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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGCGAGAGAAAGCAAGGCTAAAAGAACTCCAGAAGATGAAGAAACATAAAATCCAAGAAATATTAGATACTCAAAATGCCGCCATTGATGCTGACATGgtatatactgtctttaaatggatcctcatgtacaattgcatggtttgcacaggattaaccatttaggcttaatatatgttgtcttgatcttatatttctcaacag

Basic information

species Zea mays
transcript AC235535.1_FGT001
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC235535.1_FGT001 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 5'ss of exon 2
GAAGCGAGAGAAAGCAAGGCTAAAAGAACTCCAGAAGATGAAGAAACATAAAATCCAAGAAATATTAGATACTCAAAATGCCGCCATTGATGCTGACATGgtatatactgtctttaaatggatcctcatgtacaattgcatggtttgcacaggatta-----accatttaggcttaatatatgttgtcttgatctta-tatttctcaacag-----------------------------------
||| || |||||||| ||||| || ||| | |||||  ||||||| || ||||| ||||||||||| ||||| || ||||| ||  ||||||||||||||||      ||    || | | ||||     ||||| ||| |  |  ||||| |||       | ||| |   | |||| ||| |   | || | | | ||  | |    |                                    
GAAACGTGAGAAAGCCAGGCTCAAGGAAATGCAGAAATTGAAGAAGCAGAAAATACAAGAAATATTGGATACACAGAATGCTGCAGTTGATGCTGACATGgt-----ttgctcctataagaatccgtcaatacaaatgcctt-tcagcacatgatatggcatatcatgtgcacataatttatttcaacctgctttgaatacctttgtgtatgttgccttttgccctgattaatatttttttaacag

upper sequence: AC235535.1_FGT001 (Zea mays), 5'ss of exon 2
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 5'ss of exon 2
GAAGCGAGAGAAAGCAAGGCTAAAAGAACTCCAGAAGATGAAGAAACATAAAATCCAAGAAATATTAGATACTCAAAATGCCGCCATTGATGCTGACATGgtat-------atactgtctttaaatggatcctcatgtacaattgcatggtttgcacaggattaaccatttaggcttaatatatgttgtc-ttgat-cttatatttctcaacag
 ||||| || || || ||||| |||||| | ||||||||||||||||| || ||||| |||||||| ||| |||||||||| || |||||||| || ||||| |       ||||   ||| |||       |    ||||  |   ||| ||        | |  |  ||  |  | ||     |  || || || | ||| ||  ||  |||
CAAGCGTGAAAAGGCCAGGCTTAAAGAAATGCAGAAGATGAAGAAACAGAAGATCCAGGAAATATTGGATGCTCAAAATGCTGCTATTGATGCCGATATGgtgtgtttgtcatacatacttgaaagactcattttcctacatgttgttggctttggtgtattcagtctattgagtgtgatggccataatcattaatgcctattttaatcggcag
















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|211342489|gb|FL449460.1|FL449460
EST:     AAATCCAAGAAATATTAGATACTCAAAATGCCGCCATTGATGCTGACATG                         AACAATAAAGGGAAGGGACGGTTGAAGTACCTTCTTCAGCAGACAGAAATA
genomic: AAATCCAAGAAATATTAGATACTCAAAATGCCGCCATTGATGCTGACATGgtatatactg ... ttctcaacagAACAATAAAGGGAAGGGACGGTTGAAGTACCTTCTTCAGCAGACAGAAATA
EST: gi|149075149|gb|EE163643.2|EE163643
EST:     AAATCCAAGAAATATTAGATACTCAAAATGCCGCCATTGATGCTGACATG                         AACAATAAAGGGAAGGGACGGTTGAAGTACCTTCTTCAGCAGACAGAAATA
genomic: AAATCCAAGAAATATTAGATACTCAAAATGCCGCCATTGATGCTGACATGgtatatactg ... ttctcaacagAACAATAAAGGGAAGGGACGGTTGAAGTACCTTCTTCAGCAGACAGAAATA
EST: gi|211342491|gb|FL449462.1|FL449462
EST:     AAATCCAAGAAATATTAGATACTCAAAATGCCGCCATTGATGCTGACATG                         AACAATAAAGGGAAGGGACGGTTGAAGTACCTTCTTCAGCAGACAGAAATA
genomic: AAATCCAAGAAATATTAGATACTCAAAATGCCGCCATTGATGCTGACATGgtatatactg ... ttctcaacagAACAATAAAGGGAAGGGACGGTTGAAGTACCTTCTTCAGCAGACAGAAATA
EST: gi|22491353|gb|BU051276.1|BU051276
EST:     AAATCCAAGAAATATTAGATACTCAAAATGCCGCCATTGATGCTGACATG                         AACAATAAAGGGAAGGGACGGTTGAAGTACCTTCTTCAGCAGACAGAAATA
genomic: AAATCCAAGAAATATTAGATACTCAAAATGCCGCCATTGATGCTGACATGgtatatactg ... ttctcaacagAACAATAAAGGGAAGGGACGGTTGAAGTACCTTCTTCAGCAGACAGAAATA
EST: gi|19351041|gb|BM895573.1|BM895573
EST:     AAATCCAAGAAATATTAGATACTCAAAATGCCGCCATTGATGCTGACATG                         AACAATAAAGGGAAGGGACGGTTGAAGTACCTTCTTCAGCAGACAGAAATA
genomic: AAATCCAAGAAATATTAGATACTCAAAATGCCGCCATTGATGCTGACATGgtatatactg ... ttctcaacagAACAATAAAGGGAAGGGACGGTTGAAGTACCTTCTTCAGCAGACAGAAATA
EST: gi|18648847|gb|BM497666.1|BM497666
EST:     AAATCCAAGAAATATTAGATACTCAAAATGCCGCCATTGATGCTGACATG                         AACAATAAAGGGAAGGGACGGTTGAAGTACCTTCTTCAGCAGACAGAAATA
genomic: AAATCCAAGAAATATTAGATACTCAAAATGCCGCCATTGATGCTGACATGgtatatactg ... ttctcaacagAACAATAAAGGGAAGGGACGGTTGAAGTACCTTCTTCAGCAGACAGAAATA
EST: gi|18649308|gb|BM498127.1|BM498127
EST:     AAATCCAAGAAATATTAGATACTCAAAATGCCGCCATTGATGCTGACATG                         AACAATAAAGGGAAGGGACGGGTGAAGTACCTTCTTCAGCAGACAGAAATA
genomic: AAATCCAAGAAATATTAGATACTCAAAATGCCGCCATTGATGCTGACATGgtatatactg ... ttctcaacagAACAATAAAGGGAAGGGACGGTTGAAGTACCTTCTTCAGCAGACAGAAATA
EST: gi|32164936|gb|CD670254.1|CD670254
EST:     AAATCCAAGAAATATTAGATACTCAAAATGCCGCCATTGATGCTGACATG                         AACAATAAAGGGAAGGGACGGTTGAAGTACCTTCTTCAGCAGACAGAAATA
genomic: AAATCCAAGAAATATTAGATACTCAAAATGCCGCCATTGATGCTGACATGgtatatactg ... ttctcaacagAACAATAAAGGGAAGGGACGGTTGAAGTACCTTCTTCAGCAGACAGAAATA
EST: gi|87153564|gb|DY398353.1|DY398353
EST:     AAATCCAAGAAATATTAGATACTCAAAATGCCGCCATTGATGCTGACATG                         AACAATAAAGGGAAGGGACGGTTGAAGTACCTTCTTCAGCAGACAGAAATA
genomic: AAATCCAAGAAATATTAGATACTCAAAATGCCGCCATTGATGCTGACATGgtatatactg ... ttctcaacagAACAATAAAGGGAAGGGACGGTTGAAGTACCTTCTTCAGCAGACAGAAATA

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: 47 (upstream exon), 49 (downstream exon)
Score: 348

GAAGCGAGAGAAAGCAAGGCTAAAAGAACTCCAGAAGATGAAGAAACATAAAATCCAAGAAATATTAGATACTCAAAATGCCGCCATTGATGCTGACATGgtatatactg ... ttctcaacagAACAATAAAGGGAAGGGACGGTTGAAGTACCTTCTTCAGCAGACAGAAATATTTGCTCACTTTGCAAAAGGAAGTCAGTCCAACGAGAAAAAGCCACGCG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 173

GAAGCGAGAGAAAGCAAGGCTAAAAGAACTCCAGAAGATGAAGAAACATAAAATCCAAGAAATATTAGATACTCAAAATGCCGCCATTGATGCTGACATGgtatatactg ... ttctcaacagAACAATAAAGGGAAGGGACGGTTGAAGTACCTTCTTCAGCAGACAGAAATATTTGCTCACTTTGCAAAAGGAAGTCAGTCCAACGAGAAAAAGCCACGCG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 137

GAAGCGAGAGAAAGCAAGGCTAAAAGAACTCCAGAAGATGAAGAAACATAAAATCCAAGAAATATTAGATACTCAAAATGCCGCCATTGATGCTGACATGgtatatactg ... ttctcaacagAACAATAAAGGGAAGGGACGGTTGAAGTACCTTCTTCAGCAGACAGAAATATTTGCTCACTTTGCAAAAGGAAGTCAGTCCAACGAGAAAAAGCCACGCG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 198

GAAGCGAGAGAAAGCAAGGCTAAAAGAACTCCAGAAGATGAAGAAACATAAAATCCAAGAAATATTAGATACTCAAAATGCCGCCATTGATGCTGACATGgtatatactg ... ttctcaacagAACAATAAAGGGAAGGGACGGTTGAAGTACCTTCTTCAGCAGACAGAAATATTTGCTCACTTTGCAAAAGGAAGTCAGTCCAACGAGAAAAAGCCACGCG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGCGAGAGAAAGCAAGGCTAAAAGAACTCCAGAAGATGAAGAAACATAAAATCCAAGAAATATTAGATACTCAAAATGCCGCCATTGATGCTGACATGgtatatactgtctttaaatggatcctcatgtacaattgcatggtttgcacaggattaaccatttaggcttaatatatgttgtcttgatcttatatttctcaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG