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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGAAGAAGGGCCCGTGGACGGCGGAGGAGGACCAGAAGCTCGTCACCTTCCTCCTCATCAACGGCCAGTGCTGCTGGCGCGCCGTGCCTAAGCTCGCCGgtgagtgatcaccatataaatccggtctccctcattggccggccggcggctagctttgctttgtttttcttacacgctgccttagcctggcatgcacgccaagacgccatgaccatgaactcactcgtgcgcttgtgggtttctgaatgaacag

Basic information

species Zea mays
transcript GRMZM2G169356_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G169356_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os09g23620.1 (Oryza sativa), 5'ss of exon 1
CTGAAGAAGGGCCCGTGGACGGCGGAGGAGGACCAGAAGCTCGTCACCTTCCTCCTCATCAACGGCCAGTGCTGCTGGCGCGCCGTGCCTAAGCTCGCCGgtgagtgatcaccat----ataaatccggtctccctcattggcc-ggccgg--cggctagctttgctttgtttttcttacacg-ctgccttagcctggcatgcacgccaagacgccatgaccatgaactcactcgtgcgcttgtgggtttctgaatgaacag
||||||||||| || ||||||||||||||||||||||||||||||| ||||||||||  ||||||||| ||||||||||| ||||| || |||||||||||||||| | |  | |    | |  | | ||||| ||| ||     || ||   |    | |  ||   || | |   |      |||    ||                                                                     
CTGAAGAAGGGTCCATGGACGGCGGAGGAGGACCAGAAGCTCGTCAGCTTCCTCCTCGGCAACGGCCAATGCTGCTGGCGTGCCGTCCCCAAGCTCGCCGgtgagtcacccacctcgccagagtttcagtctctctctttaatttggtcgatccattgatcaatggactgatgtatctgtgtaactgaaacag---------------------------------------------------------------------
















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|211027698|gb|FL073325.1|FL073325
EST:     CCTCCTCATCAACGGCCAGTGCTGCTGGCGCGCCGTGCCTAAGCTCGCCG                         GACTACTGCGGTGCGGGAAGAGCTGCAGGCTGCGGTGGACCAACTACCTGC
genomic: CCTCCTCATCAACGGCCAGTGCTGCTGGCGCGCCGTGCCTAAGCTCGCCGgtgagtgatc ... gaatgaacagGACTACTGCGGTGCGGGAAGAGCTGCAGGCTGCGGTGGACCAACTACCTGC
EST: gi|211027699|gb|FL073326.1|FL073326
EST:     CCTCCTCATCAACGGCCAGTGCTGCTGGCGCGCCGTGCCTAAGCTCGCCG                         GACTACTGCGGTGCGGGAAGAGCTGCAGGCTGCGGTGGACCAACTACCTGC
genomic: CCTCCTCATCAACGGCCAGTGCTGCTGGCGCGCCGTGCCTAAGCTCGCCGgtgagtgatc ... gaatgaacagGACTACTGCGGTGCGGGAAGAGCTGCAGGCTGCGGTGGACCAACTACCTGC
EST: gi|211027700|gb|FL073327.1|FL073327
EST:     CCTCCTCATCAACGGCCAGTGCTGCTGGCGCGCCGTGCCTAAGCTCGCCG                         GACTACTGCGGTGCGGGAAGAGCTGCAGGCTGCGGTGGACCAACTACCTGC
genomic: CCTCCTCATCAACGGCCAGTGCTGCTGGCGCGCCGTGCCTAAGCTCGCCGgtgagtgatc ... gaatgaacagGACTACTGCGGTGCGGGAAGAGCTGCAGGCTGCGGTGGACCAACTACCTGC
EST: gi|211027702|gb|FL073329.1|FL073329
EST:     CCTCCTCATCAACGGCCAGTGCTGCTGGCGCGCCGTGCCTAAGCTCGCCG                         GACTACTGCGGTGCGGGAAGAGCTGCAGGCTGCGGTGGACCAACTACCTGC
genomic: CCTCCTCATCAACGGCCAGTGCTGCTGGCGCGCCGTGCCTAAGCTCGCCGgtgagtgatc ... gaatgaacagGACTACTGCGGTGCGGGAAGAGCTGCAGGCTGCGGTGGACCAACTACCTGC
EST: gi|211027697|gb|FL073324.1|FL073324
EST:     CCTCCTCATCAACGGCCAGTGCTGCTGGCGCGCCGTGCCTAAGCTCGCCG                         GACTACTGCGGTGCGGGAAGAGCTGCAGGCTGCGGTGGACCAACTACCTGC
genomic: CCTCCTCATCAACGGCCAGTGCTGCTGGCGCGCCGTGCCTAAGCTCGCCGgtgagtgatc ... gaatgaacagGACTACTGCGGTGCGGGAAGAGCTGCAGGCTGCGGTGGACCAACTACCTGC
EST: gi|211027704|gb|FL073331.1|FL073331
EST:     CCTCCTCATCAACGGCCAGTGCTGCTGGCGCGCCGTGCCTAAGCTCGCCG                         GACTACTGCGGTGCGGGAAGAGCTGCAGGCTGCGGTGGACCAACTACCTGC
genomic: CCTCCTCATCAACGGCCAGTGCTGCTGGCGCGCCGTGCCTAAGCTCGCCGgtgagtgatc ... gaatgaacagGACTACTGCGGTGCGGGAAGAGCTGCAGGCTGCGGTGGACCAACTACCTGC
EST: gi|211027696|gb|FL073323.1|FL073323
EST:     CCTCCTCATCAACGGCCAGTGCTGCTGGCGCGCCGTGCCTAAGCTCGCCG                         GACTACTGCGGTGCGGGAAGAGCTGCAGGCTCCGGTGGACCAACTACCTGC
genomic: CCTCCTCATCAACGGCCAGTGCTGCTGGCGCGCCGTGCCTAAGCTCGCCGgtgagtgatc ... gaatgaacagGACTACTGCGGTGCGGGAAGAGCTGCAGGCTGCGGTGGACCAACTACCTGC
EST: gi|211027701|gb|FL073328.1|FL073328
EST:     CCTCCTCATCAACGGCCAGTGCTGCTGGCGCGCCGTGCCTAAGCTCGCCG                         GACTACTGCGGTGCGGGAAGAGCTGCAGGCTGCGGTGGACCAACTACCTGC
genomic: CCTCCTCATCAACGGCCAGTGCTGCTGGCGCGCCGTGCCTAAGCTCGCCGgtgagtgatc ... gaatgaacagGACTACTGCGGTGCGGGAAGAGCTGCAGGCTGCGGTGGACCAACTACCTGC
EST: gi|211027703|gb|FL073330.1|FL073330
EST:     CCTCCTCATCAACGGCCAGTGCTGCTGGCGCGCCGTGCCTAAGCTCGCCG                         GACTACTGCGGTGCGGGAAGAGCTGCAGGCTGCGGTGGACCAACTACCTGC
genomic: CCTCCTCATCAACGGCCAGTGCTGCTGGCGCGCCGTGCCTAAGCTCGCCGgtgagtgatc ... gaatgaacagGACTACTGCGGTGCGGGAAGAGCTGCAGGCTGCGGTGGACCAACTACCTGC

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: 37 (upstream exon), 47 (downstream exon)
Score: 3

CTGAAGAAGGGCCCGTGGACGGCGGAGGAGGACCAGAAGCTCGTCACCTTCCTCCTCATCAACGGCCAGTGCTGCTGGCGCGCCGTGCCTAAGCTCGCCGgtgagtgatc ... gaatgaacagGACTACTGCGGTGCGGGAAGAGCTGCAGGCTGCGGTGGACCAACTACCTGCGCCCGGACCTCAAGCGCGGGCTGCTGTCGGAGGAGGAGGAGAGGACGGT


Block sizes: 48 (upstream exon), 36 (downstream exon)
Score: 17

CTGAAGAAGGGCCCGTGGACGGCGGAGGAGGACCAGAAGCTCGTCACCTTCCTCCTCATCAACGGCCAGTGCTGCTGGCGCGCCGTGCCTAAGCTCGCCGgtgagtgatc ... gaatgaacagGACTACTGCGGTGCGGGAAGAGCTGCAGGCTGCGGTGGACCAACTACCTGCGCCCGGACCTCAAGCGCGGGCTGCTGTCGGAGGAGGAGGAGAGGACGGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 71

CTGAAGAAGGGCCCGTGGACGGCGGAGGAGGACCAGAAGCTCGTCACCTTCCTCCTCATCAACGGCCAGTGCTGCTGGCGCGCCGTGCCTAAGCTCGCCGgtgagtgatc ... gaatgaacagGACTACTGCGGTGCGGGAAGAGCTGCAGGCTGCGGTGGACCAACTACCTGCGCCCGGACCTCAAGCGCGGGCTGCTGTCGGAGGAGGAGGAGAGGACGGT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGAAGAAGGGCCCGTGGACGGCGGAGGAGGACCAGAAGCTCGTCACCTTCCTCCTCATCAACGGCCAGTGCTGCTGGCGCGCCGTGCCTAAGCTCGCCGgtgagtgatcaccatataaatccggtctccctcattggccggccggcggctagctttgctttgtttttcttacacgctgccttagcctggcatgcacgccaagacgccatgaccatgaactcactcgtgcgcttgtgggtttctgaatgaacag

- - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT