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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTCCCAGTCCCAGTTGTCCAGATAGATCAGGACTCAGACCGTGATGCGACCATTGTGCAGCTAAGTTTTGGAGATCGCTTGGGGGCACTACTTGACACGgtatatattttacatgcgccactgatgctgtctttacattgttgctgctcaaaattgtgatgtttaagtttttgtcatatctgccaattatttttcctggtattcactgtttgcag

Basic information

species Zea mays
transcript GRMZM5G825902_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G825902_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os12g05650.1 (Oryza sativa), 5'ss of exon 3
AGTCCCAGTCCCAGTTGTCCAGATAGATCAGGACTCAGACCGTGATGCGACCATTGTGCAGCTAAGTTTTGGAGATCGCTTGGGGGCACTACTTGACACGgtatatattttacatgcgccactgatgctgtctttacattgttgctgctcaaaat---tgtgatgttta--agtttttgtcatatctgccaattatttt-tcctggtattcactgtttgcag
| | |||   |||||||| | ||||||||| ||||||||||||||||| ||||| |||||||| ||||||||||| ||  ||||||||||||||||||||||||| ||||| | |  || |  | |||| | |||    || |  || | || ||   | |  |  |||  | |||||||  |||| |  ||||||||| ||||||||||||||||||||||
AATTCCACAGCCAGTTGTTCTGATAGATCAAGACTCAGACCGTGATGCAACCATAGTGCAGCTGAGTTTTGGAGACCGTCTGGGGGCACTACTTGACACGgtata-attttcc-tatgctatgggtgctctatttgatctgatcttgtttaagatatatttcgtaattagtaatttttgttgtatcagtaaattattttgtcctggtattcactgtttgcag
















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|6020732|gb|AW065540.1|AW065540
EST:     CCATTGTGCAGCTAAGTTTTGGAGATCGCTTGGGGGCACTACTTGACACG                         ATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA
genomic: CCATTGTGCAGCTAAGTTTTGGAGATCGCTTGGGGGCACTACTTGACACGgtatatattt ... ctgtttgcagATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA
EST: gi|31351917|gb|CD436274.1|CD436274
EST:     CCATTGTGCAGCTAAGTTTTGGAGATCGTTTGGGGGCGCTACTTGACACG                         ATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA
genomic: CCATTGTGCAGCTAAGTTTTGGAGATCGCTTGGGGGCACTACTTGACACGgtatatattt ... ctgtttgcagATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA
EST: gi|213192723|gb|FM191866.1|FM191866
EST:     CCATTGTGCAGCTAAGTTTTGGAGATCGTTTGGGGGCGCTACTTGACACG                         ATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA
genomic: CCATTGTGCAGCTAAGTTTTGGAGATCGCTTGGGGGCACTACTTGACACGgtatatattt ... ctgtttgcagATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA
EST: gi|26558566|gb|CA830801.1|CA830801
EST:     CCATTGTGCAGCTAAGTTTTGGAGATCGTTTGGGGGCGCTACTTGACACG                         ATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA
genomic: CCATTGTGCAGCTAAGTTTTGGAGATCGCTTGGGGGCACTACTTGACACGgtatatattt ... ctgtttgcagATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA
EST: gi|67035504|gb|CO464037.1|CO464037
EST:     CCATTGTGCAGCTAAGTTTTGGAGATCGTTTGGGGGCGCTACTTGACACG                         ATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA
genomic: CCATTGTGCAGCTAAGTTTTGGAGATCGCTTGGGGGCACTACTTGACACGgtatatattt ... ctgtttgcagATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA
EST: gi|5325248|gb|AI783439.1|AI783439
EST:     CCATTGTGCAGCTAAGTTTTGGAGATCGCTTGGGGGCACTACTTGACACG                         ATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA
genomic: CCATTGTGCAGCTAAGTTTTGGAGATCGCTTGGGGGCACTACTTGACACGgtatatattt ... ctgtttgcagATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA
EST: gi|31355619|gb|CD439976.1|CD439976
EST:     CCATTGTGCAGCTAAGTTTTGGAGATCGTTTGGGGGCGCTACTTGACACG                         ATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA
genomic: CCATTGTGCAGCTAAGTTTTGGAGATCGCTTGGGGGCACTACTTGACACGgtatatattt ... ctgtttgcagATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA
EST: gi|211033888|gb|FL356298.1|FL356298
EST:     CCATTGTGCAGCTAAGTTTTGGAGATCGTTTGGGGGCACTACTTGACACG                         ATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA
genomic: CCATTGTGCAGCTAAGTTTTGGAGATCGCTTGGGGGCACTACTTGACACGgtatatattt ... ctgtttgcagATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA
EST: gi|8368912|gb|BE051857.1|BE051857
EST:     CCATTGTGCAGCTAAGTTTTGGAGATCGTTTGGGGGCGCTACTTGACACG                         ATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA
genomic: CCATTGTGCAGCTAAGTTTTGGAGATCGCTTGGGGGCACTACTTGACACGgtatatattt ... ctgtttgcagATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA
EST: gi|211133671|gb|FL369481.1|FL369481
EST:     CCATTGTGCAGCTAAGTTTTGGAGATCGTTTGGGGGCGCTACTTGACACG                         ATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA
genomic: CCATTGTGCAGCTAAGTTTTGGAGATCGCTTGGGGGCACTACTTGACACGgtatatattt ... ctgtttgcagATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA
EST: gi|149100918|gb|EE187014.2|EE187014
EST:     CCATTGTGCAGCTAAGTTTTGGAGATCGTTTGGGGGCGCTACTTGACACG                         ATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA
genomic: CCATTGTGCAGCTAAGTTTTGGAGATCGCTTGGGGGCACTACTTGACACGgtatatattt ... ctgtttgcagATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA
EST: gi|87157787|gb|DY402576.1|DY402576
EST:     CCATTGTGCAGCTAAGTTTTGGAGATCGTTTGGGGGCGCTACTTGACACG                         ATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA
genomic: CCATTGTGCAGCTAAGTTTTGGAGATCGCTTGGGGGCACTACTTGACACGgtatatattt ... ctgtttgcagATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA
EST: gi|8516597|gb|BE123322.1|BE123322
EST:     CCATTGTGCAGCTAAGTTTTGGAGATCGTTTGGGGGCGCTACTTGACACG                         ATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA
genomic: CCATTGTGCAGCTAAGTTTTGGAGATCGCTTGGGGGCACTACTTGACACGgtatatattt ... ctgtttgcagATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA
EST: gi|5847192|gb|AW000271.1|AW000271
EST:     CCATTGTGCAGCTAAGTTTTGGAGATCGTTTGGGGGCGCTACTTGACACG                         ATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA
genomic: CCATTGTGCAGCTAAGTTTTGGAGATCGCTTGGGGGCACTACTTGACACGgtatatattt ... ctgtttgcagATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA
EST: gi|5325091|gb|AI783282.1|AI783282
EST:     CCATTGTGCAGCTAAGTTTTGGAGATCGTTTGGGGGCGCTACTTGACACG                         ATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA
genomic: CCATTGTGCAGCTAAGTTTTGGAGATCGCTTGGGGGCACTACTTGACACGgtatatattt ... ctgtttgcagATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA
EST: gi|22545865|gb|BU098239.1|BU098239
EST:     CCATTGTGCAGCTAAGTTTTGGAGATCGTTTGGGGGCGCTACTTGACACG                         ATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA
genomic: CCATTGTGCAGCTAAGTTTTGGAGATCGCTTGGGGGCACTACTTGACACGgtatatattt ... ctgtttgcagATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA
EST: gi|149074678|gb|EE163096.2|EE163096
EST:     CCATTGTGCAGCTAAGTTTTGGAGATCGTTTGGGGGCGCTACTTGACACG                         ATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA
genomic: CCATTGTGCAGCTAAGTTTTGGAGATCGCTTGGGGGCACTACTTGACACGgtatatattt ... ctgtttgcagATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA
EST: gi|71447368|gb|DR828418.1|DR828418
EST:     CCATTGTGCAGCTAAGTTTTGGAGATCGTTTGGGGGCGCTACTTGACACG                         ATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA
genomic: CCATTGTGCAGCTAAGTTTTGGAGATCGCTTGGGGGCACTACTTGACACGgtatatattt ... ctgtttgcagATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA
EST: gi|6526657|gb|AW215948.1|AW215948
EST:     CCATTGTGCAGCTAAGTTTTGGAGATCGTTTGGGGGCGCTACTTGACACG                         ATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA
genomic: CCATTGTGCAGCTAAGTTTTGGAGATCGCTTGGGGGCACTACTTGACACGgtatatattt ... ctgtttgcagATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA
EST: gi|148999647|gb|EE036634.2|EE036634
EST:     CCATTGTGCAGCTAAGTTTTGGAGATCGTTTGGGGGCGCTACTTGACACG                         ATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA
genomic: CCATTGTGCAGCTAAGTTTTGGAGATCGCTTGGGGGCACTACTTGACACGgtatatattt ... ctgtttgcagATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA
EST: gi|31363719|gb|CD448076.1|CD448076
EST:     CCATTGTGCAGCTAAGTTTTGGAGATCGTTTGGGGGCGCTACTTGACACG                         ATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA
genomic: CCATTGTGCAGCTAAGTTTTGGAGATCGCTTGGGGGCACTACTTGACACGgtatatattt ... ctgtttgcagATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA
EST: gi|5871295|gb|AW017766.1|AW017766
EST:     GGGGGCACTACTTGACACG                         ATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA
genomic: GGGGGCACTACTTGACACGgtatatattt ... ctgtttgcagATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA
EST: gi|5860476|gb|AW011698.1|AW011698
EST:     CCATTGTGCAGCTAAGTTTTGGAGATCGCTTGGGGGCACTACTTGACACG                         ATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA
genomic: CCATTGTGCAGCTAAGTTTTGGAGATCGCTTGGGGGCACTACTTGACACGgtatatattt ... ctgtttgcagATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA
EST: gi|211502811|gb|FL321803.1|FL321803
EST:     CCATTGTGCAGCTAAGTTTTGGAGATCGTTTGGGGGCACTACTTGACACG                         ATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA
genomic: CCATTGTGCAGCTAAGTTTTGGAGATCGCTTGGGGGCACTACTTGACACGgtatatattt ... ctgtttgcagATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACA

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: 49 (upstream exon), 49 (downstream exon)
Score: 201

AGTCCCAGTCCCAGTTGTCCAGATAGATCAGGACTCAGACCGTGATGCGACCATTGTGCAGCTAAGTTTTGGAGATCGCTTGGGGGCACTACTTGACACGgtatatattt ... ctgtttgcagATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 308

AGTCCCAGTCCCAGTTGTCCAGATAGATCAGGACTCAGACCGTGATGCGACCATTGTGCAGCTAAGTTTTGGAGATCGCTTGGGGGCACTACTTGACACGgtatatattt ... ctgtttgcagATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 519

AGTCCCAGTCCCAGTTGTCCAGATAGATCAGGACTCAGACCGTGATGCGACCATTGTGCAGCTAAGTTTTGGAGATCGCTTGGGGGCACTACTTGACACGgtatatattt ... ctgtttgcagATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 210

AGTCCCAGTCCCAGTTGTCCAGATAGATCAGGACTCAGACCGTGATGCGACCATTGTGCAGCTAAGTTTTGGAGATCGCTTGGGGGCACTACTTGACACGgtatatattt ... ctgtttgcagATGAAAGCACTCAAGGACCTTGGCCTTGATGTCACAAAAGGAAGTGTGACAACTGACTCAGCTGTCACACAAACAAAGTTCCACATCATGCGATT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTCCCAGTCCCAGTTGTCCAGATAGATCAGGACTCAGACCGTGATGCGACCATTGTGCAGCTAAGTTTTGGAGATCGCTTGGGGGCACTACTTGACACGgtatatattttacatgcgccactgatgctgtctttacattgttgctgctcaaaattgtgatgtttaagtttttgtcatatctgccaattatttttcctggtattcactgtttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC