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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGGACTACTCAGTCTATGGCAGTGACGAAGAAGCTGACGACCCTCGTGATGCTGAAACTGATGATGACCTAACTGATGAAGAAAGAGACATGCACGAGgtatggacgatttatctcagtgtccgacattttttccccttattatctagtttcaccacatcaatacactgcaaatttgaagacaatgctgaatgttctctcgcgcatcaccggatgcttgcag

Basic information

species Zea mays
transcript GRMZM2G342327_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G342327_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os02g57400.2 (Oryza sativa), 5'ss of exon 6
GGAGGACTACTCAGTCTATGGCAGTGACGAAGAAGCTGACGACCCTCGTGATGCTGAAACTGATGATGACCTAACTGATGAAGAAAGAGACATGCACGAGgtat-ggacgatttatctcagtg-tccgacattttttccccttattatc-tagtttcaccacatcaatacactgcaaatttgaagacaatgctgaatgttctctcgcgcatcaccggatgcttgcag
||| || || ||||| | ||| || || ||||| ||||| || |||| |||||||| |||||| || ||||||||||||||||||||||| ||||||||||||    |  |  |  ||   || | |  || |||     ||  || |  ||    ||| | || | |   | | || | |  | | ||   || |  |                            
GGATGATTATTCAGTTTTTGGTAGCGAAGAAGATGCTGATGATCCTCCTGATGCTGGAACTGACGAAGACCTAACTGATGAAGAAAGAGATATGCACGAGgtaccaaaaaagctccctgtatgattcagcaatttcctttctagttgtgataaacacacaatat-agttttcagaaactatataaaaaagaatgcaaataa--------------------------
















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|6538928|gb|AW225067.1|AW225067
EST:     ATGCTGAAACTGATGATGACCTAACTGATGAAGAAAGAGACATGCNCGAG                         ATAGATGCAGGCTCTGTAGACGAGCACTCAACCAAGTCGGATGAGGAATAC
genomic: ATGCTGAAACTGATGATGACCTAACTGATGAAGAAAGAGACATGCACGAGgtatggacga ... atgcttgcagATAGATGCAGGCTCTGTAGACGAGCACTCAACCAAGTCGGATGAGGAATAC
EST: gi|32841082|gb|CD980763.1|CD980763
EST:     ATGCTGAAACTGATGATGACCTAACTGATGAAGAAAGAGACATGCACGAG                         ATAGATGCAGGCCCTGTAGACGAGCACTCAACCAAGTCGGATGAGGAATAC
genomic: ATGCTGAAACTGATGATGACCTAACTGATGAAGAAAGAGACATGCACGAGgtatggacga ... atgcttgcagATAGATGCAGGCTCTGTAGACGAGCACTCAACCAAGTCGGATGAGGAATAC
EST: gi|32840469|gb|CD980150.1|CD980150
EST:     ATGCTGAAACTGATGATGACCTAACTGATGAAGAAAGAGACATGCACGAG                         ATAGATGCAGGCTCTGTAGACGAGCACTCAACCAAGTCGGATGAGGAATAC
genomic: ATGCTGAAACTGATGATGACCTAACTGATGAAGAAAGAGACATGCACGAGgtatggacga ... atgcttgcagATAGATGCAGGCTCTGTAGACGAGCACTCAACCAAGTCGGATGAGGAATAC
EST: gi|32841039|gb|CD980720.1|CD980720
EST:     ATGCTGAAACTGATGATGACCTAACTGATGAAGAAAGAGACATGCACGAG                         ATAGATGCAGGCTCTGTAGACGAGCACTCAACCAAGTCGGATGAGGAATAC
genomic: ATGCTGAAACTGATGATGACCTAACTGATGAAGAAAGAGACATGCACGAGgtatggacga ... atgcttgcagATAGATGCAGGCTCTGTAGACGAGCACTCAACCAAGTCGGATGAGGAATAC
EST: gi|32906752|gb|CF011565.1|CF011565
EST:     ATGCTGAAACTGATGATGACCTAACTGATGAAGAAAGAGACATGCACGAG                         ATAGATGCAGGCTCTGTAGACGAGCACTCAACCAAGTCGGATGAGGAATAC
genomic: ATGCTGAAACTGATGATGACCTAACTGATGAAGAAAGAGACATGCACGAGgtatggacga ... atgcttgcagATAGATGCAGGCTCTGTAGACGAGCACTCAACCAAGTCGGATGAGGAATAC
EST: gi|60348603|gb|DN215576.1|DN215576
EST:     ATGCTGAAACTGATGATGACCTAACTGATGAAGAAAGAGACATGCACGAG                         ATAGATGCAGGCTCTGTAGACGAGCACTCAACCAAGTCGGATGAGGAATAC
genomic: ATGCTGAAACTGATGATGACCTAACTGATGAAGAAAGAGACATGCACGAGgtatggacga ... atgcttgcagATAGATGCAGGCTCTGTAGACGAGCACTCAACCAAGTCGGATGAGGAATAC
EST: gi|211059349|gb|FL475168.1|FL475168
EST:     ATGCTGAAACTGATGATGMCCTAACTGATGAAGAAAGAGACATGCMCGAG                         ATAGATGCAGGYTCTGTAGACGAGCACTCAACCAAGTCGGATGAGGAATAC
genomic: ATGCTGAAACTGATGATGACCTAACTGATGAAGAAAGAGACATGCACGAGgtatggacga ... atgcttgcagATAGATGCAGGCTCTGTAGACGAGCACTCAACCAAGTCGGATGAGGAATAC
EST: gi|32840992|gb|CD980673.1|CD980673
EST:     TGCTGAAACTGATGATGACCTAACTGATGAAGAAAGAGACATGCCACGAG                         ATAGATGCAGGCTCTGTAGACGAGCACTCAACCAAGTCGGATGAGGAATA
genomic: TGCTGAAACTGATGATGACCTAACTGATGAAGAAAGAGACATGC-ACGAGgtatggacga ... atgcttgcagATAGATGCAGGCTCTGTAGACGAGCACTCAACCAAGTCGGATGAGGAATA
EST: gi|8930313|gb|BE225077.1|BE225077
EST:     ATGCTGAAACTGATGATGACCTAACTGATGAAGAAAGAGACATGCACGAG                         ATAGATGCAGGCTCTGTAGACGAGCACTCAACCAAGTCGGATGAGGAATAC
genomic: ATGCTGAAACTGATGATGACCTAACTGATGAAGAAAGAGACATGCACGAGgtatggacga ... atgcttgcagATAGATGCAGGCTCTGTAGACGAGCACTCAACCAAGTCGGATGAGGAATAC
EST: gi|32840975|gb|CD980656.1|CD980656
EST:     ATGCTGAAACTGATGATGACCTAACTGATGAAGAAAGAGACATGCACGAG                         ATAGATGCAGGCTCTGTAGACGAGCACTCAACCAAGTCGGATGAGGAATAC
genomic: ATGCTGAAACTGATGATGACCTAACTGATGAAGAAAGAGACATGCACGAGgtatggacga ... atgcttgcagATAGATGCAGGCTCTGTAGACGAGCACTCAACCAAGTCGGATGAGGAATAC
EST: gi|83278167|gb|DV942175.1|DV942175
EST:     ATGCTGAAACTGATGATGACCTAACTGATGAAGAAAGAGACATGCACGAG                         ATAGATGCAGGCTCTGTAGACGAGCACTCAACCAAGTCGGATGAGGAATAC
genomic: ATGCTGAAACTGATGATGACCTAACTGATGAAGAAAGAGACATGCACGAGgtatggacga ... atgcttgcagATAGATGCAGGCTCTGTAGACGAGCACTCAACCAAGTCGGATGAGGAATAC
EST: gi|91877217|gb|EB407174.1|EB407174
EST:     ATGCTGAAACTGATGATGACCTAACTGATGAAGAAAGAGACATGCACGAG                         ATAGATGCAGGCTCTGTAGACGAGCACTCAACCAAGTCGGATGAGGAATAC
genomic: ATGCTGAAACTGATGATGACCTAACTGATGAAGAAAGAGACATGCACGAGgtatggacga ... atgcttgcagATAGATGCAGGCTCTGTAGACGAGCACTCAACCAAGTCGGATGAGGAATAC
EST: gi|32841394|gb|CD981075.1|CD981075
EST:     ATGCTGAAACTGATGATGACCTAACTGATGAAGAAAGAGACATGCACGAG                         ATAGATGCAGGCTCTGTAGACGAGCACTCAACCAAGTCGGATGAGGAATAC
genomic: ATGCTGAAACTGATGATGACCTAACTGATGAAGAAAGAGACATGCACGAGgtatggacga ... atgcttgcagATAGATGCAGGCTCTGTAGACGAGCACTCAACCAAGTCGGATGAGGAATAC
EST: gi|32841071|gb|CD980752.1|CD980752
EST:     ATGCTGAAACTGATGATGACCTAACTGATGAAGAAAGAGACATGCACGAG                         ATAGATGCAGGCTCTGTAGACGAGCACTCAACCAAGTCGGATGAGGAATAC
genomic: ATGCTGAAACTGATGATGACCTAACTGATGAAGAAAGAGACATGCACGAGgtatggacga ... atgcttgcagATAGATGCAGGCTCTGTAGACGAGCACTCAACCAAGTCGGATGAGGAATAC
EST: gi|71445592|gb|DR826642.1|DR826642
EST:     ATGCTGAAACTGATGATGACCTAACTGATGAAGAAAGAGACATGCACGAG                         ATAGATGCAGGCTCTGTAGACGAGCACTCAACCAAGTCGGATGAGGAATAC
genomic: ATGCTGAAACTGATGATGACCTAACTGATGAAGAAAGAGACATGCACGAGgtatggacga ... atgcttgcagATAGATGCAGGCTCTGTAGACGAGCACTCAACCAAGTCGGATGAGGAATAC
EST: gi|32846015|gb|CD985696.1|CD985696
EST:     ATGCTGAAACTGATGATGACCTAACTGATGAAGAAAGAGACATGCACGAG                         ATAGATGCAGGCTCTGTAGACGAGCACTCAACCAAGTCGGATGAGGAATAC
genomic: ATGCTGAAACTGATGATGACCTAACTGATGAAGAAAGAGACATGCACGAGgtatggacga ... atgcttgcagATAGATGCAGGCTCTGTAGACGAGCACTCAACCAAGTCGGATGAGGAATAC
EST: gi|71445591|gb|DR826641.1|DR826641
EST:     ATGCTGAAACTGATGATGACCTAACTGATGAAGAAAGAGACATGCACGAG                         ATAGATGCAGGCTCTGTAGACGAGCACTCAACCAAGTCGGATGAGGAATAC
genomic: ATGCTGAAACTGATGATGACCTAACTGATGAAGAAAGAGACATGCACGAGgtatggacga ... atgcttgcagATAGATGCAGGCTCTGTAGACGAGCACTCAACCAAGTCGGATGAGGAATAC

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: 45 (upstream exon), 49 (downstream exon)
Score: 103

GGAGGACTACTCAGTCTATGGCAGTGACGAAGAAGCTGACGACCCTCGTGATGCTGAAACTGATGATGACCTAACTGATGAAGAAAGAGACATGCACGAGgtatggacga ... atgcttgcagATAGATGCAGGCTCTGTAGACGAGCACTCAACCAAGTCGGATGAGGAATACGAGGACTTAGCCATGCGTGATGTGATGGAGAATGGTGACTGGTCTGACG


Block sizes: 39 (upstream exon), 49 (downstream exon)
Score: 20

GGAGGACTACTCAGTCTATGGCAGTGACGAAGAAGCTGACGACCCTCGTGATGCTGAAACTGATGATGACCTAACTGATGAAGAAAGAGACATGCACGAGgtatggacga ... atgcttgcagATAGATGCAGGCTCTGTAGACGAGCACTCAACCAAGTCGGATGAGGAATACGAGGACTTAGCCATGCGTGATGTGATGGAGAATGGTGACTGGTCTGACG


Block sizes: 42 (upstream exon), 44 (downstream exon)
Score: 20

GGAGGACTACTCAGTCTATGGCAGTGACGAAGAAGCTGACGACCCTCGTGATGCTGAAACTGATGATGACCTAACTGATGAAGAAAGAGACATGCACGAGgtatggacga ... atgcttgcagATAGATGCAGGCTCTGTAGACGAGCACTCAACCAAGTCGGATGAGGAATACGAGGACTTAGCCATGCGTGATGTGATGGAGAATGGTGACTGGTCTGACG


Block sizes: 42 (upstream exon), 48 (downstream exon)
Score: 42

GGAGGACTACTCAGTCTATGGCAGTGACGAAGAAGCTGACGACCCTCGTGATGCTGAAACTGATGATGACCTAACTGATGAAGAAAGAGACATGCACGAGgtatggacga ... atgcttgcagATAGATGCAGGCTCTGTAGACGAGCACTCAACCAAGTCGGATGAGGAATACGAGGACTTAGCCATGCGTGATGTGATGGAGAATGGTGACTGGTCTGACG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGGACTACTCAGTCTATGGCAGTGACGAAGAAGCTGACGACCCTCGTGATGCTGAAACTGATGATGACCTAACTGATGAAGAAAGAGACATGCACGAGgtatggacgatttatctcagtgtccgacattttttccccttattatctagtttcaccacatcaatacactgcaaatttgaagacaatgctgaatgttctctcgcgcatcaccggatgcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA