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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtacagtgttggaactctttatgtttttttattttattttatttgcaaactacaaagctctgaattattgctggtacagATAAAGGAAGGGCTTGGAGGGCGTATACGTCTCATGATAGCTGGAGCAGCACCTTTGCCAGGGCAAATCGAAGAATTCATGCGGGTAACCACCTGCAGCG

Basic information

species Zea mays
transcript GRMZM2G104847_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104847_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os11g35400.2 (Oryza sativa), 3'ss of exon 13
gtgtgtacag-tgttggaactctttatgtttttttattttattttatttgcaaactacaaagctctgaattattgctggtacagATAAAGGAAGGGCTTGGAGGGCGTATACGTCTCATGATAGCTGGAGCAGCACCTTTGCCAGGGCAAATCGAAGAATTCATGCGGGTAACCACCTGCAGCG
||  || ||| | ||   ||   || |  ||||     ||| ||         |  | | |  | |  || |||  || |||||||||| |||||||||||||| || ||||| ||| |  || | |||||||||||||||||| | ||  ||||||||||||||||||| |||| |||||| |
gtacgtgcagattttaagacaacttttcattttcccccttagttagaacatctatgaaataatttt--atcatttatgttacagATAAAAGAAGGGCTTGGAGGCCGGATACGACTCCTTCTATCAGGAGCAGCACCTTTGCCAAGACACGTCGAAGAATTCATGCGGGTTACCAGCTGCAGTG
















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|67024206|gb|CO452955.1|CO452955
EST:     TGAAACAGCATGAAGCATCACCGTTTTTCGACAAGATAGTTTTCAGCAAA                         ATAAAGGAAGGGCTTGGAGGGCGTATACGTCTCATGATAGCTGGAGCAGCA
genomic: TGAAACAGCATGAAGCATCACCGTTTTTCGACAAGATAGTTTTCAGCAAAgtgtgtacag ... gctggtacagATAAAGGAAGGGCTTGGAGGGCGTATACGTCTCATGATAGCTGGAGCAGCA
EST: gi|67024157|gb|CO452906.1|CO452906
EST:     TGAAACAGCATGAAGCATCACCGTTTTTCGACAAGATAGTTTTCAGCAAA                         ATAAAGGAAGGGCTTGGAGGGCGTATACGTCTCATGATAGCTGGAGCAGCA
genomic: TGAAACAGCATGAAGCATCACCGTTTTTCGACAAGATAGTTTTCAGCAAAgtgtgtacag ... gctggtacagATAAAGGAAGGGCTTGGAGGGCGTATACGTCTCATGATAGCTGGAGCAGCA
EST: gi|74243995|gb|DT651909.1|DT651909
EST:     TGAAACAGCATGAAGCATCACCGTTTTTCGACAAGATAGTTTTCAGCAAA                         ATAAAGGAAGGGCTTGGAGGGCGTATACGTCTCATGATAGCTGGAGCAGCA
genomic: TGAAACAGCATGAAGCATCACCGTTTTTCGACAAGATAGTTTTCAGCAAAgtgtgtacag ... gctggtacagATAAAGGAAGGGCTTGGAGGGCGTATACGTCTCATGATAGCTGGAGCAGCA
EST: gi|32865224|gb|CF004906.1|CF004906
EST:     TGAAACAGCATGAAGCATCACCGTTTTTCGACAAGATAGTTTTCAGCAAA                         ATAAAGGAAGGGCTTGGAGGGCGTATACGTCTCATGATAGCTGGAGCAGCA
genomic: TGAAACAGCATGAAGCATCACCGTTTTTCGACAAGATAGTTTTCAGCAAAgtgtgtacag ... gctggtacagATAAAGGAAGGGCTTGGAGGGCGTATACGTCTCATGATAGCTGGAGCAGCA

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 239

CAAACTTGCCAATATGAGGAAAGGGCTGAAACAGCATGAAGCATCACCGTTTTTCGACAAGATAGTTTTCAGCAAAgtgtgtacag ... gctggtacagATAAAGGAAGGGCTTGGAGGGCGTATACGTCTCATGATAGCTGGAGCAGCACCTTTGCCAGGGCAAATCGAAGAATTCATGCGGGTAACCACCTGCAGCG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 132

CAAACTTGCCAATATGAGGAAAGGGCTGAAACAGCATGAAGCATCACCGTTTTTCGACAAGATAGTTTTCAGCAAAgtgtgtacag ... gctggtacagATAAAGGAAGGGCTTGGAGGGCGTATACGTCTCATGATAGCTGGAGCAGCACCTTTGCCAGGGCAAATCGAAGAATTCATGCGGGTAACCACCTGCAGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 464

CAAACTTGCCAATATGAGGAAAGGGCTGAAACAGCATGAAGCATCACCGTTTTTCGACAAGATAGTTTTCAGCAAAgtgtgtacag ... gctggtacagATAAAGGAAGGGCTTGGAGGGCGTATACGTCTCATGATAGCTGGAGCAGCACCTTTGCCAGGGCAAATCGAAGAATTCATGCGGGTAACCACCTGCAGCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttattttattttatttgcaaactacaaagctctgaattattgctggtacagATAAAGGAAGGGCTTGGAGGGCGTATACGTCTCATGATAGCTGGAGCAGCACCTTTGCCAGGGCAAATCGAAGAATTCATGCGGGTAACCACCTGCAGCG
     tattttattttatttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgtacagtgttggaactctttatgtttttttattttattttatttgcaaactacaaagctctgaattattgctggtacagATAAAGGAAGGGCTTGGAGGGCGTATACGTCTCATGATAGCTGGAGCAGCACCTTTGCCAGGGCAAATCGAAGAATTCATGCGGGTAACCACCTGCAGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG