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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttaatcaatctctgtttcctaactcacgatgtccaaagtgacaatcgtttccagctgtccccttttcactaaacatgttcttaacatctgtttcagGCAAGTTCCAGACAGAGATCGGTAAGAGCTGGGCCGCTGAAGTAAACTCGAGGAGAAAGGAGGGATGCGGAAAGCAGGAGCCTTCATCAAACTTCCACGG

Basic information

species Zea mays
transcript GRMZM2G088397_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G088397_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g45390.2 (Oryza sativa), 3'ss of exon 7
gtaatttaatcaatctctgtttcctaactcacgatgtccaaagtgacaatcgtttccagctgtccccttttcactaaacatgttcttaacatctgtt---tcagGCAAGTTCCAGACAGAGATCGGTAAGAGCTGGGCCGCTGAAGTAAACTCGAGGAGAAAGGAGGGATGCGGAAAGCAGGAGCCTTCATCAA-ACTTCCACGG
                  ||    | | |   |  | | |     | | | ||   ||  ||||| || ||   ||||||| |   |||    ||||    |||||||||||||||||||||| || ||||||||||| |||||||| ||  |||||||| |  || |||||||||| ||| ||      |    |  || ||| 
------------------gtaatgtcattgttgcaggctatttaaaaatttgtaaaca--tgtcctctgtt-gttaaacatatctgtaaatcttgttactgcagGCAAGTTCCAGACAGAGATTGGCAAGAGCTGGGCTGCTGAAGTGAATGCGAGGAGAGAACAGAGATGCGGAAAACAGAAGTAGAAGTGGCTAGCTCTACG-
















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|37398538|gb|CF636584.1|CF636584
EST:     AACATGGCAAAGTGCTAGATGAGTTCTTTCTCTCCACTGCCG                         GCAAGTTCCAGACAGAGATCGGTAAGAGCTGGGCCGCTGAAGTAAACTCGA
genomic: AACATGGCAAAGTGCTAGATGAGTTCTTTCTCTCCACTGCCGgtaatttaat ... tctgtttcagGCAAGTTCCAGACAGAGATCGGTAAGAGCTGGGCCGCTGAAGTAAACTCGA
EST: gi|32867634|gb|CF007316.1|CF007316
EST:     ATGGCAAAGTGCTAGATGAGTTCTTTCTCTCCACTGCCG                         GCAAGTTCCAGACAGAGATCGGTAAGAGCTGGGCCGCTGAAGTAAACTCGA
genomic: ATGGCAAAGTGCTAGATGAGTTCTTTCTCTCCACTGCCGgtaatttaat ... tctgtttcagGCAAGTTCCAGACAGAGATCGGTAAGAGCTGGGCCGCTGAAGTAAACTCGA
EST: gi|211216465|gb|FL469136.1|FL469136
EST:     AACATGGCAAAGTGCTAGATGAGTTCTTTCTCTCCACTGCCG                         GCAAGTTCCAGACAGAGATCGGTAAGAGCTGGGCCGCTGAAGTAAACTCGA
genomic: AACATGGCAAAGTGCTAGATGAGTTCTTTCTCTCCACTGCCGgtaatttaat ... tctgtttcagGCAAGTTCCAGACAGAGATCGGTAAGAGCTGGGCCGCTGAAGTAAACTCGA
EST: gi|37383541|gb|CF628790.1|CF628790
EST:     AACATGGCAAAGTGCTAGATGAGTTCTTTCTCTCCACTGCCG                         GCAAGTTCCAGACAGAGATCGGTAAGAGCTGGGCCGCTGAAGTAAACTCGA
genomic: AACATGGCAAAGTGCTAGATGAGTTCTTTCTCTCCACTGCCGgtaatttaat ... tctgtttcagGCAAGTTCCAGACAGAGATCGGTAAGAGCTGGGCCGCTGAAGTAAACTCGA
EST: gi|32808293|gb|CD960527.1|CD960527
EST:     AACATGGCAAAGTGCTAGGTGAGTTCTTTCTCTCCACTGCCG                         GCAAGTTCCAGACAGAGATC
genomic: AACATGGCAAAGTGCTAGATGAGTTCTTTCTCTCCACTGCCGgtaatttaat ... tctgtttcagGCAAGTTCCAGACAGAGATC
EST: gi|32840843|gb|CD980524.1|CD980524
EST:     AACATGGCAAAGTGCTAGATGAGTTCTTTCTCTCCACTGCCG                         GCAAGTTCCAGACAGAGATCGGTAAGAGCTGGGCCGCTGAAGTAAACTCGA
genomic: AACATGGCAAAGTGCTAGATGAGTTCTTTCTCTCCACTGCCGgtaatttaat ... tctgtttcagGCAAGTTCCAGACAGAGATCGGTAAGAGCTGGGCCGCTGAAGTAAACTCGA
EST: gi|194717181|gb|FK934334.1|FK934334
EST:     AACATGGCAAAGTGCTAGATGAGTTCTTTCTCTCCACTGCCG                         GCAAGTTCCAGACAGAGATCGGTAAGAGCTGGGCCGCTGAAGTAAACTCGA
genomic: AACATGGCAAAGTGCTAGATGAGTTCTTTCTCTCCACTGCCGgtaatttaat ... tctgtttcagGCAAGTTCCAGACAGAGATCGGTAAGAGCTGGGCCGCTGAAGTAAACTCGA
EST: gi|32945555|gb|CF050374.1|CF050374
EST:     AACATGGCAAAGTGCTAGATGAGTTCTTTCTCTCCACTGCCG                         GCAAGTTCCAGACAGAGATCGGTAAGAGCTGGGCCGCTGAAGTAAACTCGA
genomic: AACATGGCAAAGTGCTAGATGAGTTCTTTCTCTCCACTGCCGgtaatttaat ... tctgtttcagGCAAGTTCCAGACAGAGATCGGTAAGAGCTGGGCCGCTGAAGTAAACTCGA

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: 46 (upstream exon), 39 (downstream exon)
Score: 29

AACATGGCAAAGTGCTAGATGAGTTCTTTCTCTCCACTGCCGgtaatttaat ... tctgtttcagGCAAGTTCCAGACAGAGATCGGTAAGAGCTGGGCCGCTGAAGTAAACTCGAGGAGAAAGGAGGGATGCGGAAAGCAGGAGCCTTCATCAAACTTCCACGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 28

AACATGGCAAAGTGCTAGATGAGTTCTTTCTCTCCACTGCCGgtaatttaat ... tctgtttcagGCAAGTTCCAGACAGAGATCGGTAAGAGCTGGGCCGCTGAAGTAAACTCGAGGAGAAAGGAGGGATGCGGAAAGCAGGAGCCTTCATCAAACTTCCACGG


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

AACATGGCAAAGTGCTAGATGAGTTCTTTCTCTCCACTGCCGgtaatttaat ... tctgtttcagGCAAGTTCCAGACAGAGATCGGTAAGAGCTGGGCCGCTGAAGTAAACTCGAGGAGAAAGGAGGGATGCGGAAAGCAGGAGCCTTCATCAAACTTCCACGG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 32

AACATGGCAAAGTGCTAGATGAGTTCTTTCTCTCCACTGCCGgtaatttaat ... tctgtttcagGCAAGTTCCAGACAGAGATCGGTAAGAGCTGGGCCGCTGAAGTAAACTCGAGGAGAAAGGAGGGATGCGGAAAGCAGGAGCCTTCATCAAACTTCCACGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatcgtttccagctgtccccttttcactaaacatgttcttaacatctgtttcagGCAAGTTCCAGACAGAGATCGGTAAGAGCTGGGCCGCTGAAGTAAACTCGAGGAGAAAGGAGGGATGCGGAAAGCAGGAGCCTTCATCAAACTTCCACGG
                                     tcttaac  putative branch site (score: 32)
                                             tctgtttc  CT-rich tract
                            taaacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttaatcaatctctgtttcctaactcacgatgtccaaagtgacaatcgtttccagctgtccccttttcactaaacatgttcttaacatctgtttcagGCAAGTTCCAGACAGAGATCGGTAAGAGCTGGGCCGCTGAAGTAAACTCGAGGAGAAAGGAGGGATGCGGAAAGCAGGAGCCTTCATCAAACTTCCACGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG