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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACAAAATCAATAATTGGAGGGCCACAGCTCTTATTTTGACATCCATCCTTTTCGCTGCTGTTGTGTTCTGGTTCATTGgtaagtttcacaatataataggctacagtttcacaaattatcggttctctttttttttctttcagactttcacatgctgatgaaaaaccttcattaaagc...

Basic information

species Zea mays
transcript GRMZM2G062024_T01
intron # 15
splice site 5'
intron type U2

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|32840593|gb|CD980274.1|CD980274
EST:     TCTTATTTTGACATCCATCCTTTTCGCTGCTGTTGTGTTCTGGTTCATTG                         GCATATTTATCCCCAGCGTCGATCGTTTCAATGAAGAGAGCGAGCATGGCC
genomic: TCTTATTTTGACATCCATCCTTTTCGCTGCTGTTGTGTTCTGGTTCATTGgtaagtttca ... gtctttgcagGCATATTTATCCCCAGCGTCGATCGTTTCAATGAAGAGAGCGAGCATGGCC
EST: gi|32840289|gb|CD979970.1|CD979970
EST:     TCTTATTTTGACATCCATCCTTTTCGCTGCTGTTGTGTTCTGGTTCATTG                         GCATATTTATCCCCAGCGTCGATCGTTTCAATGAAGAGAGCGAGCATGGCC
genomic: TCTTATTTTGACATCCATCCTTTTCGCTGCTGTTGTGTTCTGGTTCATTGgtaagtttca ... gtctttgcagGCATATTTATCCCCAGCGTCGATCGTTTCAATGAAGAGAGCGAGCATGGCC
EST: gi|32840250|gb|CD979931.1|CD979931
EST:     TCTTATTTTGACATCCATCCTTTTCGCTGCTGTTGTGTTCTGGTTCATTG                         GCATATTTATCCCCAGCGTCGATCGTTTCAATGAAGAGAGCGAGCATGGCC
genomic: TCTTATTTTGACATCCATCCTTTTCGCTGCTGTTGTGTTCTGGTTCATTGgtaagtttca ... gtctttgcagGCATATTTATCCCCAGCGTCGATCGTTTCAATGAAGAGAGCGAGCATGGCC
EST: gi|6012686|gb|AW062123.1|AW062123
EST:     TCTTATTTTGACATCCATCCTTTTCGCTGCTGTTGTGTTCTGGTTCATTG                         GCATATTTATCCCCAGCGTCGATCGTTTCAATGAAGAGAGCGAGCATGCCC
genomic: TCTTATTTTGACATCCATCCTTTTCGCTGCTGTTGTGTTCTGGTTCATTGgtaagtttca ... gtctttgcagGCATATTTATCCCCAGCGTCGATCGTTTCAATGAAGAGAGCGAGCATGGCC
EST: gi|91875800|gb|EB405757.1|EB405757
EST:     TCTTATTTTGACATCCATCCTTTTCGCTGCTGTTGTGTTCTGGTTCATTG                         GCATATTTATCCCCAGCGTCGATCGTTTCAATGAAGAGAGCGAGCATGGCC
genomic: TCTTATTTTGACATCCATCCTTTTCGCTGCTGTTGTGTTCTGGTTCATTGgtaagtttca ... gtctttgcagGCATATTTATCCCCAGCGTCGATCGTTTCAATGAAGAGAGCGAGCATGGCC
EST: gi|32840295|gb|CD979976.1|CD979976
EST:     TCTTATTTTGACATCCATCCTTTTCGCTGCTGTTGTGTTCTGGTTCATTG                         GCATATTTATCCCCAGCGTCGATCGTTTCAATGAAGAGAGCGAGCATGGCC
genomic: TCTTATTTTGACATCCATCCTTTTCGCTGCTGTTGTGTTCTGGTTCATTGgtaagtttca ... gtctttgcagGCATATTTATCCCCAGCGTCGATCGTTTCAATGAAGAGAGCGAGCATGGCC
EST: gi|32840590|gb|CD980271.1|CD980271
EST:     TCTTATTTTGACATCCATCCTTTTCGCTGCTGTTGTGTTCTGGTTCATTG                         GCATATTTATCCCCAGCGTCGATCGTTTCAATGAAGAGAGCGAGCATGGCC
genomic: TCTTATTTTGACATCCATCCTTTTCGCTGCTGTTGTGTTCTGGTTCATTGgtaagtttca ... gtctttgcagGCATATTTATCCCCAGCGTCGATCGTTTCAATGAAGAGAGCGAGCATGGCC
EST: gi|211124332|gb|FL444268.1|FL444268
EST:     TCTTATTTTGACATCCATCCTTTTCGCTGCTGTTGTGTTCTGGTTCATTG                         GCATATTTATCCCCAGCGTCGATCGTTTCAATGAAGAGAGCGAGCATGGCC
genomic: TCTTATTTTGACATCCATCCTTTTCGCTGCTGTTGTGTTCTGGTTCATTGgtaagtttca ... gtctttgcagGCATATTTATCCCCAGCGTCGATCGTTTCAATGAAGAGAGCGAGCATGGCC
EST: gi|32840308|gb|CD979989.1|CD979989
EST:     TCTTATTTTGACATCCATCCTTTTCGCTGCTGTTGTGTTCTGGTTCATTG                         GCATATTTATCCCCAGCGTCGATCGTTTCAATGAAGAGAGCGAGCATGGCC
genomic: TCTTATTTTGACATCCATCCTTTTCGCTGCTGTTGTGTTCTGGTTCATTGgtaagtttca ... gtctttgcagGCATATTTATCCCCAGCGTCGATCGTTTCAATGAAGAGAGCGAGCATGGCC
EST: gi|5108252|gb|AI739965.1|AI739965
EST:     TCTTATTTTGACATCCATCCTTTTCGCTGCTGTTGTGTTCTGGTTCATTG                         GCATATTTATCCCCAGCGTCGATCGTTTCAATGAAGAGAGCGAGCATGGCC
genomic: TCTTATTTTGACATCCATCCTTTTCGCTGCTGTTGTGTTCTGGTTCATTGgtaagtttca ... gtctttgcagGCATATTTATCCCCAGCGTCGATCGTTTCAATGAAGAGAGCGAGCATGGCC
EST: gi|74236979|gb|DT644893.1|DT644893
EST:     TCTTATTTTGACATCCATCCTTTTCGCTGCTGTTGTGTTCTGGTTCATTG                         GCATATTTATCCCCAGCGTCGATCGTTTCAATGAAGAGAGCGAGCATGGCC
genomic: TCTTATTTTGACATCCATCCTTTTCGCTGCTGTTGTGTTCTGGTTCATTGgtaagtttca ... gtctttgcagGCATATTTATCCCCAGCGTCGATCGTTTCAATGAAGAGAGCGAGCATGGCC
EST: gi|32840674|gb|CD980355.1|CD980355
EST:     TCTTATTTTGACATCCATCCTTTTCGCTGCTGTTGTGTTCTGGTTCATTG                         GCATATTTATCCCCAGCGTCGATCGTTTCAATGAAGAGAGCGAGCATGGCC
genomic: TCTTATTTTGACATCCATCCTTTTCGCTGCTGTTGTGTTCTGGTTCATTGgtaagtttca ... gtctttgcagGCATATTTATCCCCAGCGTCGATCGTTTCAATGAAGAGAGCGAGCATGGCC
EST: gi|29545180|gb|CB605358.1|CB605358
EST:     TCTTATTTTGACATCCATCCTTTTCGCTGCTGTTGTGTTCTGGTTCATTG                         GCATATTTATCCCCAGCGTCGATCGTTTCAATGAAGAGAGCGAGCATGGCC
genomic: TCTTATTTTGACATCCATCCTTTTCGCTGCTGTTGTGTTCTGGTTCATTGgtaagtttca ... gtctttgcagGCATATTTATCCCCAGCGTCGATCGTTTCAATGAAGAGAGCGAGCATGGCC
EST: gi|32840071|gb|CD979752.1|CD979752
EST:     TCTTATTTTGGCATCCATCCTTTTCGCTGCTGTTGTGTTCTGGTTCATTG                         GCATATTTATCCCCAGCGTCGATCGTTTCAATGAAGAGAGCGAGCATGGCC
genomic: TCTTATTTTGACATCCATCCTTTTCGCTGCTGTTGTGTTCTGGTTCATTGgtaagtttca ... gtctttgcagGCATATTTATCCCCAGCGTCGATCGTTTCAATGAAGAGAGCGAGCATGGCC
EST: gi|32840235|gb|CD979916.1|CD979916
EST:     TCTTATTTTGACATCCATCCTTTTCGCTGCTGTTGTGTTCTGGTTCATTG                         GCATATTTATCCCCAGCGTCGATCGTTTCAATGAAGAGAGCGAGGCATGGC
genomic: TCTTATTTTGACATCCATCCTTTTCGCTGCTGTTGTGTTCTGGTTCATTGgtaagtttca ... gtctttgcagGCATATTTATCCCCAGCGTCGATCGTTTCAATGAAGAGAGCGAG-CATGGC
EST: gi|32840128|gb|CD979809.1|CD979809
EST:     TCTTATTTTGACATCCATCCTTTTCGCTGCTGTTGTGTTCTGGTTCATTG                         GCATATTTATCCCCAGCGTCGATCGTTTCAATGAAGAGAGCGAGCATGGCC
genomic: TCTTATTTTGACATCCATCCTTTTCGCTGCTGTTGTGTTCTGGTTCATTGgtaagtttca ... gtctttgcagGCATATTTATCCCCAGCGTCGATCGTTTCAATGAAGAGAGCGAGCATGGCC

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: 48 (upstream exon), 49 (downstream exon)
Score: 51

GACAAAATCAATAATTGGAGGGCCACAGCTCTTATTTTGACATCCATCCTTTTCGCTGCTGTTGTGTTCTGGTTCATTGgtaagtttca ... gtctttgcagGCATATTTATCCCCAGCGTCGATCGTTTCAATGAAGAGAGCGAGCATGGCCTTACTGTCGCCGAGAGATCAAATCTCAGGCCGCTCCTTGATGAAAAGGA


Block sizes: 42 (upstream exon), 48 (downstream exon)
Score: 19

GACAAAATCAATAATTGGAGGGCCACAGCTCTTATTTTGACATCCATCCTTTTCGCTGCTGTTGTGTTCTGGTTCATTGgtaagtttca ... gtctttgcagGCATATTTATCCCCAGCGTCGATCGTTTCAATGAAGAGAGCGAGCATGGCCTTACTGTCGCCGAGAGATCAAATCTCAGGCCGCTCCTTGATGAAAAGGA


Block sizes: 44 (upstream exon), 45 (downstream exon)
Score: 16

GACAAAATCAATAATTGGAGGGCCACAGCTCTTATTTTGACATCCATCCTTTTCGCTGCTGTTGTGTTCTGGTTCATTGgtaagtttca ... gtctttgcagGCATATTTATCCCCAGCGTCGATCGTTTCAATGAAGAGAGCGAGCATGGCCTTACTGTCGCCGAGAGATCAAATCTCAGGCCGCTCCTTGATGAAAAGGA


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 65

GACAAAATCAATAATTGGAGGGCCACAGCTCTTATTTTGACATCCATCCTTTTCGCTGCTGTTGTGTTCTGGTTCATTGgtaagtttca ... gtctttgcagGCATATTTATCCCCAGCGTCGATCGTTTCAATGAAGAGAGCGAGCATGGCCTTACTGTCGCCGAGAGATCAAATCTCAGGCCGCTCCTTGATGAAAAGGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACAAAATCAATAATTGGAGGGCCACAGCTCTTATTTTGACATCCATCCTTTTCGCTGCTGTTGTGTTCTGGTTCATTGgtaagtttcacaatataataggctacagtttcacaaattatcggttctctttttttttctttcagactttcacatgctgatgaaaaaccttcattaaagc

- - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgaaaaa