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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGGACAAGACTATTGGCAAGATAAGAACGTAATTGAAGAGATGCCATGCTGCCGGCAGATGTTCAATATTTTTCATCCTTTTGACCCTGTAGCATACAGgtttgtagttgtcttacacttttttcttatctcatgtttggagagtttgtaaaacatacaataccacaacagaactaaacaatggcaatctgatatgaaa...

Basic information

species Zea mays
transcript GRMZM2G318860_T02
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G318860_T02 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os08g01920.1 (Oryza sativa), 5'ss of exon 15
AAGGACAAGACTATTGGCAAGATAAGAACGTAATTGAAGAGATGCCATGCTGCCGGCAGATGTTCAATATTTTTCATCCTTTTGACCCTGTAGCATACAGgtttgtagttgtcttacacttttt-----tcttatc-tcatgtttggagagtttgtaaaacatacaataccacaacagaactaaacaatggcaatctgatatgaaa--------------------
  || ||||| ||||||||| || ||||| || |||||||||||||||||||||| ||||||||||| ||||||||||| ||||| ||||||||||||||||||| || | || ||||  | ||     | || || |||  | |    |  |  |  |  | ||  | |          | || | | |   || |   |||||                     
GGGGGCAAGATTATTGGCAAAATGAGAACATAGTTGAAGAGATGCCATGCTGCCGTCAGATGTTCAACATTTTTCATCCCTTTGATCCTGTAGCATACAGgtttgcagctttcgtacatatattaatgatgttttcatcacttctctttatgtactggagaagactgtccttatctgttgcaaagcgaggagcatgtctcatgaatctaagttggcttttatacag

upper sequence: GRMZM2G318860_T02 (Zea mays), 5'ss of exon 15
lower sequence: GLYMA09G36920.1 (Glycine max), 5'ss of exon 16
AAGGACAAGACTATTGGCAAGATAAGAACGTAATTGAAGAGATGCCATGCTGCCGGCAGATGTTCAATATTTTTCATCCTTTTGACCCTGTAGCATACAGgtttgtagttgtcttacacttttttcttatctcatgtttggagagtttgtaaaacatacaataccacaacagaactaaacaatggcaatctgatatgaaa---
 ||| ||||| |||||| |  |  | ||  |||  || ||||||||    || |||||||||||||| |||||||| || | ||| || ||||||||||||||||      |  ||  ||    |    | |||  |   ||   |  ||| |  |   || |  | ||   || |     |   || | |||| || |    
GAGGCCAAGAATATTGGGAGCAGGAAAATATAAGAGAGGAGATGCCGGCTTGTCGGCAGATGTTCAACATTTTTCACCCCTATGATCCCGTAGCATACAGgtttgctacaattcta-gctccaatgaagtatcac-tagtgattatgagtagagtaatgaacattataatttaatttcttgacatcagt-tgatttgtatagt
















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|67015052|gb|CO443801.1|CO443801
EST:     TGCCGGCAGATGTTCAATATTTTTCATCCTTTTGACCCTGTAGCATACAG                         AATTGAACCACTTGTATGTGAAGATTATCTAAAGAAGCGTCCTGTAATTGT
genomic: TGCCGGCAGATGTTCAATATTTTTCATCCTTTTGACCCTGTAGCATACAGgtttgtagtt ... ttttatacagAATTGAACCACTTGTATGTGAAGATTATCTAAAGAAGCGTCCTGTAATTGT
EST: gi|78075263|gb|DV503697.1|DV503697
EST:     TGCCGGCAGATGTTCAATATTTTTCATCCTTTTGACCCTGTAGCATACAG                         AATTGAACCACTTGTATGTGAAGATTATCTAAAGAAGCGTCCTGTAATTGT
genomic: TGCCGGCAGATGTTCAATATTTTTCATCCTTTTGACCCTGTAGCATACAGgtttgtagtt ... ttttatacagAATTGAACCACTTGTATGTGAAGATTATCTAAAGAAGCGTCCTGTAATTGT
EST: gi|71767650|gb|DR965587.1|DR965587
EST:     TGCCGGCAGATGTTCAATATTTTTCATCCTTTTGACCCTGTAGCATACAG                         AATTGAACCACTTGTATGTGAAGATTATCTAAAGAAGCGTCCTGTAATTGT
genomic: TGCCGGCAGATGTTCAATATTTTTCATCCTTTTGACCCTGTAGCATACAGgtttgtagtt ... ttttatacagAATTGAACCACTTGTATGTGAAGATTATCTAAAGAAGCGTCCTGTAATTGT
EST: gi|211270821|gb|FL023496.1|FL023496
EST:     TTTGACCCTGTAGCATACAG                         AATTGAACCACTTGTATGTGAAGATTATCTAAAGAAGCGTCCTGTAATTGT
genomic: TTTGACCCTGTAGCATACAGgtttgtagtt ... ttttatacagAATTGAACCACTTGTATGTGAAGATTATCTAAAGAAGCGTCCTGTAATTGT

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: 48 (upstream exon), 47 (downstream exon)
Score: 74

AAGGACAAGACTATTGGCAAGATAAGAACGTAATTGAAGAGATGCCATGCTGCCGGCAGATGTTCAATATTTTTCATCCTTTTGACCCTGTAGCATACAGgtttgtagtt ... ttttatacagAATTGAACCACTTGTATGTGAAGATTATCTAAAGAAGCGTCCTGTAATTGTTCCCTACCATAGAGGCGGAAAGAGGATACATGTTGGAGTGCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 108

AAGGACAAGACTATTGGCAAGATAAGAACGTAATTGAAGAGATGCCATGCTGCCGGCAGATGTTCAATATTTTTCATCCTTTTGACCCTGTAGCATACAGgtttgtagtt ... ttttatacagAATTGAACCACTTGTATGTGAAGATTATCTAAAGAAGCGTCCTGTAATTGTTCCCTACCATAGAGGCGGAAAGAGGATACATGTTGGAGTGCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 162

AAGGACAAGACTATTGGCAAGATAAGAACGTAATTGAAGAGATGCCATGCTGCCGGCAGATGTTCAATATTTTTCATCCTTTTGACCCTGTAGCATACAGgtttgtagtt ... ttttatacagAATTGAACCACTTGTATGTGAAGATTATCTAAAGAAGCGTCCTGTAATTGTTCCCTACCATAGAGGCGGAAAGAGGATACATGTTGGAGTGCAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 68

AAGGACAAGACTATTGGCAAGATAAGAACGTAATTGAAGAGATGCCATGCTGCCGGCAGATGTTCAATATTTTTCATCCTTTTGACCCTGTAGCATACAGgtttgtagtt ... ttttatacagAATTGAACCACTTGTATGTGAAGATTATCTAAAGAAGCGTCCTGTAATTGTTCCCTACCATAGAGGCGGAAAGAGGATACATGTTGGAGTGCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGGACAAGACTATTGGCAAGATAAGAACGTAATTGAAGAGATGCCATGCTGCCGGCAGATGTTCAATATTTTTCATCCTTTTGACCCTGTAGCATACAGgtttgtagttgtcttacacttttttcttatctcatgtttggagagtttgtaaaacatacaataccacaacagaactaaacaatggcaatctgatatgaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaacata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caacagaa