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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTACAACAGCAACAAGTCAAACCTCAAGTTGTATGTTAGAAGAGTGTTCATCTCTGATGAATTTGATGACCTTCTTCCGAAGTATCTCAGCTTTTTGAGGgtactatattgctacttcaagagcaaatatacaattaatttgaaaggcatatgttatactaaatcttacagtgatattctctctag

Basic information

species Zea mays
transcript GRMZM2G399073_T03
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G399073_T02 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os06g50300.1 (Oryza sativa), 5'ss of exon 10
CTACAACAGCAACAAGTCAAACCTCAAGTTGTATGTTAGAAGAGTGTTCATCTCTGATGAATTTGATGACCTTCTTCCGAAGTATCTCAGCTTTTTGAGGgtactatattgctacttcaagagcaaatatacaattaatttgaaaggcatatgttatactaaatcttacagtgatattctctctag
|||||||   |||||||||||||| ||||||||||||||||| || ||||||||||||||||||||||| |||||||||||||||||||||||||||| ||||||| ||| ||| |||| || | |  |    |||   || |  | | ||||     ||||| ||   ||   |||| ||| |||
CTACAACTCTAACAAGTCAAACCTTAAGTTGTATGTTAGAAGGGTTTTCATCTCTGATGAATTTGATGAGCTTCTTCCGAAGTATCTCAGCTTTTTGAAGgtactagattactatttcatgaacga-cacggtattccattcattgacttatgcagc-ctaaacctataagc--tattatctgtag

upper sequence: GRMZM2G399073_T02 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA17G37820.1 (Glycine max), 5'ss of exon 10
-CTACAACAGCAACAAGTCAAACCTCAAGTTGTATGTTAGAAGAGTGTTCATCTCTGATGAATTTGATGACCTTCTTCCGAAGTATCTCAGCTTTTTGAGGgtac---------tatattgctacttcaagagcaa-atatacaattaatttgaaaggcatatgttatactaaatcttacagt-gatattctctctag
  || |||   ||||| || ||||| ||||||||||||||| | |||||||| || ||||||||| |||| ||  | || ||||| || | |||||||  ||||          |   ||| || | ||     || ||||   || |   | | |   || | |  || ||||| ||||  | ||  ||      | 
ATTATAACGCAAACAAATCCAACCTGAAGTTGTATGTTAGACGTGTGTTCATTTCAGATGAATTTAATGAACTGTTGCCTAAGTACCTAAACTTTTTGCTggtaggaattgttgtgctttgttattgcagataaaatatattttatgatgatcagaataatttttgctaataaatgttacttttgacgttgggaaca-

upper sequence: GRMZM2G399073_T02 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA14G40320.3 (Glycine max), 5'ss of exon 10
CTACAACAGCAACAAGTCAAACCTCAAGTTGTATGTTAGAAGAGTGTTCATCTCTGATGAATTTGATGACCTTCTTCCGAAGTATCTCAGCTTTTTGAGGgtac-tatattgctacttcaagagcaaatatacaattaatttgaaaggcatatgttatactaaatcttac--agtgatattctctctag------------
 || |||   ||||| || ||||| ||||||||||||||| | |||||||| || ||||||||| |||| ||  | || ||||| || | |||||||  ||||   ||  |  | |||    |    | ||| |  || |||   |||      | ||| ||| | || |  |   || ||   | |              
TTATAACGCAAACAAATCGAACCTGAAGTTGTATGTTAGACGTGTGTTCATTTCAGATGAATTTAATGAACTGTTGCCCAAGTACCTAAACTTTTTGCTGgtaggcattgttgtgctttgttattgcagataaatatattttatgagg-----atcataataatttttgctaacaaatgtttcttttgacgttgggaacag

upper sequence: GRMZM2G399073_T02 (Zea mays), 5'ss of exon 12
lower sequence: AT4G24190.2 (Arabidopsis thaliana), 5'ss of exon 10
CTACAACAGCAACAAGTCAAACCTCAAGTTGTATGTTAGAAGAGTGTTCATCTCTGATGAATTTGATGACCTTCTTCCGAAGTATCTCAGCTTTTTGAGGgtactatattgctacttcaagagcaaatatacaattaatttgaaaggcatatgttatactaaatct-tacagtgatattctctc-tag
 ||||||||||||||| | ||| | ||| | ||||| || || ||||||||||| |||||||||||||| ||||| || |||||| | || || |||| ||||        |||||| ||   ||||   |    |  ||| ||    |  |  |   |||||||  ||  ||||  | || |   ||
TTACAACAGCAACAAGGCGAACTTGAAGCTATATGTCAGGAGGGTGTTCATCTCAGATGAATTTGATGAGCTTCTGCCTAAGTATTTGAGTTTCTTGAAGgtaa------actacttgaaagacaaactaaggggttctttcaatacaaatttatgggctaaatccctaacgtgagttgcttttgcag

upper sequence: GRMZM2G399073_T02 (Zea mays), 5'ss of exon 12
lower sequence: Vv18s0001g14500.t01 (Vitis vinifera), 5'ss of exon 10
CTACAACAGCAACAAGTCAAACCTCAAGTTGTATGTTAGAAGAGTGTTCATCTCTGATGAATTTGATGACCTTCTTCCGAAGTATCTCAGCTTTTTGAGGgtactatattgctacttcaagagcaaatatacaattaatttgaaaggcatatgttat--actaaatcttacagtgatattctctctag----------------
||| |||| ||| || || ||| | ||||||||||||||| | || ||||| ||||| ||||||||||| ||| | || |||||||| | |||||||| |||  || ||    | || |  |     |||    ||  | | ||  | | |  ||||  | ||  | |   ||||||  |||   | |                
CTATAACACCAAGAAATCCAACTTGAAGTTGTATGTTAGACGTGTATTCATTTCTGAAGAATTTGATGAGCTTTTGCCCAAGTATCTGAACTTTTTGAAGgttataaatc---aatttataaattcctattgggttcttgtaaactggagaatttatgaattaggtttagaagtgat--tctaaatgggtgacgttttgagcag

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|211478283|gb|FL245116.1|FL245116
EST:     TCTCTGATGAATTTGATGACCTTCTTCCGAAGTATCTCAGCTTTTTGAGG                         GGTATTGTTGACTCAGACACACTGCCGCTGAATGTGTCACGAGAAATGCTC
genomic: TCTCTGATGAATTTGATGACCTTCTTCCGAAGTATCTCAGCTTTTTGAGGgtactatatt ... ttctctctagGGTATTGTTGACTCAGACACACTGCCGCTGAATGTGTCACGAGAAATGCTC
EST: gi|32834169|gb|CD973847.1|CD973847
EST:     TCTCTGATGAATTTGATGACCTTCTTCCGAAGTATCTCAGCTTTTTGAGG                         GGTATTGTTGACTCAGACACACTGCCGCTGAATGTGTCACGAGAAATGCTC
genomic: TCTCTGATGAATTTGATGACCTTCTTCCGAAGTATCTCAGCTTTTTGAGGgtactatatt ... ttctctctagGGTATTGTTGACTCAGACACACTGCCGCTGAATGTGTCACGAGAAATGCTC
EST: gi|22489665|gb|BU049575.1|BU049575
EST:     TCTCTGATGAATTTGATGACCTTCTTCCGAAGTATCTCAGCTTTTTGAGG                         GGTATTGTTGACTCAGACACACTGCCGCTGAATGTGTCACGAGAAATGCTC
genomic: TCTCTGATGAATTTGATGACCTTCTTCCGAAGTATCTCAGCTTTTTGAGGgtactatatt ... ttctctctagGGTATTGTTGACTCAGACACACTGCCGCTGAATGTGTCACGAGAAATGCTC
EST: gi|31358114|gb|CD442471.1|CD442471
EST:     TCTCTGATGAATTTGATGACCTTCTTCCGAAGTATCTCAGCTTTTTGAGG                         GGTATTGTTGACTCAGACACACTGCCGCTTAATGTGTCACGAGAGGGGCTC
genomic: TCTCTGATGAATTTGATGACCTTCTTCCGAAGTATCTCAGCTTTTTGAGGgtactatatt ... ttctctctagGGTATTGTTGACTCAGACACACTGCCGCTGAATGTGTCACGAGAAATGCTC
EST: gi|19822479|gb|BQ048503.1|BQ048503
EST:     TCTCTGATGAATTTGATGACCTTCTTCCGAAGTATCTCAGCTTTTTGAGG                         GGTATTGTTGACTCAGACACACTGCCGCTGAATGTGTCACGAGAAATGCTC
genomic: TCTCTGATGAATTTGATGACCTTCTTCCGAAGTATCTCAGCTTTTTGAGGgtactatatt ... ttctctctagGGTATTGTTGACTCAGACACACTGCCGCTGAATGTGTCACGAGAAATGCTC
EST: gi|211478285|gb|FL245118.1|FL245118
EST:     TCTCTGATGAATTTGATGACCTTCTTCCGAAGTATCTCAGCTTTTTGAGG                         GGTATTGTTGACTCAGACACACTGCCGCTGAATGTGTCACGAGAAATGCTC
genomic: TCTCTGATGAATTTGATGACCTTCTTCCGAAGTATCTCAGCTTTTTGAGGgtactatatt ... ttctctctagGGTATTGTTGACTCAGACACACTGCCGCTGAATGTGTCACGAGAAATGCTC
EST: gi|211354990|gb|FL245115.1|FL245115
EST:     TCTCTGATGAATTTGATGACCTTCTTCCGAAGTATCTCAGCTTTTTGAGG                         GGTATTGTTGACTCAGACACACTGCCGCTGAATGTGTCACGAGAAATGCTC
genomic: TCTCTGATGAATTTGATGACCTTCTTCCGAAGTATCTCAGCTTTTTGAGGgtactatatt ... ttctctctagGGTATTGTTGACTCAGACACACTGCCGCTGAATGTGTCACGAGAAATGCTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTACAACAGCAACAAGTCAAACCTCAAGTTGTATGTTAGAAGAGTGTTCATCTCTGATGAATTTGATGACCTTCTTCCGAAGTATCTCAGCTTTTTGAGGgtactatattgctacttcaagagcaaatatacaattaatttgaaaggcatatgttatactaaatcttacagtgatattctctctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT