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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAATTGTTTGTAGCTGTTAGAAGCGAGTTAAATCTGGACTTAAAGAACATTAAGACAGAACAAGCAAAGTTCTGGAAGCAGCATCCATCACTAGTAAAGgttggccttttctgactagattctatgatgcacaagatataaactgatctccacaatctgaaaagctataattttaatttcttcattttattgcag

Basic information

species Zea mays
transcript GRMZM2G007871_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G007871_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os04g24180.1 (Oryza sativa), 5'ss of exon 7
AAAATTGTTTGTAGCTGTTAGAAGCGAGTTAAATCTGGACTTAAAGAACATTAAGACAGAACAAGCAAAGTTCTGGAAGCAGCATCCATCACTAGTAAAGgttggccttttctgactagattctatgatgcacaagatataaactg--atctccacaatctgaaaagctataattttaatttcttcattttattgcag
 ||||| |||||||||||||| || || |||||||| ||||| ||||| ||||  ||||||||||| || |||||||||||||||||||| ||||| |||||||| |||||    |||  |  ||||   |||||  |   | |||  |  |    |||||   |||||  ||| |   |    |  | ||   |   
GAAATTATTTGTAGCTGTTAGGAGTGAATTAAATCTAGACTTGAAGAATATTAGAACAGAACAAGCTAAATTCTGGAAGCAGCATCCATCTCTAGTGAAGgttggtctttttctgctaagtgttatggcacacaaacttatatctgtgacatgacaaatcttgcaagctcaaatatctgtcatctactcttgcag---

upper sequence: GRMZM2G007871_T02 (Zea mays), 5'ss of exon 6
lower sequence: Vv16s0050g01460.t01 (Vitis vinifera), 5'ss of exon 6
AAAATTGTTTGTAGCTGTTAGAAGCGAGTTAAATCTGGACTTAAAGAACATTAAGACAGAACAAGCAAAGTTCTGGAAGCAGCATCCATCACTAGTAAAGgttggccttttctgactagattctatgatgcacaagatataaac-tgatctccacaatct-----gaaaagctataattttaatttctt--cattttattgcag
 ||| ||||  |    || || || ||||||||  ||||| | ||||||||||||  ||| || |||||||| ||||||||||||||||||||||| |||||     || |    | || ||     ||  | |  |  ||||  | | |  |  | |||     |||     |   | ||| ||  ||  | |||  || |||
GAAACTGTTCATGTTAGTAAGGAGTGAGTTAAACTTGGACCTTAAGAACATTAAGCAAGAGCAGGCAAAGTTTTGGAAGCAGCATCCATCACTAGTTAAGgtaa--tttgttcaccaagttttggctatataaagcagttaaagatcagcgtcttagtctttaatgaagcatcagcttcttacttctttgccttttcctttcag
















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|32838158|gb|CD977836.1|CD977836
EST:     TTAAGACAGAACAAGCAAAGTTCTGGAAGCAGCATCCATCACTAGTAAAG                         ATGGAACTGCTGATTCAGGCGCATCTCACTTGTGAGTCATTCGCTTTGACG
genomic: TTAAGACAGAACAAGCAAAGTTCTGGAAGCAGCATCCATCACTAGTAAAGgttggccttt ... tttattgcagATGGAACTGCTGATTCAGGCGCATCTCACTTGTGAGTCATTCGCTTTGACG
EST: gi|22715113|gb|BU197585.1|BU197585
EST:     TTAAGACAGAACAAGCAAAGTTCTGGAAGCAGCATCCATCACTAGTAAAG                         ATGGAACTGCTGATTCAGGCGCATCTCACTTGTGAGTCATTCGCTTTGACG
genomic: TTAAGACAGAACAAGCAAAGTTCTGGAAGCAGCATCCATCACTAGTAAAGgttggccttt ... tttattgcagATGGAACTGCTGATTCAGGCGCATCTCACTTGTGAGTCATTCGCTTTGACG
EST: gi|26559135|gb|CA831370.1|CA831370
EST:     TTAAGACAGAACAAGCAAAGATCTGGAAGCAGCATCCATCACTAGTAAAG                         ATGGAACTGCTGATTCAGGCGCATCTCACTTGTGAGTCATTCGCTTTGACG
genomic: TTAAGACAGAACAAGCAAAGTTCTGGAAGCAGCATCCATCACTAGTAAAGgttggccttt ... tttattgcagATGGAACTGCTGATTCAGGCGCATCTCACTTGTGAGTCATTCGCTTTGACG
EST: gi|22935564|gb|BU571839.1|BU571839
EST:     TTAAGACAGAACAAGCAAAGTTCTGGAAGCAGCATCCATCACTAGTAAAG                         ATGGAACTGCTGATTCAGGCGCATCTCACTTGTGAGTCATTCGCTTTGACG
genomic: TTAAGACAGAACAAGCAAAGTTCTGGAAGCAGCATCCATCACTAGTAAAGgttggccttt ... tttattgcagATGGAACTGCTGATTCAGGCGCATCTCACTTGTGAGTCATTCGCTTTGACG
EST: gi|26560014|gb|CA832249.1|CA832249
EST:     TTAAGACAGAACAAGCAAAGTTCTGGAAGCAGCATCCATCACTAGTAAAG                         ATGGAACTGCTGATTCAGGCGCATCTCACTTGTGAGTCATTCGCTTTGACG
genomic: TTAAGACAGAACAAGCAAAGTTCTGGAAGCAGCATCCATCACTAGTAAAGgttggccttt ... tttattgcagATGGAACTGCTGATTCAGGCGCATCTCACTTGTGAGTCATTCGCTTTGACG
EST: gi|32837602|gb|CD977280.1|CD977280
EST:     TTAAGACAGAACAAGCAAAGTTCTGGAAGCAGCATCCATCACTAGTAAAG                         ATGGAACTGCTGATTCAGGCGCATCTCACTTGTGAGTCATTCGCTTTGACG
genomic: TTAAGACAGAACAAGCAAAGTTCTGGAAGCAGCATCCATCACTAGTAAAGgttggccttt ... tttattgcagATGGAACTGCTGATTCAGGCGCATCTCACTTGTGAGTCATTCGCTTTGACG
EST: gi|87156492|gb|DY401281.1|DY401281
EST:     TTAAGACAGAACAAGCAAAGTTCTGGAAGCAGCATCCATCACTAGTAAAG                         ATGGAACTGCTGATTCAGGCGCATCTCACTTGTGAGTCATTCGCTTTGACG
genomic: TTAAGACAGAACAAGCAAAGTTCTGGAAGCAGCATCCATCACTAGTAAAGgttggccttt ... tttattgcagATGGAACTGCTGATTCAGGCGCATCTCACTTGTGAGTCATTCGCTTTGACG
EST: gi|32836675|gb|CD976353.1|CD976353
EST:     TTAAGACAGAACAAGCAAAGTTCTGGAAGCAGCATCCATCACTAGTAAAG                         ATGGAACTGCTGATTCAGGCGCATCTCACTTGTGAGTCATTCGCTTTGACG
genomic: TTAAGACAGAACAAGCAAAGTTCTGGAAGCAGCATCCATCACTAGTAAAGgttggccttt ... tttattgcagATGGAACTGCTGATTCAGGCGCATCTCACTTGTGAGTCATTCGCTTTGACG
EST: gi|22542214|gb|BU092652.1|BU092652
EST:     TTAAGACAGAACAAGCAAAGTTCTGGAAGCAGCATCCATCACTAGTAAAG                         ATGGAACTGCTGATTCAGGCGCATCTCACTTGTGAGTCATTCGCTTTGACG
genomic: TTAAGACAGAACAAGCAAAGTTCTGGAAGCAGCATCCATCACTAGTAAAGgttggccttt ... tttattgcagATGGAACTGCTGATTCAGGCGCATCTCACTTGTGAGTCATTCGCTTTGACG
EST: gi|87157186|gb|DY401975.1|DY401975
EST:     TTAAGACAGAACAAGCAAAGTTCTGGAAGCAGCATCCATCACTAGTAAAG                         ATGGAACTGCTGATTCAGGCGCATCTCACTTGTGAGTCATTCGCTTTGACG
genomic: TTAAGACAGAACAAGCAAAGTTCTGGAAGCAGCATCCATCACTAGTAAAGgttggccttt ... tttattgcagATGGAACTGCTGATTCAGGCGCATCTCACTTGTGAGTCATTCGCTTTGACG
EST: gi|87157024|gb|DY401813.1|DY401813
EST:     TTAAGACAGAACAAGCAAAGTTCTGGAAGCAGCATCCATCACTAGTAAAG                         ATGGAACTGCTGATTCAGGCGCATCTCACTTGTGAGTCATTCGCTTTGACG
genomic: TTAAGACAGAACAAGCAAAGTTCTGGAAGCAGCATCCATCACTAGTAAAGgttggccttt ... tttattgcagATGGAACTGCTGATTCAGGCGCATCTCACTTGTGAGTCATTCGCTTTGACG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAATTGTTTGTAGCTGTTAGAAGCGAGTTAAATCTGGACTTAAAGAACATTAAGACAGAACAAGCAAAGTTCTGGAAGCAGCATCCATCACTAGTAAAGgttggccttttctgactagattctatgatgcacaagatataaactgatctccacaatctgaaaagctataattttaatttcttcattttattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG