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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctggcgtgtctactaaaaacgaaccataatttttttggggtaaacttgccttgtgttctccattaagtgtcagttaacatctgtcatctggtacttgcagTTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTCCTAAAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGG

Basic information

species Zea mays
transcript GRMZM2G022876_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G022876_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g34950.1 (Oryza sativa), 3'ss of exon 1
ctggcgtgtctactaaaaac-gaaccataatttttttggggtaaacttgccttgtgttctccattaagtgtcagttaacatctgtcatctggtacttgcagTTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTCCTAAAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGG
 ||||   | ||       | |||  |||   ||||| |  |     |    |       |  | ||  |  |  |  |||     |||| | || ||||||||||||| | |  ||||| |  |||||||| |||||||| ||||||||||| || ||||| || |||||||| ||||||||||||||||||||  ||| 
-tggcacatatagagttctctgaaatatatagttttttgtatttttgttaagtaaaaaagctgtcaatggaaaaatctcatgcagaatctcgcacatgcagTTGTTGGTATAGTTAATGCAAAGACTGGGGTCAACAAACCCGAATTGCTTCCCAAGGAATTCACCACCGTCATTGATGTTGCTGGTTTTCTCTCCCCAG-

upper sequence: GRMZM2G022876_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g34950.2 (Oryza sativa), 3'ss of exon 1
ctggcgtgtctac-taaaaacgaaccataatttttttggggtaaacttgccttgtgt-tctccattaagt---------gtcagttaa-------catctgtcatctggtacttgcagTTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTCCTAAAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGG
 |  | ||| |    ||   |  |     | || | ||   || | | |  || ||| | |   ||||||         |||| |  |       |||     |||| | || ||||||||||||| | |  ||||| |  |||||||| |||||||| ||||||||||| || ||||| || |||||||| ||||||||||                
-ttacatgtatttgcaatggcacatatagagttctctgaaatata-tagttttttgtatttttgttaagtaaaaaagctgtcaatggaaaaatctcatgcagAATCTCGCACATGCAGTTGTTGGTATAGTTAATGCAAAGACTGGGGTCAACAAACCCGAATTGCTTCCCAAGGAATTCACCACCGTCATTGATGTTGCTG----------------

upper sequence: GRMZM2G022876_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT5G52970.1 (Arabidopsis thaliana), 3'ss of exon 1
ctggcgtgtctactaaaaacgaaccataatttttttggggtaaact-tgcct-tgtgttctccattaagtgtcagttaacatctgtcatctggtacttgcagTTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTCCTAAAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGG
 | | |    |     |      |  | |||   |     | |||  ||| | ||   | || |     |  | || || | || | |     |  ||||||  || || || ||  |||| | |  ||| || |||||||||||||||||||||||||| || ||| | || || |||||||||| ||| |||||    ||
-ttgtgaaatt-tcggacctagtctcttattccataactatgaacaatgcatatgcaatttcaagattttagctgtcaataactttgaatctctttttgcagGCGTGGGGTTTGCAGATGCAAAAGTTGGTGTTAACAAACCAGAATTGCTTCCTAAAGAGTTCACTTCTGTTATAGATGTTGCTGATTTCCTCTCTAATGG

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|211533933|gb|FL079631.1|FL079631
EST:     GAAGGCCGCGGTCTCCGGCGTGGTCGCCCTCGCCGTCTCCTTCACCTGCC                         TTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTC
genomic: GAAGGCCGCGGTCTCCGGCGTGGTCGCCCTCGCCGTCTCCTTCACCTGCCgtaagcttgc ... gtacttgcagTTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTC
EST: gi|13125853|gb|BG316423.1|BG316423
EST:     GAAGGCCGCGGTCTCCGGCGTGGTCGCCCTCGCCGTCTCCTTCACCTGCC                         TTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTC
genomic: GAAGGCCGCGGTCTCCGGCGTGGTCGCCCTCGCCGTCTCCTTCACCTGCCgtaagcttgc ... gtacttgcagTTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTC
EST: gi|22819283|gb|BU499373.1|BU499373
EST:     GAAGGCCGCGGTCTCCGGCGTGGTCGCCCTCGCCGTCTCCTTCACCTGCC                         TTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTC
genomic: GAAGGCCGCGGTCTCCGGCGTGGTCGCCCTCGCCGTCTCCTTCACCTGCCgtaagcttgc ... gtacttgcagTTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTC
EST: gi|211533938|gb|FL079636.1|FL079636
EST:     GAAGGCCGCGGTCTCCGGCGTGGTCGCCCTCGCCGTCTCCTTCACCTGCC                         TTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTC
genomic: GAAGGCCGCGGTCTCCGGCGTGGTCGCCCTCGCCGTCTCCTTCACCTGCCgtaagcttgc ... gtacttgcagTTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTC
EST: gi|211533932|gb|FL079630.1|FL079630
EST:     GAAGGCCGCGGTCTCCGGCGTGGTCGCCCTCGCCGTCTCCTTCACCTGCC                         TTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTC
genomic: GAAGGCCGCGGTCTCCGGCGTGGTCGCCCTCGCCGTCTCCTTCACCTGCCgtaagcttgc ... gtacttgcagTTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTC
EST: gi|211536947|gb|FL079648.1|FL079648
EST:     GAAGGCCGCGGTCTCCGGCGTGGTCGCCCTCGCCGTCTCCTTCACCTGCC                         TTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTC
genomic: GAAGGCCGCGGTCTCCGGCGTGGTCGCCCTCGCCGTCTCCTTCACCTGCCgtaagcttgc ... gtacttgcagTTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTC
EST: gi|211539949|gb|FL079654.1|FL079654
EST:     GAAGGCCGCGGTCTCCGGCGTGGTCGCCCTCGCCGTCTCCTTCACCTGCC                         TTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTC
genomic: GAAGGCCGCGGTCTCCGGCGTGGTCGCCCTCGCCGTCTCCTTCACCTGCCgtaagcttgc ... gtacttgcagTTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTC
EST: gi|211533925|gb|FL079623.1|FL079623
EST:     GAAGGCCGCGGTCTCCGGCGTGGTCGCCCTCGCCGTCTCCTTCACCTGCC                         TTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTC
genomic: GAAGGCCGCGGTCTCCGGCGTGGTCGCCCTCGCCGTCTCCTTCACCTGCCgtaagcttgc ... gtacttgcagTTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTC
EST: gi|211539956|gb|FL079661.1|FL079661
EST:     GAAGGCCGCGGTCTCCGGCGTGGTCGCCCTCGCCGTCTCCTTCACCTGCC                         TTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTC
genomic: GAAGGCCGCGGTCTCCGGCGTGGTCGCCCTCGCCGTCTCCTTCACCTGCCgtaagcttgc ... gtacttgcagTTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTC
EST: gi|149071910|gb|EE160296.2|EE160296
EST:     GAAGGCCGCGGTCTCCGGCGTGGTCGCCCTCGCCGTCTCCTTCACCTGCC                         TTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTC
genomic: GAAGGCCGCGGTCTCCGGCGTGGTCGCCCTCGCCGTCTCCTTCACCTGCCgtaagcttgc ... gtacttgcagTTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTC
EST: gi|211533931|gb|FL079629.1|FL079629
EST:     GAAGGCCGCGGTCTCCGGCGTGGTCGCCCTCGCCGTCTCCTTCACCTGCC                         TTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTC
genomic: GAAGGCCGCGGTCTCCGGCGTGGTCGCCCTCGCCGTCTCCTTCACCTGCCgtaagcttgc ... gtacttgcagTTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTC
EST: gi|211536940|gb|FL079641.1|FL079641
EST:     GAAGGCCGCGGTCTCCGGCGTGGTCGCCCTCGCCGTCTCCTTCACCTGCC                         TTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTC
genomic: GAAGGCCGCGGTCTCCGGCGTGGTCGCCCTCGCCGTCTCCTTCACCTGCCgtaagcttgc ... gtacttgcagTTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTC
EST: gi|211539950|gb|FL079655.1|FL079655
EST:     GAAGGCCGCGGTCTCCGGCGTGGTCGCCCTCGCCGTCTCCTTCACCTGCC                         TTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTC
genomic: GAAGGCCGCGGTCTCCGGCGTGGTCGCCCTCGCCGTCTCCTTCACCTGCCgtaagcttgc ... gtacttgcagTTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTC
EST: gi|211533939|gb|FL079637.1|FL079637
EST:     GAAGGCCGCGGTCTCCGGCGTGGTCGCCCTCGCCGTCTCCTTCACCTGCC                         TTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTC
genomic: GAAGGCCGCGGTCTCCGGCGTGGTCGCCCTCGCCGTCTCCTTCACCTGCCgtaagcttgc ... gtacttgcagTTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTC
EST: gi|211533934|gb|FL079632.1|FL079632
EST:     GAAGGCCGCGGTCTCCGGCGTGGTCGCCCTCGCCGTCTCCTTCACCTGCC                         TTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTC
genomic: GAAGGCCGCGGTCTCCGGCGTGGTCGCCCTCGCCGTCTCCTTCACCTGCCgtaagcttgc ... gtacttgcagTTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTC
EST: gi|211530935|gb|FL079622.1|FL079622
EST:     GAAGGCCGCGGTCTCCGGCGTGGTCGCCCTCGCCGTCTCCTTCACCTGCC                         TTGTTGGTTTGGCCAATGCCAGAACTGGGGTWAACAAACCAGAATTGCTTC
genomic: GAAGGCCGCGGTCTCCGGCGTGGTCGCCCTCGCCGTCTCCTTCACCTGCCgtaagcttgc ... gtacttgcagTTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTC
EST: gi|211533928|gb|FL079626.1|FL079626
EST:     GAAGGCCGCGGTCTCCGGCGTGGTCGCCCTCGCCGTCTCCTTCACCTGCC                         TTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTC
genomic: GAAGGCCGCGGTCTCCGGCGTGGTCGCCCTCGCCGTCTCCTTCACCTGCCgtaagcttgc ... gtacttgcagTTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTC
EST: gi|211536951|gb|FL079652.1|FL079652
EST:     GAAGGCCGCGGTCTCCGGCGTGGTCGCCCTCGCCGTCTCCTTCACCTGCC                         TTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTC
genomic: GAAGGCCGCGGTCTCCGGCGTGGTCGCCCTCGCCGTCTCCTTCACCTGCCgtaagcttgc ... gtacttgcagTTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTC
EST: gi|211536937|gb|FL079638.1|FL079638
EST:     GAAGGCCGCGGTCTCCGGCGTGGTCGCCCTCGCCGTCTCCTTCACCTGCC                         TTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTC
genomic: GAAGGCCGCGGTCTCCGGCGTGGTCGCCCTCGCCGTCTCCTTCACCTGCCgtaagcttgc ... gtacttgcagTTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTC
EST: gi|211536944|gb|FL079645.1|FL079645
EST:     GAAGGCCGCGGTCTCCGGCGTGGTCGCCCTCGCCGTCTCCTTCACCTGCC                         TTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTC
genomic: GAAGGCCGCGGTCTCCGGCGTGGTCGCCCTCGCCGTCTCCTTCACCTGCCgtaagcttgc ... gtacttgcagTTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTC
EST: gi|211539948|gb|FL079653.1|FL079653
EST:     GAAGGCCGCGGTCTCCGGCGTGGTCGCCCTCGCCGTCTCCTTCACCTGCC                         TTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTC
genomic: GAAGGCCGCGGTCTCCGGCGTGGTCGCCCTCGCCGTCTCCTTCACCTGCCgtaagcttgc ... gtacttgcagTTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTC
EST: gi|211536943|gb|FL079644.1|FL079644
EST:     GAAGGCCGCGGTCTCCGGCGTGGTCGCCCTCGCCGTCTCCTTCACCTGCC                         TTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTC
genomic: GAAGGCCGCGGTCTCCGGCGTGGTCGCCCTCGCCGTCTCCTTCACCTGCCgtaagcttgc ... gtacttgcagTTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgccttgtgttctccattaagtgtcagttaacatctgtcatctggtacttgcagTTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTCCTAAAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGG
                          agttaac  putative branch site (score: 3)
                attaagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctggcgtgtctactaaaaacgaaccataatttttttggggtaaacttgccttgtgttctccattaagtgtcagttaacatctgtcatctggtacttgcagTTGTTGGTTTGGCCAATGCCAGAACTGGGGTAAACAAACCAGAATTGCTTCCTAAAGAATTTACTACCGTCATCGATGTTGCTGGTTTTCTCTCGTCAGG

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