGGTCATCTGTCCAAAAGCACTGAAGTGATGAAAA
genomic: GAACAAGGCTCAACTAAATTCAGTATCAATGCACCTTGGAGAAATTGTCGgtatggcttt ... caattttcagCAACTGCAAGAACAGTGGGTCATCTGTCCAAAAGCACTGAAGTGATGAAAA
EST: gi|71765371|gb|DR963308.1|DR963308
EST:     GAACAAGGCTCAACTAAATTCAGTATCAATGCACCTTGGAGAAATTGTCG                         CAACTGCAAGAACAGTGGGTCATCTGTCCAAAAGCACTGAAGTGATGAAAA
genomic: GAACAAGGCTCAACTAAATTCAGTATCAATGCACCTTGGAGAAATTGTCGgtatggcttt ... caattttcagCAACTGCAAGAACAGTGGGTCATCTGTCCAAAAGCACTGAAGTGATGAAAA
EST: gi|32867970|gb|CF007652.1|CF007652
EST:     AACTAAATTCAGTATCAATGCACCTTGGAGAAATTGTCG                         CAACTGCAAGAACAGTGGGTCATCTGTCCAAAAGCACTGAAGTGATGAAAA
genomic: AACTAAATTCAGTATCAATGCACCTTGGAGAAATTGTCGgtatggcttt ... caattttcagCAACTGCAAGAACAGTGGGTCATCTGTCCAAAAGCACTGAAGTGATGAAAA
EST: gi|211495220|gb|FL000400.1|FL000400
EST:     GAACAAGGCTCAACTAAATTCAGTATCAATGCACCTTGGAGAAATTGTCG                         CAACTGCAAGAACAGTGGGTCATCTGTCCAAAAGCACTGAAGTGATGAAAA
genomic: GAACAAGGCTCAACTAAATTCAGTATCAATGCACCTTGGAGAAATTGTCGgtatggcttt ... caattttcagCAACTGCAAGAACAGTGGGTCATCTGTCCAAAAGCACTGAAGTGATGAAAA
EST: gi|78074982|gb|DV503416.1|DV503416
EST:     CTAAATTCAGTATCAATGCACCTTGGAGAAATTGTCG                         CAACTGCAAGAACAGTGGGTCATCTGTCCAAAAGCACTGAAGTGATGAAAA
genomic: CTAAATTCAGTATCAATGCACCTTGGAGAAATTGTCGgtatggcttt ... caattttcagCAACTGCAAGAACAGTGGGTCATCTGTCCAAAAGCACTGAAGTGATGAAAA
EST: gi|76281952|gb|DV021520.1|DV021520
EST:     AAATTCAGTATCAATGCACCTTGGAGAAATTGTCG                         CAACTGCAAGAACAGTGGGTCATCTGTCCAAAAGCACTGAAGTGATGAAAA
genomic: AAATTCAGTATCAATGCACCTTGGAGAAATTGTCGgtatggcttt ... caattttcagCAACTGCAAGAACAGTGGGTCATCTGTCCAAAAGCACTGAAGTGATGAAAA
EST: gi|32867969|gb|CF007651.1|CF007651
EST:     AACTAAATTCAGTATCAATGCACCTTGGAGAAATTGTCG                         CAACTGCAAGAACAGTGGGTCATCTGTCCAAAAGCACTGAAGTGATGAAAA
genomic: AACTAAATTCAGTATCAATGCACCTTGGAGAAATTGTCGgtatggcttt ... caattttcagCAACTGCAAGAACAGTGGGTCATCTGTCCAAAAGCACTGAAGTGATGAAAA
EST: gi|76933730|gb|DV173563.1|DV173563
EST:     GAACAAGGCTCAACTAAATTCAGTATCAATGCACCTTGGAGAAATTGTCG                         CAACTGCAAGAACAGTGGGTCATCTGTCCAAAAGCACTGAAGTGATGAAAA
genomic: GAACAAGGCTCAACTAAATTCAGTATCAATGCACCTTGGAGAAATTGTCGgtatggcttt ... caattttcagCAACTGCAAGAACAGTGGGTCATCTGTCCAAAAGCACTGAAGTGATGAAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGCTAAGGAACTTGTAAGATCAAGACGTGCTGTTAATCGTCTTTATGAGAACAAGGCTCAACTAAATTCAGTATCAATGCACCTTGGAGAAATTGTCGgtatggcttttttatgatttttttttgttggtttggtgtctgacgttgtccaagagaatgtccttttaatttctggaagagtgattctgttagttaatat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA