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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTGAAAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAGAGGGAGCGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGTCTGCAGgtactttcctctctgatgtactctaatcaattacgcatcagtttggccaactgacatcttttaaatggtatgacttttgaaaaagttctaatcattgcaatccatgcag

Basic information

species Zea mays
transcript GRMZM2G386991_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G386991_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os01g62080.2 (Oryza sativa), 5'ss of exon 13
TGCTGAAAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAGAGGGAGCGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGTCTGCAGgtactttcctctctgatgtactc----taatcaattacgcat-----cagtttggccaactgacatcttttaaatggtatgacttttgaaaaagttctaatcattgcaatccatgcag
|||||||||||| ||||  || ||| |||||||||||||||||||||| || |||||||| || ||| |||||||||||||||||||||||||||||||||||||||  | ||||||||| ||    |  ||   |  ||||     |   || ||||| || |  ||  ||  ||||||  || |||| |    || |||  |   ||  |||||||
TGCTGAAAAGTATTTCAGACGTGGATTAAGGTTGGACTGGCCAGAGGGGGCTGCCTCACGGGAAAGCCTGAAGGCAGTCTGGAAATTGCCTCGTCTGCAGgtactttgttatctgatgtagtcagtatgttcctcttagcattttcccctctttgccaagtgtcg-ctcataggtggtatc-ctcttgaca---ctcgaattgtgctaactcatgcag
















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|211421941|gb|FL433263.1|FL433263
EST:     CGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGTCTGCAG                         AACCTTGTGATGCAACATGTTGATCATTCTGCTGGAGATCTAATTGATCTT
genomic: CGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGTCTGCAGgtactttcct ... atccatgcagAACCTTGTGATGCAACATGTTGATCATTCTGCTGGAGATCTAATTGATCTT
EST: gi|32930586|gb|CF035398.1|CF035398
EST:     CGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGTCTGCAG                         AACCTTGTGATGCAACATGTTGATCATTCTGCTGGAGATCTAATTGATCTT
genomic: CGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGTCTGCAGgtactttcct ... atccatgcagAACCTTGTGATGCAACATGTTGATCATTCTGCTGGAGATCTAATTGATCTT
EST: gi|113702476|gb|EE679980.1|EE679980
EST:     CGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGTCTGCAG                         AACCTTGTGATGCAACATGTTGATCATTCTGCTGGAGATCTAATTGATCTT
genomic: CGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGTCTGCAGgtactttcct ... atccatgcagAACCTTGTGATGCAACATGTTGATCATTCTGCTGGAGATCTAATTGATCTT
EST: gi|6021499|gb|AW066427.1|AW066427
EST:     CGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGTCTGCAG                         AACCTTGTGATGCAACATGTTGATCATTCTGCTGGAGATCTAATTGATCTT
genomic: CGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGTCTGCAGgtactttcct ... atccatgcagAACCTTGTGATGCAACATGTTGATCATTCTGCTGGAGATCTAATTGATCTT
EST: gi|211073306|gb|FL473576.1|FL473576
EST:     CGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGTCTGCAG                         AACCTTGTGATGCAACATGTTGATCATTCTGCTGGAGATCTAATTGATCTT
genomic: CGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGTCTGCAGgtactttcct ... atccatgcagAACCTTGTGATGCAACATGTTGATCATTCTGCTGGAGATCTAATTGATCTT
EST: gi|19822133|gb|BQ048157.1|BQ048157
EST:     CGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGTCTGCAG                         AACCTTGTGATGCAACATGTTGATCATTCTGCTGGAGATCTAATTGATCTT
genomic: CGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGTCTGCAGgtactttcct ... atccatgcagAACCTTGTGATGCAACATGTTGATCATTCTGCTGGAGATCTAATTGATCTT
EST: gi|19769731|gb|BQ034452.1|BQ034452
EST:     CGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGTCTGCAG                         AACCTTGTGATGCAACATGTTGATCATTCTGCTGGAGATCTAATTGATCTT
genomic: CGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGTCTGCAGgtactttcct ... atccatgcagAACCTTGTGATGCAACATGTTGATCATTCTGCTGGAGATCTAATTGATCTT
EST: gi|19769965|gb|BQ034686.1|BQ034686
EST:     CGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGTCTGCAG                         AACCTTGTGATGCAACATGTTGATCATTCTGCTGGAGATCTAATTGATCTT
genomic: CGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGTCTGCAGgtactttcct ... atccatgcagAACCTTGTGATGCAACATGTTGATCATTCTGCTGGAGATCTAATTGATCTT
EST: gi|31997648|gb|CD661693.1|CD661693
EST:     CGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGTCTGCAG                         AACCTTGTGATGCAACATGTTGATCATTCTGCTGGAGATCTAATTGATCTT
genomic: CGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGTCTGCAGgtactttcct ... atccatgcagAACCTTGTGATGCAACATGTTGATCATTCTGCTGGAGATCTAATTGATCTT
EST: gi|211122243|gb|FL474055.1|FL474055
EST:     CGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGTCTGCAG                         AACCTTGTGATGCAACATGTTGATCATTCTGCTGGAGATCTAATTGATCTT
genomic: CGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGTCTGCAGgtactttcct ... atccatgcagAACCTTGTGATGCAACATGTTGATCATTCTGCTGGAGATCTAATTGATCTT
EST: gi|19822056|gb|BQ048080.1|BQ048080
EST:     CGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGTCTGCAG                         AACCTTGTGATGCAACATGTTGATCATTCTGCTGGAGATCTAATTGATCTT
genomic: CGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGTCTGCAGgtactttcct ... atccatgcagAACCTTGTGATGCAACATGTTGATCATTCTGCTGGAGATCTAATTGATCTT
EST: gi|15426933|gb|BI542755.1|BI542755
EST:     CGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGTCTGCAG                         AACCTTGTGATGCAACATGTTGATCATTCTGCTGGAGATCTAATTGATCTT
genomic: CGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGTCTGCAGgtactttcct ... atccatgcagAACCTTGTGATGCAACATGTTGATCATTCTGCTGGAGATCTAATTGATCTT
EST: gi|15352988|gb|BI502599.1|BI502599
EST:     CGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGTCTGCAG                         AACCTTGTGATGCAACATGTTGATCATTCTGCTGGAGATCTAATTGATCTT
genomic: CGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGTCTGCAGgtactttcct ... atccatgcagAACCTTGTGATGCAACATGTTGATCATTCTGCTGGAGATCTAATTGATCTT
EST: gi|14245195|gb|BG873777.1|BG873777
EST:     CGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGTCTGCAG                         AACCTTGTGATGCAACATGTTGATCATTCTGCTGGAGATCTAATTGATCTT
genomic: CGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGTCTGCAGgtactttcct ... atccatgcagAACCTTGTGATGCAACATGTTGATCATTCTGCTGGAGATCTAATTGATCTT
EST: gi|60343108|gb|DN210081.1|DN210081
EST:     CGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGTCTGCAG                         AACCTTGTGATGCAACATGTTGATCATTCTGCTGGAGATCTAATTGATCTT
genomic: CGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGTCTGCAGgtactttcct ... atccatgcagAACCTTGTGATGCAACATGTTGATCATTCTGCTGGAGATCTAATTGATCTT
EST: gi|60354602|gb|DN221575.1|DN221575
EST:     CGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGTCTGCAG                         AACCTTGTGATGCAACATGTTGATCATTCTGCTGGAGATCTAATTGATCTT
genomic: CGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGTCTGCAGgtactttcct ... atccatgcagAACCTTGTGATGCAACATGTTGATCATTCTGCTGGAGATCTAATTGATCTT
EST: gi|113672090|gb|DW823682.1|DW823682
EST:     GGAAATTGCCTCGTCTGCAG                         AACCTTGTGATGCAACATGTTGATCATTCTGCTGGAGATCTAATTGATCTT
genomic: GGAAATTGCCTCGTCTGCAGgtactttcct ... atccatgcagAACCTTGTGATGCAACATGTTGATCATTCTGCTGGAGATCTAATTGATCTT
EST: gi|113556745|gb|DW733538.1|DW733538
EST:     CTGGAAATTGCCTCGTCTGCAG                         AACCTTGTGATGCAACATGTTGATCATTCTGCTGGAGATCTAATTGATCTT
genomic: CTGGAAATTGCCTCGTCTGCAGgtactttcct ... atccatgcagAACCTTGTGATGCAACATGTTGATCATTCTGCTGGAGATCTAATTGATCTT
EST: gi|45847998|gb|CN071941.1|CN071941
EST:     CGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGTCTGCAG                         AACCTTGTGATGCAACATGTTGATCATTCTGCTGGAGATCTAATTGATCTT
genomic: CGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGTCTGCAGgtactttcct ... atccatgcagAACCTTGTGATGCAACATGTTGATCATTCTGCTGGAGATCTAATTGATCTT
EST: gi|6127284|gb|AW129809.1|AW129809
EST:     CGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGTCTGCAG                         AACCTTGTGATGCAACATGTTGATCATTCTGCTGGAGATCTAATTGATCTT
genomic: CGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGTCTGCAGgtactttcct ... atccatgcagAACCTTGTGATGCAACATGTTGATCATTCTGCTGGAGATCTAATTGATCTT

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), 49 (downstream exon)
Score: 144

TGCTGAAAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAGAGGGAGCGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGTCTGCAGgtactttcct ... atccatgcagAACCTTGTGATGCAACATGTTGATCATTCTGCTGGAGATCTAATTGATCTTCTTCAAGGACTTCTTCGGTATGATCCTAATGAGCGCCTGAAAGCACATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 181

TGCTGAAAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAGAGGGAGCGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGTCTGCAGgtactttcct ... atccatgcagAACCTTGTGATGCAACATGTTGATCATTCTGCTGGAGATCTAATTGATCTTCTTCAAGGACTTCTTCGGTATGATCCTAATGAGCGCCTGAAAGCACATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 158

TGCTGAAAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAGAGGGAGCGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGTCTGCAGgtactttcct ... atccatgcagAACCTTGTGATGCAACATGTTGATCATTCTGCTGGAGATCTAATTGATCTTCTTCAAGGACTTCTTCGGTATGATCCTAATGAGCGCCTGAAAGCACATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 142

TGCTGAAAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAGAGGGAGCGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGTCTGCAGgtactttcct ... atccatgcagAACCTTGTGATGCAACATGTTGATCATTCTGCTGGAGATCTAATTGATCTTCTTCAAGGACTTCTTCGGTATGATCCTAATGAGCGCCTGAAAGCACATG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTGAAAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAGAGGGAGCGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGTCTGCAGgtactttcctctctgatgtactctaatcaattacgcatcagtttggccaactgacatcttttaaatggtatgacttttgaaaaagttctaatcattgcaatccatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG