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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttaattgcaatcaacttgctatgttatgtcatgcaggttggaactataagtgtttattaatattaatgtttcagGCACCATGGATGGGTCTTCTATTGGGTACGTGCCTCTTGCACATTTTGATTGGAAACAAACATAGGGAGATGGCAAGTGGCACTGTCATACCAATTGGAA

Basic information

species Zea mays
transcript GRMZM2G153434_T01
intron # 7
splice site 3'
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|32837225|gb|CD976903.1|CD976903
EST:     CTCCGGAACATTCTGCACCATCTACTGTTACAAAAAATGCCCTCTCAGTG                         GCACCATGGATGGGTCTTCTATTGGGTA
genomic: CTCCGGAACATTCTGCACCATCTACTGTTACAAAAAATGCCCTCTCAGTGgtaagttaat ... aatgtttcagGCACCATGGATGGGTCTTCTATTGGGTA
EST: gi|22549090|gb|BU101291.1|BU101291
EST:     CTCCGGAACATTCTGCACCATCTACTGTTACAAAAAATGCCCTCTCAGTG                         GCACCATGGATGGGTCTTCTATTGGGTACGTGCCTCTTGCACATTTTGATT
genomic: CTCCGGAACATTCTGCACCATCTACTGTTACAAAAAATGCCCTCTCAGTGgtaagttaat ... aatgtttcagGCACCATGGATGGGTCTTCTATTGGGTACGTGCCTCTTGCACATTTTGATT
EST: gi|26559131|gb|CA831366.1|CA831366
EST:     CTCCGGAACATTCTGCACCATCTACTGTTACAAAAAATGCCCTCTCAGTG                         GCACCATGGATGGGTCTTCTATTGGGTACGTGCCTCTTGCACATTTTGATT
genomic: CTCCGGAACATTCTGCACCATCTACTGTTACAAAAAATGCCCTCTCAGTGgtaagttaat ... aatgtttcagGCACCATGGATGGGTCTTCTATTGGGTACGTGCCTCTTGCACATTTTGATT
EST: gi|32836692|gb|CD976370.1|CD976370
EST:     CTCCGGAACATTCTGCACCATCTACTGTTACAAAAAATGCCCTCTCAGTG                         GCACCATGGATGGGTCTTCTATTGGGTA
genomic: CTCCGGAACATTCTGCACCATCTACTGTTACAAAAAATGCCCTCTCAGTGgtaagttaat ... aatgtttcagGCACCATGGATGGGTCTTCTATTGGGTA
EST: gi|211278622|gb|FL264828.1|FL264828
EST:     CTCCGGAACATTCTGCACCATCTACTGTTACAAAAAATGCCCTCTCAGTG                         GCACCATGGATGGGTCTTCTATTGGGTACGTGCCTCTTGCACATTTTGATT
genomic: CTCCGGAACATTCTGCACCATCTACTGTTACAAAAAATGCCCTCTCAGTGgtaagttaat ... aatgtttcagGCACCATGGATGGGTCTTCTATTGGGTACGTGCCTCTTGCACATTTTGATT
EST: gi|89106847|gb|DY577064.1|DY577064
EST:     CTCCGGAACATTCTGCACCATCTACTGTTACAAAAAATGCCCTCTCAGTG                         GCACCATGGATGGGTCTTCTATTGGGTACGTGCCTCTTGCACATTTTGATT
genomic: CTCCGGAACATTCTGCACCATCTACTGTTACAAAAAATGCCCTCTCAGTGgtaagttaat ... aatgtttcagGCACCATGGATGGGTCTTCTATTGGGTACGTGCCTCTTGCACATTTTGATT
EST: gi|32838489|gb|CD978167.1|CD978167
EST:     CTCCGGAACATTCTGCACCATCTACTGTTACAAAAAATGCCCTCTCAGTG                         GCACCATGGATGGGTCTTCTATTGGGTA
genomic: CTCCGGAACATTCTGCACCATCTACTGTTACAAAAAATGCCCTCTCAGTGgtaagttaat ... aatgtttcagGCACCATGGATGGGTCTTCTATTGGGTA
EST: gi|89106878|gb|DY577095.1|DY577095
EST:     CTCCGGAACATTCTGCACCATCTACTGTTACAAAAAATGCCCTCTCAGTG                         GCACCATGGATGGGTCTTCTATTGGGTACGTGCCTCTTGCACATTTTGATT
genomic: CTCCGGAACATTCTGCACCATCTACTGTTACAAAAAATGCCCTCTCAGTGgtaagttaat ... aatgtttcagGCACCATGGATGGGTCTTCTATTGGGTACGTGCCTCTTGCACATTTTGATT
EST: gi|22521517|gb|BU080328.1|BU080328
EST:     CTCCGGAACATTCTGCACCATCTACTGTTACAAAAAATGCCCTCTCAGTG                         GCACCATGGATGGGTCTTCTATTGGGTACGTGCCTCTTGCACATTTTGATT
genomic: CTCCGGAACATTCTGCACCATCTACTGTTACAAAAAATGCCCTCTCAGTGgtaagttaat ... aatgtttcagGCACCATGGATGGGTCTTCTATTGGGTACGTGCCTCTTGCACATTTTGATT
EST: gi|26558987|gb|CA831222.1|CA831222
EST:     CTCCGGAACATTCTGCACCATCTACTGTTACAAAAAATGCCCTCTCAGTG                         GCACCATGGATGGGTCTTCTATTGGGTACGTGCCTCTTGCACATTTTGATT
genomic: CTCCGGAACATTCTGCACCATCTACTGTTACAAAAAATGCCCTCTCAGTGgtaagttaat ... aatgtttcagGCACCATGGATGGGTCTTCTATTGGGTACGTGCCTCTTGCACATTTTGATT
EST: gi|78082255|gb|DV510667.1|DV510667
EST:     CTCCGGAACATTCTGCACCATCTACTGTTACAAAAAATGCCCTCTCAGTG                         GCACCATGGATGGGTCTTCTATTGGGTACGTGCCTCTTGCACATTTTGATT
genomic: CTCCGGAACATTCTGCACCATCTACTGTTACAAAAAATGCCCTCTCAGTGgtaagttaat ... aatgtttcagGCACCATGGATGGGTCTTCTATTGGGTACGTGCCTCTTGCACATTTTGATT
EST: gi|32837681|gb|CD977359.1|CD977359
EST:     CTCCGGAACATTCTGCACCATCTACTGTTACAAAAAATGCCCTCTCAGTG                         GCACCATGGATGGGTCTTCTATTGGGTA
genomic: CTCCGGAACATTCTGCACCATCTACTGTTACAAAAAATGCCCTCTCAGTGgtaagttaat ... aatgtttcagGCACCATGGATGGGTCTTCTATTGGGTA
EST: gi|211278621|gb|FL264827.1|FL264827
EST:     CTCCGGAACATTCTGCACCATCTACTGTTACAAAAAATGCCCTCTCAGTG                         GCACCATGGATGGGTCTTCTATTGGGTACGTGCCTCTTGCACATTTTGATT
genomic: CTCCGGAACATTCTGCACCATCTACTGTTACAAAAAATGCCCTCTCAGTGgtaagttaat ... aatgtttcagGCACCATGGATGGGTCTTCTATTGGGTACGTGCCTCTTGCACATTTTGATT

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), 43 (downstream exon)
Score: 47

AAGTCCTCCACAAATGAATGATCAAAGGGGATCTTTAATTGGTGAGATCGCTCCGGAACATTCTGCACCATCTACTGTTACAAAAAATGCCCTCTCAGTGgtaagttaat ... aatgtttcagGCACCATGGATGGGTCTTCTATTGGGTACGTGCCTCTTGCACATTTTGATTGGAAACAAACATAGGGAGATGGCAAGTGGCACTGTCATACCAATTGGAA


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 47

AAGTCCTCCACAAATGAATGATCAAAGGGGATCTTTAATTGGTGAGATCGCTCCGGAACATTCTGCACCATCTACTGTTACAAAAAATGCCCTCTCAGTGgtaagttaat ... aatgtttcagGCACCATGGATGGGTCTTCTATTGGGTACGTGCCTCTTGCACATTTTGATTGGAAACAAACATAGGGAGATGGCAAGTGGCACTGTCATACCAATTGGAA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 17

AAGTCCTCCACAAATGAATGATCAAAGGGGATCTTTAATTGGTGAGATCGCTCCGGAACATTCTGCACCATCTACTGTTACAAAAAATGCCCTCTCAGTGgtaagttaat ... aatgtttcagGCACCATGGATGGGTCTTCTATTGGGTACGTGCCTCTTGCACATTTTGATTGGAAACAAACATAGGGAGATGGCAAGTGGCACTGTCATACCAATTGGAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 106

AAGTCCTCCACAAATGAATGATCAAAGGGGATCTTTAATTGGTGAGATCGCTCCGGAACATTCTGCACCATCTACTGTTACAAAAAATGCCCTCTCAGTGgtaagttaat ... aatgtttcagGCACCATGGATGGGTCTTCTATTGGGTACGTGCCTCTTGCACATTTTGATTGGAAACAAACATAGGGAGATGGCAAGTGGCACTGTCATACCAATTGGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgttatgtcatgcaggttggaactataagtgtttattaatattaatgtttcagGCACCATGGATGGGTCTTCTATTGGGTACGTGCCTCTTGCACATTTTGATTGGAAACAAACATAGGGAGATGGCAAGTGGCACTGTCATACCAATTGGAA
                                         tattaat  putative branch site (score: 106)
                      aactataagtgtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttaattgcaatcaacttgctatgttatgtcatgcaggttggaactataagtgtttattaatattaatgtttcagGCACCATGGATGGGTCTTCTATTGGGTACGTGCCTCTTGCACATTTTGATTGGAAACAAACATAGGGAGATGGCAAGTGGCACTGTCATACCAATTGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG