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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAATgtgagtaggcaccgcctcttctactctcatgttatgttacttgtggtgtttatgcggttaacataacaacatatgtaacatgttgcttgtctcatttatt...

Basic information

species Zea mays
transcript GRMZM2G016296_T06
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G016296_T06 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os08g37960.1 (Oryza sativa), 5'ss of exon 4
GCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAATgtgagtagg---caccgcctcttctactctcatgttatgttacttgtggtgtttatgc--ggttaacataacaacatatgtaacatgttgcttgtctcatttatt
| ||| ||||||||||||| |||||||||||||||||||| ||||| || |||||||| |||||||||||||||||   |  ||     |||| | | |||| |  |  || ||  | | | |||  || ||   |   |   | || ||||||       | | ||||   
GGCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCCAAGTATGGGCCCAATGCGGAGCCAATgtgagtagggttcctcgttcgatctattgtgatgtca-atatctagttatatatgtgcatgggtaggttcttattgtttg-aacatggcaaccatgttattt---
















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|87157632|gb|DY402421.1|DY402421
EST:     AGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAAT                         CCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG
genomic: AGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAATgtgagtaggc ... ctttctgtagCCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG
EST: gi|33100209|gb|CF060169.1|CF060169
EST:     ACGGCCCCAATGCTGAGCCAAT                         CCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG
genomic: ACGGCCCCAATGCTGAGCCAATgtgagtaggc ... ctttctgtagCCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG
EST: gi|33100317|gb|CF060277.1|CF060277
EST:     ACGGCCCCAATGCTGAGCCAAT                         CCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG
genomic: ACGGCCCCAATGCTGAGCCAATgtgagtaggc ... ctttctgtagCCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG
EST: gi|18384287|gb|BM417486.1|BM417486
EST:     AGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAAT                         CCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG
genomic: AGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAATgtgagtaggc ... ctttctgtagCCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG
EST: gi|71766439|gb|DR964376.1|DR964376
EST:     AGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAAT                         CCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG
genomic: AGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAATgtgagtaggc ... ctttctgtagCCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG
EST: gi|33098747|gb|CF058707.1|CF058707
EST:     ACGGCCCCAATGCTGAGCCAAT                         CCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG
genomic: ACGGCCCCAATGCTGAGCCAATgtgagtaggc ... ctttctgtagCCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG
EST: gi|74235570|gb|DT643484.1|DT643484
EST:     AGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAAT                         CCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG
genomic: AGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAATgtgagtaggc ... ctttctgtagCCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG
EST: gi|71421374|gb|DR805394.1|DR805394
EST:     AGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAAT                         CCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG
genomic: AGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAATgtgagtaggc ... ctttctgtagCCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG
EST: gi|211456040|gb|FL150302.1|FL150302
EST:     AGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAAT                         CCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG
genomic: AGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAATgtgagtaggc ... ctttctgtagCCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG
EST: gi|211422683|gb|FL350037.1|FL350037
EST:     AGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAAT                         CCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG
genomic: AGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAATgtgagtaggc ... ctttctgtagCCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG
EST: gi|6022225|gb|AW067153.1|AW067153
EST:     AGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAAT                         CCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG
genomic: AGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAATgtgagtaggc ... ctttctgtagCCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG
EST: gi|32830771|gb|CD970449.1|CD970449
EST:     ACGGCCCCATTGCTGAG-CAATT                         CGGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAA
genomic: ACGGCCCCAATGCTGAGCCAA-Tgtgagtaggc ... ctttctgtagCCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAA
EST: gi|76280364|gb|DV019932.1|DV019932
EST:     AGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAAT                         CCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG
genomic: AGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAATgtgagtaggc ... ctttctgtagCCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG
EST: gi|71317634|gb|DR795571.1|DR795571
EST:     AGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAAT                         CCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG
genomic: AGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAATgtgagtaggc ... ctttctgtagCCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG
EST: gi|22489702|gb|BU049625.1|BU049625
EST:     AGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAAT                         CCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG
genomic: AGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAATgtgagtaggc ... ctttctgtagCCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG
EST: gi|211456031|gb|FL150293.1|FL150293
EST:     AGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAAT                         CCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGA
genomic: AGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAATgtgagtaggc ... ctttctgtagCCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGA
EST: gi|26558961|gb|CA831196.1|CA831196
EST:     AGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAAT                         CCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG
genomic: AGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAATgtgagtaggc ... ctttctgtagCCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG
EST: gi|33099574|gb|CF059534.1|CF059534
EST:     ACGGCCCCAATGCTGAGCCAAT                         CCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG
genomic: ACGGCCCCAATGCTGAGCCAATgtgagtaggc ... ctttctgtagCCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG
EST: gi|76936777|gb|DV174882.1|DV174882
EST:     AGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAAT                         CCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG
genomic: AGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAATgtgagtaggc ... ctttctgtagCCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG
EST: gi|50336916|gb|CO532042.1|CO532042
EST:     AGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAAT                         CCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG
genomic: AGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAATgtgagtaggc ... ctttctgtagCCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG
EST: gi|22545919|gb|BU098278.1|BU098278
EST:     AGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAAT                         CCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG
genomic: AGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAATgtgagtaggc ... ctttctgtagCCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG
EST: gi|74232258|gb|DT640172.1|DT640172
EST:     AGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAAT                         CCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG
genomic: AGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAATgtgagtaggc ... ctttctgtagCCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG
EST: gi|211456033|gb|FL150295.1|FL150295
EST:     AGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAAT                         CCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG
genomic: AGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAATgtgagtaggc ... ctttctgtagCCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG
EST: gi|211456029|gb|FL150291.1|FL150291
EST:     AGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAAT                         CCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG
genomic: AGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAATgtgagtaggc ... ctttctgtagCCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG
EST: gi|91873269|gb|EB403226.1|EB403226
EST:     AGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAAT                         CCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG
genomic: AGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAATgtgagtaggc ... ctttctgtagCCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG
EST: gi|211456038|gb|FL150300.1|FL150300
EST:     AGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAAT                         CCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG
genomic: AGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAATgtgagtaggc ... ctttctgtagCCGCAAAGGAAGGGTTAAAGAGGGGGTTGAGAAATCACAAGACAGATCAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAATgtgagtaggcaccgcctcttctactctcatgttatgttacttgtggtgtttatgcggttaacataacaacatatgtaacatgttgcttgtctcatttatt

- - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG