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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATCCTCAGATGGGGTAGCATCAACTGAATTCTCTTTCCCTCAGCTGTCTTTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAGgttagttcttctgtcacctaaggcggtggtagtccgctattacctgcctcaccgagtctgaggtttatcatagtgtgtcgtccgatattatcttgactag...

Basic information

species Zea mays
transcript GRMZM2G127739_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G127739_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os12g40190.1 (Oryza sativa), 5'ss of exon 7
CATCCTCAGATGGGGTAGCATCAACTGAATTCTCTTTCCCTCAGCTGTCTTTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAGgttagttcttctgtcacctaaggcgg--tggtagtccgctattacctgcctcaccgagtctgaggtttatcatagtgtgtcgtccgatattatcttgactag------------------------
|||||||||||||| ||||||| || || ||||| ||||| || ||| ||||||  || | |||| |||||||||| ||| |||||||||||||||||||||  ||||||  |||||  ||   ||  ||||||||    || |||||  |  |      |   ||   |   |   |       ||||  |   |||  |                         
CATCCTCAGATGGGTTAGCATCTACAGATTTCTCCTTCCCACAACTGGCTTTGGACGGGCGGGGTTTTGATGAGCCAGATCCACAAGACACTTTGCTAAGgtctgttcttaagtcactgaaaagggcatggtagtctaa-ataacctgtgtttctagtctttctgtaactttcatctttgttaatgataacagtatgaacaatgaaacattttgttctattttcag
















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|71310498|gb|DR791544.1|DR791544
EST:     TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAG                         GTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
genomic: TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAGgttagttctt ... ttgttttcagGTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
EST: gi|94473931|gb|EB702889.1|EB702889
EST:     TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAG                         GTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
genomic: TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAGgttagttctt ... ttgttttcagGTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
EST: gi|148972405|gb|EE023335.2|EE023335
EST:     TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAG                         GTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
genomic: TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAGgttagttctt ... ttgttttcagGTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
EST: gi|71763610|gb|DR961547.1|DR961547
EST:     TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAG                         GTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
genomic: TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAGgttagttctt ... ttgttttcagGTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
EST: gi|76017187|gb|DT944357.1|DT944357
EST:     TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAG                         GTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
genomic: TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAGgttagttctt ... ttgttttcagGTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
EST: gi|78110170|gb|DV528585.1|DV528585
EST:     TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAG                         GTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
genomic: TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAGgttagttctt ... ttgttttcagGTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
EST: gi|94475631|gb|EB704589.1|EB704589
EST:     TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAG                         GTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
genomic: TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAGgttagttctt ... ttgttttcagGTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
EST: gi|71322062|gb|DR797719.1|DR797719
EST:     TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAG                         GTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
genomic: TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAGgttagttctt ... ttgttttcagGTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
EST: gi|149070928|gb|EE159335.2|EE159335
EST:     TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAG                         GTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
genomic: TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAGgttagttctt ... ttgttttcagGTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
EST: gi|78119468|gb|DV537852.1|DV537852
EST:     TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAG                         GTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
genomic: TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAGgttagttctt ... ttgttttcagGTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
EST: gi|71308379|gb|DR790418.1|DR790418
EST:     TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAG                         GTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
genomic: TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAGgttagttctt ... ttgttttcagGTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
EST: gi|71760704|gb|DR958641.1|DR958641
EST:     TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAG                         GTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
genomic: TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAGgttagttctt ... ttgttttcagGTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
EST: gi|76014164|gb|DT941334.1|DT941334
EST:     TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAG                         GTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
genomic: TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAGgttagttctt ... ttgttttcagGTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
EST: gi|71328662|gb|DR801008.1|DR801008
EST:     TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAG                         GTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
genomic: TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAGgttagttctt ... ttgttttcagGTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
EST: gi|89252509|gb|DY624295.1|DY624295
EST:     TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAG                         GTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
genomic: TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAGgttagttctt ... ttgttttcagGTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
EST: gi|71773347|gb|DR971251.1|DR971251
EST:     TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAG                         GTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
genomic: TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAGgttagttctt ... ttgttttcagGTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
EST: gi|74241916|gb|DT649830.1|DT649830
EST:     TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAG                         GTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
genomic: TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAGgttagttctt ... ttgttttcagGTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
EST: gi|71758063|gb|DR956000.1|DR956000
EST:     TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAG                         GTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
genomic: TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAGgttagttctt ... ttgttttcagGTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
EST: gi|148979414|gb|EE026650.2|EE026650
EST:     TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAG                         GTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
genomic: TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAGgttagttctt ... ttgttttcagGTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
EST: gi|26457126|gb|CA828709.1|CA828709
EST:     TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAG                         GTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
genomic: TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAGgttagttctt ... ttgttttcagGTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
EST: gi|93283625|gb|EB675889.1|EB675889
EST:     TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAG                         GTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
genomic: TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAGgttagttctt ... ttgttttcagGTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
EST: gi|74237568|gb|DT645482.1|DT645482
EST:     TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAG                         GTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
genomic: TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAGgttagttctt ... ttgttttcagGTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
EST: gi|148929836|gb|EE285518.2|EE285518
EST:     TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAG                         GTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
genomic: TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAGgttagttctt ... ttgttttcagGTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
EST: gi|149075131|gb|EE163624.2|EE163624
EST:     TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAG                         GTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
genomic: TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAGgttagttctt ... ttgttttcagGTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
EST: gi|149100969|gb|EE187066.2|EE187066
EST:     TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAG                         GTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
genomic: TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAGgttagttctt ... ttgttttcagGTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
EST: gi|149061146|gb|EE157406.2|EE157406
EST:     TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAG                         GTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
genomic: TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAGgttagttctt ... ttgttttcagGTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
EST: gi|86469211|gb|DY235581.1|DY235581
EST:     TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAG                         GTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
genomic: TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAGgttagttctt ... ttgttttcagGTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
EST: gi|149109394|gb|EE293282.2|EE293282
EST:     TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAG                         GTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG
genomic: TTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAGgttagttctt ... ttgttttcagGTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 167

CATCCTCAGATGGGGTAGCATCAACTGAATTCTCTTTCCCTCAGCTGTCTTTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAGgttagttctt ... ttgttttcagGTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATGGCTGCAAATGTTCGATGACGTAAGGCTTGTTATCTTCTGTGTTGCTGCT


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 72

CATCCTCAGATGGGGTAGCATCAACTGAATTCTCTTTCCCTCAGCTGTCTTTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAGgttagttctt ... ttgttttcagGTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATGGCTGCAAATGTTCGATGACGTAAGGCTTGTTATCTTCTGTGTTGCTGCT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 62

CATCCTCAGATGGGGTAGCATCAACTGAATTCTCTTTCCCTCAGCTGTCTTTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAGgttagttctt ... ttgttttcagGTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATGGCTGCAAATGTTCGATGACGTAAGGCTTGTTATCTTCTGTGTTGCTGCT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 104

CATCCTCAGATGGGGTAGCATCAACTGAATTCTCTTTCCCTCAGCTGTCTTTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAGgttagttctt ... ttgttttcagGTACCAATTGATCAGGATAAACAGTAGAGGTTTGCATGGGAACTGCAAATGGCTGCAAATGTTCGATGACGTAAGGCTTGTTATCTTCTGTGTTGCTGCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATCCTCAGATGGGGTAGCATCAACTGAATTCTCTTTCCCTCAGCTGTCTTTGGGTGGACTGGGTGTTGATGAGCCCGATGCACAAGACACTTTGCTAAGgttagttcttctgtcacctaaggcggtggtagtccgctattacctgcctcaccgagtctgaggtttatcatagtgtgtcgtccgatattatcttgactag

- - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA