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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccgtgcaattaattcctagcttcccggcccttttatttgcctgcatgcttcaattcggacgaattcgatcggacgaaatcaaatttgctaaccttaattttataataataataatataagGATCGAGGACGTGATCACGAGGTACATCAATCTCCCGGAGCACGACAGAGGAGG

Basic information

species Zea mays
transcript GRMZM2G334225_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G334225_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os06g11970.1 (Oryza sativa), 3'ss of exon 1
gtccgtgcaattaattcctagctt--cccggcccttttatttgcctgcatgcttcaattcggacgaattcgatcggacgaaatcaaatttgctaaccttaattttataataataataatataagGATCGAGGACGTGATCACGAGGTACATCAATCTCCCGGAGCACGACAGAGGAGG
||   |  |||||| |   |       |    |   ||| ||  |  ||||| |  |||||        |   |  |    |||| || |  | |  | |||||| |       |   | || |||||||||||||| |||| ||||||||||||||||| ||    |||||||||||
gtaaat-taattaagtttaaatcaaatcaaatcaaattaattaaccacatgcatgcattcgacttcgagcatgcaaatttgatcatatatagtcatgt-aattttttg----cgactttgta-gGATCGAGGACGTGCTCACAAGGTACATCAATCTCCCAGAAAGTGACAGAGGAGG
















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|71771389|gb|DR969326.1|DR969326
EST:     ATCATGTTCTCGCCCTCCAATCGCCTCAGCCACTTCTCCGGCAGGCGCAG                         GATCGAGGACGTGATCACGAGGTACATCAATCTCCCGGAGCACGACAGAGG
genomic: ATCATGTTCTCGCCCTCCAATCGCCTCAGCCACTTCTCCGGCAGGCGCAGgtccgtgcaa ... ataatataagGATCGAGGACGTGATCACGAGGTACATCAATCTCCCGGAGCACGACAGAGG
EST: gi|211397005|gb|FL238530.1|FL238530
EST:     ATCATGTTCTCGCCCTCCAATCGCCTCAGCCACTTCTCCGGCAGGCGCAG                         GATCGAGGACGTGATCACGAGGTACATCAATCTCCCGGAGCACGACAGAGG
genomic: ATCATGTTCTCGCCCTCCAATCGCCTCAGCCACTTCTCCGGCAGGCGCAGgtccgtgcaa ... ataatataagGATCGAGGACGTGATCACGAGGTACATCAATCTCCCGGAGCACGACAGAGG
EST: gi|211397006|gb|FL238531.1|FL238531
EST:     ATCATGTTCTCGCCCTCCAATCGCCTCAGCCACTTCTCCGGCAGGCGCAG                         GATCGAGGACGTGATCACGAGGTACATCAATCTCCCGGAGCACGACAGAGG
genomic: ATCATGTTCTCGCCCTCCAATCGCCTCAGCCACTTCTCCGGCAGGCGCAGgtccgtgcaa ... ataatataagGATCGAGGACGTGATCACGAGGTACATCAATCTCCCGGAGCACGACAGAGG
EST: gi|211397001|gb|FL238526.1|FL238526
EST:     ATCATGTTCTCGCCCTCCAATCGCCTCAGCCACTTCTCCGGCAGGCGCAG                         GATCGAGGACGTGATCACGAGGTACATCAATCTCCCGGAGCACGACAGAGG
genomic: ATCATGTTCTCGCCCTCCAATCGCCTCAGCCACTTCTCCGGCAGGCGCAGgtccgtgcaa ... ataatataagGATCGAGGACGTGATCACGAGGTACATCAATCTCCCGGAGCACGACAGAGG
EST: gi|211520163|gb|FL238537.1|FL238537
EST:     ATCATGTTCTCGCCCTCCAATCGCCTCAGCCACTTCTCCGGCAGGCGCAG                         GATCGAGGACGTGATCACGAGGTACATCAATCTCCCGGAGCACGACAGAGG
genomic: ATCATGTTCTCGCCCTCCAATCGCCTCAGCCACTTCTCCGGCAGGCGCAGgtccgtgcaa ... ataatataagGATCGAGGACGTGATCACGAGGTACATCAATCTCCCGGAGCACGACAGAGG
EST: gi|211397002|gb|FL238527.1|FL238527
EST:     ATCATGTTCTCGCCCTCCAATCGCCTCAGCCACTTCTCCGGCAGGCGCAG                         GATCGAGGACGTGATCACGAGGTACATCAATCTCCCGGAGCACGACAGAGG
genomic: ATCATGTTCTCGCCCTCCAATCGCCTCAGCCACTTCTCCGGCAGGCGCAGgtccgtgcaa ... ataatataagGATCGAGGACGTGATCACGAGGTACATCAATCTCCCGGAGCACGACAGAGG
EST: gi|74233594|gb|DT641508.1|DT641508
EST:     ATCATGTTCTCGCCCTCCAATCGCCTCAGCCACTTCTCCGGCAGGCGCAG                         GATCGAGGACGTGATCACGAGGTACATCAATCTCCCGGAGCACGACAGAGG
genomic: ATCATGTTCTCGCCCTCCAATCGCCTCAGCCACTTCTCCGGCAGGCGCAGgtccgtgcaa ... ataatataagGATCGAGGACGTGATCACGAGGTACATCAATCTCCCGGAGCACGACAGAGG
EST: gi|211520159|gb|FL238533.1|FL238533
EST:     ATCATGTTCTCGCCCTCCAATCGCCTCAGCCACTTCTCCGGCAGGCGCAG                         GATCGAGGACGTGATCACGAGGTACATCAATCTCCCGGAGCACGACAGAGG
genomic: ATCATGTTCTCGCCCTCCAATCGCCTCAGCCACTTCTCCGGCAGGCGCAGgtccgtgcaa ... ataatataagGATCGAGGACGTGATCACGAGGTACATCAATCTCCCGGAGCACGACAGAGG
EST: gi|211520162|gb|FL238536.1|FL238536
EST:     ATCATGTTCTCGCCCTCCAATCGCCTCAGCCACTTCTCCGGCAGGCGCAG                         GATCGAGGACGTGATCACGAGGTACATCAATCTCCCGGAGCACGACAGAGG
genomic: ATCATGTTCTCGCCCTCCAATCGCCTCAGCCACTTCTCCGGCAGGCGCAGgtccgtgcaa ... ataatataagGATCGAGGACGTGATCACGAGGTACATCAATCTCCCGGAGCACGACAGAGG
EST: gi|211397004|gb|FL238529.1|FL238529
EST:     ATCATGTTCTCGCCCTCCAATCGCCTCAGCCACTTCTCCGGCAGGCGCAG                         GATCGAGGACGTGATCACGAGGTACATCAATCTCCCGGAGCACGACAGAGG
genomic: ATCATGTTCTCGCCCTCCAATCGCCTCAGCCACTTCTCCGGCAGGCGCAGgtccgtgcaa ... ataatataagGATCGAGGACGTGATCACGAGGTACATCAATCTCCCGGAGCACGACAGAGG
EST: gi|211397003|gb|FL238528.1|FL238528
EST:     ATCATGTTCTCGCCCTCCAATCGCCTCAGCCACTTCTCCGGCAGGCGCAG                         GATCGAGGACGTGATCACGAGGTACATCAATCTCCCGGAGCACGACAGAGG
genomic: ATCATGTTCTCGCCCTCCAATCGCCTCAGCCACTTCTCCGGCAGGCGCAGgtccgtgcaa ... ataatataagGATCGAGGACGTGATCACGAGGTACATCAATCTCCCGGAGCACGACAGAGG
EST: gi|211520161|gb|FL238535.1|FL238535
EST:     ATCATGTTCTCGCCCTCCAATCGCCTCAGCCACTTCTCCGGCAGGCGCAG                         GATCGAGGACGTGATCACGAGGTACATCAATCTCCCGGAGCACGACAGANG
genomic: ATCATGTTCTCGCCCTCCAATCGCCTCAGCCACTTCTCCGGCAGGCGCAGgtccgtgcaa ... ataatataagGATCGAGGACGTGATCACGAGGTACATCAATCTCCCGGAGCACGACAGAGG
EST: gi|50333189|gb|CO528315.1|CO528315
EST:     ATCATGTTCTCGCCCTCCAATCGCCTCAGCCACTTCTCCGGCAGGCGCAG                         GATCGAGGACGTGATCACGAGGTACATCAATCTCCCGGAGCACGACAGAGG
genomic: ATCATGTTCTCGCCCTCCAATCGCCTCAGCCACTTCTCCGGCAGGCGCAGgtccgtgcaa ... ataatataagGATCGAGGACGTGATCACGAGGTACATCAATCTCCCGGAGCACGACAGAGG
EST: gi|211520160|gb|FL238534.1|FL238534
EST:     ATCATGTTCTCGCCCTCCAATCGCCTCAGCCACTTCTCCGGCAGGCGCAG                         GATCGAGGACGTGATCACGAGGTACATCAATCTCCCGGAGCACGACAGAGG
genomic: ATCATGTTCTCGCCCTCCAATCGCCTCAGCCACTTCTCCGGCAGGCGCAGgtccgtgcaa ... ataatataagGATCGAGGACGTGATCACGAGGTACATCAATCTCCCGGAGCACGACAGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgatcggacgaaatcaaatttgctaaccttaattttataataataataatataagGATCGAGGACGTGATCACGAGGTACATCAATCTCCCGGAGCACGACAGAGGAGG
               aaatttgctaacctta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtccgtgcaattaattcctagcttcccggcccttttatttgcctgcatgcttcaattcggacgaattcgatcggacgaaatcaaatttgctaaccttaattttataataataataatataagGATCGAGGACGTGATCACGAGGTACATCAATCTCCCGGAGCACGACAGAGGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG