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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtgctgtatcttctcaggcatcaatgattgagcgcttcgtgtttgcaggatgcgtactcctgtcatgcgttttgctcgtgcaatttttacaatgcagtagcatttgatggttgtgtctggctctgattgattctaactgatgagcctgcattctgaaacagACATCTCTACGGGAGCTCACTACCCTTGGAATCAAGAATGCTGAGAATTTAGCAATTCCAAGTGTTAGAAATGAT

Basic information

species Zea mays
transcript GRMZM2G004352_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G004352_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g54640.2 (Oryza sativa), 3'ss of exon 2
gtcagtgctgtatcttctcaggcatcaatgattgagcgcttcgtgtttgcaggatgcgtactcctgt-catgcgttttgctcgt---gcaatttttacaatgcagtagcatttgatggttgtgtctggctctgattgat-tctaactgatgagcctgcattctgaaacagACATCTCTACGGGAGCTCACTACCCTTGGAATCAAGAATGCTGAGAATTTAGCAATTCCAAGTGTTAGAAATGAT
||||||||  ||||||| |  ||| |||    |  |   || |   ||||||   || | || |  | | |  ||| |   |||   | |   |||    | || |    ||  ||||  |   || |  ||||||| | |     |  |     |      ||  |||||||||||| || |||||||| || ||||| || ||||| ||||||||  | || ||||| ||||| |||||||||
gtcagtgcgatatcttcccgagcaccaagcgcttcgaattt-gcagttgcagagagcattcttccctacttctgttgtcagcgtcaggtagagttttgggt-caatgcggttgcatgggag---cttgaactgattggtgttctttttttttttttatgaattgtgacagACATCTCTGCGAGAGCTCACCACGCTTGGGATAAAGAACGCTGAGAACCTGGCGATTCCGAGTGTCAGAAATGAT

upper sequence: GRMZM2G004352_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv07s0031g01560.t01 (Vitis vinifera), 3'ss of exon 2
----------gtcagtgctgt-atcttctcaggcatcaatgattgagcgct--tcgtgtttgcagg---atgcgtactcctgtcatgcgttttgctcgtgcaatttttacaatgcagtagcatttgatggttgtgtctggctctgattgattctaactgatgagcctgcattc-tgaaacagACATCTCTACGGGAGCTCACTACCCTTGGAATCAAGAATGCTGAGAATTTAGCAATTCCAAGTGTTAGAAATGAT
           | |    ||| |  ||||  |  |    |  |  | |  |   |   | | ||     |||| |||   |  ||||  |  ||    |     |  | |  |  ||   || |   | |||   | |||||   |   |       | |||  ||  ||||  || | ||||||||||| |||||||| || ||||||||||| |||||||| || ||  | ||||||||||||||||||||||||
gtcagtccccattacaagtgtgaagttctgggaaagtgctactcaaacattagccacatctacaaacccatgcatacatgta-catgaataatgtctatctgtatactgccttaaagatccactcatttgttaaatttggctggaaaataaatagtatcatgttccaacatttgtgcaccagACATCTCTTCGGGAGCTGACAACCCTTGGAATGAAGAATGCGGAAAACCTTGCAATTCCAAGTGTTAGAAATGAT
















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|211057845|gb|FL422564.1|FL422564
EST:     GCGGATGGGCCAAGCGGTGGGGCTCGCAGCCCTATGTGTCGCGCCGGACG                         ACATCTCTACGGGARCTCACTACCCTTGGAATCAAGAATGCTGAGAATTTA
genomic: GCGGATGGGCCAAGCGGTGGGGCTCGCAGCCCTATGTGTCGCGCCGGACGgtcagtgctg ... tctgaaacagACATCTCTACGGGAGCTCACTACCCTTGGAATCAAGAATGCTGAGAATTTA
EST: gi|50329898|gb|CO525024.1|CO525024
EST:     GCGGATGGGCCAAGCGGTGGGGCTCGCAGCCCTATGTGTCGCGCCGGACG                         ACATCTCTACGGGAGCTCACTACCCTTGGAATCAAGAATGCTGAGAATTTA
genomic: GCGGATGGGCCAAGCGGTGGGGCTCGCAGCCCTATGTGTCGCGCCGGACGgtcagtgctg ... tctgaaacagACATCTCTACGGGAGCTCACTACCCTTGGAATCAAGAATGCTGAGAATTTA
EST: gi|211212631|gb|FL412327.1|FL412327
EST:     GCGGATGGGCCAAGCGGTGGGGCTCGCAGCCCTATGTGTCGCGCCGGACG                         ACATCTCTACGGGAGCTCACTACCCTTGGAATCAAGAATGCTGAGAATTTA
genomic: GCGGATGGGCCAAGCGGTGGGGCTCGCAGCCCTATGTGTCGCGCCGGACGgtcagtgctg ... tctgaaacagACATCTCTACGGGAGCTCACTACCCTTGGAATCAAGAATGCTGAGAATTTA
EST: gi|148954649|gb|EC900096.2|EC900096
EST:     GCGGATGGGCCAAGCGGTGGGGCTCGCAGCCCTATGTGTCGCGCCGGACG                         ACATCTCTACGGGAGCTCACTACCCTTGGAATCAAGAATGCTGAGAATTTA
genomic: GCGGATGGGCCAAGCGGTGGGGCTCGCAGCCCTATGTGTCGCGCCGGACGgtcagtgctg ... tctgaaacagACATCTCTACGGGAGCTCACTACCCTTGGAATCAAGAATGCTGAGAATTTA
EST: gi|149084909|gb|EE174419.2|EE174419
EST:     GCGGATGGGCCAAGCGGTGGGGCTCGCAGCCCTATGTGTCGCGCCGGACG                         ACATCTCTACGGGAGCTCACTACCCTTGGAATCAAGAATGCTGAGAATTTA
genomic: GCGGATGGGCCAAGCGGTGGGGCTCGCAGCCCTATGTGTCGCGCCGGACGgtcagtgctg ... tctgaaacagACATCTCTACGGGAGCTCACTACCCTTGGAATCAAGAATGCTGAGAATTTA
EST: gi|211463633|gb|FL380567.1|FL380567
EST:     GCGGATGGGCCAAGCGGTGGGGCTCGCAGCCCTATGTGTCGCGCCGGACG                         ACATCTCTACGGGAGCTCACTACCCTTGGAATCAAGAATGCTGAGAATTTA
genomic: GCGGATGGGCCAAGCGGTGGGGCTCGCAGCCCTATGTGTCGCGCCGGACGgtcagtgctg ... tctgaaacagACATCTCTACGGGAGCTCACTACCCTTGGAATCAAGAATGCTGAGAATTTA
EST: gi|211057978|gb|FL426568.1|FL426568
EST:     GCGGATGGGCCAAGCGGTGGGGCTCGCAGCCCTATGTGTCGCGCCGGACG                         ACATCTCTACTGGAGCTCACTACCCTTGGAATCAAGAATGCTGAGAATTTA
genomic: GCGGATGGGCCAAGCGGTGGGGCTCGCAGCCCTATGTGTCGCGCCGGACGgtcagtgctg ... tctgaaacagACATCTCTACGGGAGCTCACTACCCTTGGAATCAAGAATGCTGAGAATTTA
EST: gi|211087785|gb|FL400777.1|FL400777
EST:     GCGGATGGGCCAAGCGGTGGGGCTCGCAGCCCTATGTGTCGCGCCGGACG                         ACATCTCTACGGGAGCTCACTACCCTTGGAATCAAGAATGCTGAGAATTTA
genomic: GCGGATGGGCCAAGCGGTGGGGCTCGCAGCCCTATGTGTCGCGCCGGACGgtcagtgctg ... tctgaaacagACATCTCTACGGGAGCTCACTACCCTTGGAATCAAGAATGCTGAGAATTTA
EST: gi|76010526|gb|DT937696.1|DT937696
EST:     GCGGATGGGCCAAGCGGTGGGGCTCGCAGCCCTATGTGTCGCGCCGGACG                         ACATCTCTACGGGAGCTCACTACCCTTGGAATCAAGAATGCTGAGAATTTA
genomic: GCGGATGGGCCAAGCGGTGGGGCTCGCAGCCCTATGTGTCGCGCCGGACGgtcagtgctg ... tctgaaacagACATCTCTACGGGAGCTCACTACCCTTGGAATCAAGAATGCTGAGAATTTA
EST: gi|71313543|gb|DR793346.1|DR793346
EST:     GCGGATGGGCCAAGCGGTGGGGCTCGCAGCCCTATGTGTCGCGCCGGACG                         ACATCTCTACGGGAGCTCACTACCCTTGGAATCAAGAATGCTGAGAATTTA
genomic: GCGGATGGGCCAAGCGGTGGGGCTCGCAGCCCTATGTGTCGCGCCGGACGgtcagtgctg ... tctgaaacagACATCTCTACGGGAGCTCACTACCCTTGGAATCAAGAATGCTGAGAATTTA
EST: gi|211403691|gb|FL424169.1|FL424169
EST:     GCGGATGGGCCAAGCGGTGGGGCTCGCAGCCCTATGTGTCGCGCCGGACG                         ACATCTCTACGGGAGCTCACTACCCTTGGAATCAAGAATGCTGAGAATTTA
genomic: GCGGATGGGCCAAGCGGTGGGGCTCGCAGCCCTATGTGTCGCGCCGGACGgtcagtgctg ... tctgaaacagACATCTCTACGGGAGCTCACTACCCTTGGAATCAAGAATGCTGAGAATTTA
EST: gi|211110152|gb|FL388603.1|FL388603
EST:     GCGGATGGGCCAAGCGGTGGGGCTCGCAGCCCTATGTGTCGCGCCGGACG                         ACATCTCTACGGGAGCTCACTACCCTTGGAATCAAGAATGCTGAGAATTTA
genomic: GCGGATGGGCCAAGCGGTGGGGCTCGCAGCCCTATGTGTCGCGCCGGACGgtcagtgctg ... tctgaaacagACATCTCTACGGGAGCTCACTACCCTTGGAATCAAGAATGCTGAGAATTTA
EST: gi|211493014|gb|FL369799.1|FL369799
EST:     GCGGATGGGCCAAGCGGTGGGGCTCGCAGCCCTATGTGTCGCGCCGGACG                         ACATCTCTACGGGAGCTCACTACCCTTGGAATCAAGAATGCTGAGAATTTA
genomic: GCGGATGGGCCAAGCGGTGGGGCTCGCAGCCCTATGTGTCGCGCCGGACGgtcagtgctg ... tctgaaacagACATCTCTACGGGAGCTCACTACCCTTGGAATCAAGAATGCTGAGAATTTA
EST: gi|37417290|gb|CF646298.1|CF646298
EST:     GCGGATGGGCCAAGCGGTGGGGCTCGCAGCCCTATGTGTCGCGCCGGACG                         ACATCTCTACGGGAGCTCACTACCCTTGGAATCAAGAATGCTGAGAATTTA
genomic: GCGGATGGGCCAAGCGGTGGGGCTCGCAGCCCTATGTGTCGCGCCGGACGgtcagtgctg ... tctgaaacagACATCTCTACGGGAGCTCACTACCCTTGGAATCAAGAATGCTGAGAATTTA
EST: gi|149100298|gb|EE186363.2|EE186363
EST:     GCGGATGGGCCAAGCGGTGGGGCTCGCAGCCCTATGTGTCGCGCCGGACG                         ACATCTCTACGGGAGCTCACTACCCTTGGAATCAAGAATGCTGAGAATTTA
genomic: GCGGATGGGCCAAGCGGTGGGGCTCGCAGCCCTATGTGTCGCGCCGGACGgtcagtgctg ... tctgaaacagACATCTCTACGGGAGCTCACTACCCTTGGAATCAAGAATGCTGAGAATTTA
EST: gi|211472091|gb|FL427745.1|FL427745
EST:     GCGGATGGGCCAAGCGGTGGGGCTCGCAGCCCTATGTGTCGCGCCGGACG                         ACATCTCTACGGGAGCTCACTACCCTTGGAATCAAGAATGCTGAGAATTTA
genomic: GCGGATGGGCCAAGCGGTGGGGCTCGCAGCCCTATGTGTCGCGCCGGACGgtcagtgctg ... tctgaaacagACATCTCTACGGGAGCTCACTACCCTTGGAATCAAGAATGCTGAGAATTTA
EST: gi|148930743|gb|EC873038.2|EC873038
EST:     GCGGATGGGCCAAGCGGTGGGGCTCGCAGCCCTATGTGTCGCGCCGGACG                         ACATCTCTACGGGAGCTCACTACCCTTGGAATCAAGAATGCTGAGAATTTA
genomic: GCGGATGGGCCAAGCGGTGGGGCTCGCAGCCCTATGTGTCGCGCCGGACGgtcagtgctg ... tctgaaacagACATCTCTACGGGAGCTCACTACCCTTGGAATCAAGAATGCTGAGAATTTA
EST: gi|71317339|gb|DR795363.1|DR795363
EST:     GCGGATGGGCCAAGCGGTGGGGCTCGCAGCCCTATGTGTCGCGCCGGACG                         ACATCTCTACGGGAGCTCACTACCCTTGGAATCAAGAATGCTGAGAATTTA
genomic: GCGGATGGGCCAAGCGGTGGGGCTCGCAGCCCTATGTGTCGCGCCGGACGgtcagtgctg ... tctgaaacagACATCTCTACGGGAGCTCACTACCCTTGGAATCAAGAATGCTGAGAATTTA
EST: gi|91872113|gb|EB402070.1|EB402070
EST:     GCGGATGGGCCAAGCGGTGGGGCTCGCAGCCCTATGTGTCGAGCCGGACG                         ACATATCTACGGGAGCTCAATACCCTTGGAATCAAGAATG
genomic: GCGGATGGGCCAAGCGGTGGGGCTCGCAGCCCTATGTGTCGCGCCGGACGgtcagtgctg ... tctgaaacagACATCTCTACGGGAGCTCACTACCCTTGGAATCAAGAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggttgtgtctggctctgattgattctaactgatgagcctgcattctgaaacagACATCTCTACGGGAGCTCACTACCCTTGGAATCAAGAATGCTGAGAATTTAGCAATTCCAAGTGTTAGAAATGAT
                   attgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtgctgtatcttctcaggcatcaatgattgagcgcttcgtgtttgcaggatgcgtactcctgtcatgcgttttgctcgtgcaatttttacaatgcagtagcatttgatggttgtgtctggctctgattgattctaactgatgagcctgcattctgaaacagACATCTCTACGGGAGCTCACTACCCTTGGAATCAAGAATGCTGAGAATTTAGCAATTCCAAGTGTTAGAAATGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG