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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcagctttgctctctcacctgaaatgtgcatgtagttttcttgctgttttctccccccagtctcctatgatcccctgtatcctaccatcttgcttgcagGTTGAGTTTGCCCACGATGGAACATGCCATGGGTTCGCTGTTTGGATCGACTGGGTACTTGACAAGGAAAATTCCATAGTGATAAGCACCGGGCCAG

Basic information

species Zea mays
transcript GRMZM2G037624_T03
intron # 11
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|60398284|gb|DN231100.1|DN231100
EST:     TGGATTTGAACTTTTCTGAGCCTATCCACTCTTGTTTTGGTGAAACAAAG                         GTTGAGTTTGCCCACGATGGAACATGCCATGGGTTCGCTGTTTGGATCGAC
genomic: TGGATTTGAACTTTTCTGAGCCTATCCACTCTTGTTTTGGTGAAACAAAGgtatcatttt ... ttgcttgcagGTTGAGTTTGCCCACGATGGAACATGCCATGGGTTCGCTGTTTGGATCGAC
EST: gi|149009603|gb|EE154023.2|EE154023
EST:     TGGATTTGAACTTTTCTGAGCCTATCCACTCTTGTTTTGGTGAAACAAAG                         GTTGAGTTTGCCCACGATGGAACATGCCATGGGTTCGCTGTTTGGATCGAC
genomic: TGGATTTGAACTTTTCTGAGCCTATCCACTCTTGTTTTGGTGAAACAAAGgtatcatttt ... ttgcttgcagGTTGAGTTTGCCCACGATGGAACATGCCATGGGTTCGCTGTTTGGATCGAC
EST: gi|149056982|gb|EE156538.2|EE156538
EST:     TGGATTTGAACTTTTCTGAGCCTATCCACTCTTGTTTTGGTGAAACAAAG                         GTTGAGTTTGCCCCCGATGGAACATGCCATGGGTTCGCTGTTTGGATCGAC
genomic: TGGATTTGAACTTTTCTGAGCCTATCCACTCTTGTTTTGGTGAAACAAAGgtatcatttt ... ttgcttgcagGTTGAGTTTGCCCACGATGGAACATGCCATGGGTTCGCTGTTTGGATCGAC
EST: gi|71450153|gb|DR831203.1|DR831203
EST:     TGGATTTGAACTTTTCTGAGCCTATCCACTCTTGTTTTGGTGAAACAAAG                         GTTGAGTTTGCCCACGATGGAACATGCCATGGGTTCGCTGTTTGGATCGAC
genomic: TGGATTTGAACTTTTCTGAGCCTATCCACTCTTGTTTTGGTGAAACAAAGgtatcatttt ... ttgcttgcagGTTGAGTTTGCCCACGATGGAACATGCCATGGGTTCGCTGTTTGGATCGAC
EST: gi|78025068|gb|DV493455.1|DV493455
EST:     TGGATTTGAACTTTTCTGAGCCTATCCACTCTTGTTTTGGTGAAACAAAG                         GTTGAGTTTGCCCACGATGGAACATGCCATGGGTTCGCTGTTTGGATCGAC
genomic: TGGATTTGAACTTTTCTGAGCCTATCCACTCTTGTTTTGGTGAAACAAAGgtatcatttt ... ttgcttgcagGTTGAGTTTGCCCACGATGGAACATGCCATGGGTTCGCTGTTTGGATCGAC
EST: gi|91869810|gb|EB400552.1|EB400552
EST:     TGGATTTGAACTTTTCTGAGCCTATCCACTCTTGTTTTGGTGAAACAAAG                         GTTGAGTTTGCCCACGATGGAACATGCCATGGGTTCGCTGTTTGGATCGAC
genomic: TGGATTTGAACTTTTCTGAGCCTATCCACTCTTGTTTTGGTGAAACAAAGgtatcatttt ... ttgcttgcagGTTGAGTTTGCCCACGATGGAACATGCCATGGGTTCGCTGTTTGGATCGAC
EST: gi|5499114|gb|AI854981.1|AI854981
EST:     GCCTATCCACTCTTGTTTTGGTGAAACAAAG                         GTTGAGTTTGCCCACGATGGAACATGCCATGGGTTCGCTGTTTGGATCGAC
genomic: GCCTATCCACTCTTGTTTTGGTGAAACAAAGgtatcatttt ... ttgcttgcagGTTGAGTTTGCCCACGATGGAACATGCCATGGGTTCGCTGTTTGGATCGAC
EST: gi|91056761|gb|EB167179.1|EB167179
EST:     TGGATTTGAACTTTTTTGAGCCTATCCACTCTTGTTTTGGTGAAACAAAG                         GTTGAGTTTGCCCACGATGGAACATGCCATGGGTTCGCTGTTTGGATCGAC
genomic: TGGATTTGAACTTTTCTGAGCCTATCCACTCTTGTTTTGGTGAAACAAAGgtatcatttt ... ttgcttgcagGTTGAGTTTGCCCACGATGGAACATGCCATGGGTTCGCTGTTTGGATCGAC

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: 47 (upstream exon), 43 (downstream exon)
Score: 44

AAATTAAGTGAAGTTTACTCTCTCATGGATTTGAACTTTTCTGAGCCTATCCACTCTTGTTTTGGTGAAACAAAGgtatcatttt ... ttgcttgcagGTTGAGTTTGCCCACGATGGAACATGCCATGGGTTCGCTGTTTGGATCGACTGGGTACTTGACAAGGAAAATTCCATAGTGATAAGCACCGGGCCAG


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 30

AAATTAAGTGAAGTTTACTCTCTCATGGATTTGAACTTTTCTGAGCCTATCCACTCTTGTTTTGGTGAAACAAAGgtatcatttt ... ttgcttgcagGTTGAGTTTGCCCACGATGGAACATGCCATGGGTTCGCTGTTTGGATCGACTGGGTACTTGACAAGGAAAATTCCATAGTGATAAGCACCGGGCCAG


Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 22

AAATTAAGTGAAGTTTACTCTCTCATGGATTTGAACTTTTCTGAGCCTATCCACTCTTGTTTTGGTGAAACAAAGgtatcatttt ... ttgcttgcagGTTGAGTTTGCCCACGATGGAACATGCCATGGGTTCGCTGTTTGGATCGACTGGGTACTTGACAAGGAAAATTCCATAGTGATAAGCACCGGGCCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 21

AAATTAAGTGAAGTTTACTCTCTCATGGATTTGAACTTTTCTGAGCCTATCCACTCTTGTTTTGGTGAAACAAAGgtatcatttt ... ttgcttgcagGTTGAGTTTGCCCACGATGGAACATGCCATGGGTTCGCTGTTTGGATCGACTGGGTACTTGACAAGGAAAATTCCATAGTGATAAGCACCGGGCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttttctccccccagtctcctatgatcccctgtatcctaccatcttgcttgcagGTTGAGTTTGCCCACGATGGAACATGCCATGGGTTCGCTGTTTGGATCGACTGGGTACTTGACAAGGAAAATTCCATAGTGATAAGCACCGGGCCAG
                                           tcttgctt  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcagctttgctctctcacctgaaatgtgcatgtagttttcttgctgttttctccccccagtctcctatgatcccctgtatcctaccatcttgcttgcagGTTGAGTTTGCCCACGATGGAACATGCCATGGGTTCGCTGTTTGGATCGACTGGGTACTTGACAAGGAAAATTCCATAGTGATAAGCACCGGGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
-gcagctt
- - - - - - - - cacctga
- - - - - - - - - - - - - -tgcatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctacca