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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgttagatactttttaagatgaagtgttgggacagctcacgagtttggttcagtaacatgtttgtcagaaatttcctaagactactctcacacattgcagGAAACAAATGCTAACTTGGATGAGATAGTTGAGCTGGCAAAGCAGCTCCAG

Basic information

species Zea mays
transcript GRMZM2G005493_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G005493_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os07g47290.1 (Oryza sativa), 3'ss of exon 6
cgttagatactttttaagatgaagtgttgggacagctcacgagtttggttcagtaacatgttt---gtcagaaatttcctaagactactctcacacattgcagGAAACAAATGCTAACTTGGATGAGATAGTTGAGCTGGCAAAGCAGCTCCAG
  |  | ||  ||||  ||   | |  ||||         ||  | | |   |  ||  ||     ||| |  ||||  ||||  |  | |  |||||||||||||||||||   || ||||||||||||||||| ||||||||| | ||||||
tttctgttaaatttttgga---atttctgggtttctgtgtgatgtagctctggccaccagtggaaggtctggtattttataagcttcttgtttcacattgcagGAAACAAATAAAAATTTGGATGAGATAGTTGAACTGGCAAAGAAACTCCAG
















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|149080694|gb|EE169755.2|EE169755
EST:     AATGGTGCTTCCATGATAGGGATATTGCCCCTGATGGGGAAACTCTCGAA                         GAAACAAATGCTAACTTGGATGAGATAGTTGAGCTGGCAAAG
genomic: AATGGTGCTTCCATGATAGGGATATTGCCCCTGATGGGAAAACTCTCGAAgtatgtcctt ... cacattgcagGAAACAAATGCTAACTTGGATGAGATAGTTGAGCTGGCAAAG
EST: gi|211302405|gb|FL012357.1|FL012357
EST:     AATGGTGCTTCCATGATAGGGATATTGCCCCTGATGGGAAAACTCTCGAA                         GAA-CAAATGCTAACTTGGATGAGATAGTTGAGCTGGCAAAGCAGCTCCAG
genomic: AATGGTGCTTCCATGATAGGGATATTGCCCCTGATGGGAAAACTCTCGAAgtatgtcctt ... cacattgcagGAAACAAATGCTAACTTGGATGAGATAGTTGAGCTGGCAAAGCAGCTCCAG
EST: gi|67027757|gb|CO456506.1|CO456506
EST:     AATGGTGCTTCCATGATAGGGATATTGCCCCTGATGGGAAAACTCTCGAA                         GAAACAAATGCTAACTTGGATGAGATAGTTGAGCTGGCAAAGCAGCTCCAG
genomic: AATGGTGCTTCCATGATAGGGATATTGCCCCTGATGGGAAAACTCTCGAAgtatgtcctt ... cacattgcagGAAACAAATGCTAACTTGGATGAGATAGTTGAGCTGGCAAAGCAGCTCCAG
EST: gi|67019408|gb|CO448157.1|CO448157
EST:     AATGGTGCTTCCATGATAGGGATATTGCCCCTGATGGGAAAACTCTCGAA                         GAAACAAATGCTAACTTGGATGAGATAGTTGAGCTGGCAAAGCAGCTCCAG
genomic: AATGGTGCTTCCATGATAGGGATATTGCCCCTGATGGGAAAACTCTCGAAgtatgtcctt ... cacattgcagGAAACAAATGCTAACTTGGATGAGATAGTTGAGCTGGCAAAGCAGCTCCAG
EST: gi|148950087|gb|EC895623.2|EC895623
EST:     AATGGTGCTTCCATGATAGGGATATTGCCCCTGATGGGAAAACTCTCGAA                         GAAACAAATGCTAACTTGGATGAGATAGTTGAGCTGGCAAAGCAGCTCCAG
genomic: AATGGTGCTTCCATGATAGGGATATTGCCCCTGATGGGAAAACTCTCGAAgtatgtcctt ... cacattgcagGAAACAAATGCTAACTTGGATGAGATAGTTGAGCTGGCAAAGCAGCTCCAG
EST: gi|76286923|gb|DV026491.1|DV026491
EST:     AATGGTGCTTCCATGATAGGGATATTGCCCCTGATGGGAAAACTCTCGAA                         GAAACAAATGCTAACTTGGATGAGATAGTTGAGCTGGCAAAGCAGCTCCAG
genomic: AATGGTGCTTCCATGATAGGGATATTGCCCCTGATGGGAAAACTCTCGAAgtatgtcctt ... cacattgcagGAAACAAATGCTAACTTGGATGAGATAGTTGAGCTGGCAAAGCAGCTCCAG
EST: gi|21389921|gb|BQ527970.1|BQ527970
EST:     AATGGTGCTTCCATGATAGGGATATTGCCCCTGATGGGAAAACTCTCGAA                         GAAACAAATGCTAACTTGGATGAGA
genomic: AATGGTGCTTCCATGATAGGGATATTGCCCCTGATGGGAAAACTCTCGAAgtatgtcctt ... cacattgcagGAAACAAATGCTAACTTGGATGAGA

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: 488

TGAGAGCTCACTTTGAGTTCATGGAGAAGCTGGGGGTTGACAAATGGTGCTTCCATGATAGGGATATTGCCCCTGATGGGAAAACTCTCGAAgtatgtcctt ... cacattgcagGAAACAAATGCTAACTTGGATGAGATAGTTGAGCTGGCAAAGCAGCTCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 718

TGAGAGCTCACTTTGAGTTCATGGAGAAGCTGGGGGTTGACAAATGGTGCTTCCATGATAGGGATATTGCCCCTGATGGGAAAACTCTCGAAgtatgtcctt ... cacattgcagGAAACAAATGCTAACTTGGATGAGATAGTTGAGCTGGCAAAGCAGCTCCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 559

TGAGAGCTCACTTTGAGTTCATGGAGAAGCTGGGGGTTGACAAATGGTGCTTCCATGATAGGGATATTGCCCCTGATGGGAAAACTCTCGAAgtatgtcctt ... cacattgcagGAAACAAATGCTAACTTGGATGAGATAGTTGAGCTGGCAAAGCAGCTCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 753

TGAGAGCTCACTTTGAGTTCATGGAGAAGCTGGGGGTTGACAAATGGTGCTTCCATGATAGGGATATTGCCCCTGATGGGAAAACTCTCGAAgtatgtcctt ... cacattgcagGAAACAAATGCTAACTTGGATGAGATAGTTGAGCTGGCAAAGCAGCTCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggttcagtaacatgtttgtcagaaatttcctaagactactctcacacattgcagGAAACAAATGCTAACTTGGATGAGATAGTTGAGCTGGCAAAGCAGCTCCAG
                                       ctctcac  CT-rich tract
                     agaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgttagatactttttaagatgaagtgttgggacagctcacgagtttggttcagtaacatgtttgtcagaaatttcctaagactactctcacacattgcagGAAACAAATGCTAACTTGGATGAGATAGTTGAGCTGGCAAAGCAGCTCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - tgttggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtttgt