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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCAGCAACTGAACTTCGTCAGCATGGGTTTTCAGAATCTCCAGGTTCTGGCTTGAGGCAGCATTTTGCAGCTGAAAGGAAATGGGCCCTTGGTCTTCAGgtaattttcttgttaagtacatcttatgatgtgtttcatgaattattccgaattccgattcatttatctgtaattgtctaacag

Basic information

species Zea mays
transcript GRMZM2G077278_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G077278_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os05g45420.3 (Oryza sativa), 5'ss of exon 9
TTCAGCAACTGAACTTCGTCAGCATGGGTTTTCAGAATCTCCAGGTTCTGGCTTGAGGCAGCATTTTGCAGCTGAAAGGAAATGGGCCCTTGGTCTTCAGgt--aattttcttgttaagtacatcttatg-atgtgtttcatgaattattccgaattccgattcatttatctgtaattgtctaacag
 ||||| ||||| | ||| |||||||||  |   |||||||| || | |||||||||||| ||||| |||||||| ||||||||||||||||||||||||||   ||  | ||  ||      ||||||  ||    || ||  |||||     || |  |||||||| |||||| || | ||||||
CTCAGCCACTGATCATCGGCAGCATGGGCATATGGAATCTCCTGGGTTTGGCTTGAGGCATCATTTCGCAGCTGACAGGAAATGGGCCCTTGGTCTTCAGgttttatgctgttactataaggttcttatttattcactttatttattataagttatcctaattcatttgtctgtatttatttaacag

upper sequence: GRMZM2G077278_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA18G49770.1 (Glycine max), 5'ss of exon 10
TTCAGCAACTGAACTTCGTCAGCATGGGTTTTCAGAATCTCCAGGTTCTGGCTTGAGGCAGCATTTTGCAGCTGAAAGGAAATGGGCCCTTGGTCTTCAGgtaattttcttgttaagtacatc--ttatgatgtgtttcatgaattattcc---gaattcc--gattcatttatctg--taattgtctaacag-------
|||||    || |   ||    |  || |     |||| ||||||    || | |||||| || ||  | | ||||||||||||||||||||| |||||||||   |   | | |   |      |  || ||| |   | ||| ||||     ||  |||  | || |||| |     |  |||| ||| ||       
TTCAGTTGTTGGAAACCGCTTTCCAGGCTACATGGAATATCCAGGAGTAGGATCGAGGCAACAGTTCCCTGTTGAAAGGAAATGGGCCCTTGGGCTTCAGgtatgatgaatatcactcatggtaatcttgctgtttgagaggaaatatttgttagatgtccttgtttaatttgttccatttgttgtataaaagtatgggc

upper sequence: GRMZM2G077278_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA08G26180.1 (Glycine max), 5'ss of exon 9
TTCAGCAACTGAACTTCGTCAGCATGGGTTTTCAGAATCTCCAGGTTCTGGCTTGAGGCAGCATTTTGCAGCTGAAAGGAAATGGGCCCTTGGTCTTCAGgtaattttcttgttaagtacatcttatgatgtgtttcatgaattattccgaattccgattcatttatctgta--attgtctaacag---------------------
|||||    || |   |||   |  || |  |  || | ||| ||    || | |||||| || ||  | | ||||||||||||||||||||| |||||||||       ||   | ||   || |||||    ||  ||  | |     |||     || |||| |||||   ||    | |  |                     
TTCAGTTGTTGGAAACCGTTTTCCAGGCTACTTGGAGTATCCGGGAGTAGGATCGAGGCAACAGTTCCCTGTTGAAAGGAAATGGGCCCTTGGGCTTCAGgta-------tgacgaatatcactcatgataatcttgctgtttgaaaggaaatatttgttaatttgtctgttgtatgaaattatgggcttttgaatttgttgtttat

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|31351266|gb|CD435623.1|CD435623
EST:     GCTTGAGGCAGCATTTTGCAGCTGAAAGGAAATGGGCCCTTGGTCTTCAG                         TCTCGAGCACATCCACGAGAAATAATAAGTGAAGTGCTTAAAGCTCTGCAA
genomic: GCTTGAGGCAGCATTTTGCAGCTGAAAGGAAATGGGCCCTTGGTCTTCAGgtaattttct ... tgtctaacagTCTCGAGCACATCCACGAGAAATAATAAGTGAAGTGCTTAAAGCTCTGCAA
EST: gi|76933414|gb|DV173440.1|DV173440
EST:     GCTTGAGGCAGCATTTTGCAGCTGAAAGGAAATGGGCCCTTGGTCTTCAG                         TCTCGAGCACATCCACGAGAAATAATAAGTGAAGTGCTTAAAGCTCTGCAA
genomic: GCTTGAGGCAGCATTTTGCAGCTGAAAGGAAATGGGCCCTTGGTCTTCAGgtaattttct ... tgtctaacagTCTCGAGCACATCCACGAGAAATAATAAGTGAAGTGCTTAAAGCTCTGCAA
EST: gi|60344416|gb|DN211389.1|DN211389
EST:     GCTTGAGGCAGCATTTTGCAGCTGAAAGGAAATGGGCCCTTGGTCTTCAG                         TCTCGAGCACATCCACGAGAAATAATAAGTGAAGTGCTTAAAGCTCTGCAA
genomic: GCTTGAGGCAGCATTTTGCAGCTGAAAGGAAATGGGCCCTTGGTCTTCAGgtaattttct ... tgtctaacagTCTCGAGCACATCCACGAGAAATAATAAGTGAAGTGCTTAAAGCTCTGCAA
EST: gi|6307878|gb|AW163845.1|AW163845
EST:     GCTTGAGGCAGCATTTTGCAGCTGAAAGGAAATGGGCCCTTGGTCTTCAG                         TCTCGAGCACATCCACGAGAAATAATAAGTGAAGTGCTTAAAGCTCTGCAA
genomic: GCTTGAGGCAGCATTTTGCAGCTGAAAGGAAATGGGCCCTTGGTCTTCAGgtaattttct ... tgtctaacagTCTCGAGCACATCCACGAGAAATAATAAGTGAAGTGCTTAAAGCTCTGCAA
EST: gi|91878197|gb|EB408154.1|EB408154
EST:     GAGGCAGCATTTTGCAGCTGAAAGGAAATGGGCCCTGGGTCTTCAT                         TCTCGAGCACATCCACGAGAAATAATAAGTGAAGTGCTTAAAGCTCTGCAA
genomic: GAGGCAGCATTTTGCAGCTGAAAGGAAATGGGCCCTTGGTCTTCAGgtaattttct ... tgtctaacagTCTCGAGCACATCCACGAGAAATAATAAGTGAAGTGCTTAAAGCTCTGCAA
EST: gi|211090137|gb|FL283399.1|FL283399
EST:     GCTTGAGGCAGCATTTTGCAGCTGAAAGGAAATGGGCCCTTGGTCTTCAG                         TCTCGAGCACATCCACGAGAAATAATAAGTGAAGTGCTTAAAGCTCTGCAA
genomic: GCTTGAGGCAGCATTTTGCAGCTGAAAGGAAATGGGCCCTTGGTCTTCAGgtaattttct ... tgtctaacagTCTCGAGCACATCCACGAGAAATAATAAGTGAAGTGCTTAAAGCTCTGCAA
EST: gi|76934830|gb|DV174040.1|DV174040
EST:     GCTTGAGGCAGCATTTTGCAGCTGAAAGGAAATGGGCCCTTGGTCTTCAG                         TCTCGAGCACATCCACGAGAAATAATAAGTGAAGTGCTTAAAGCTCTGCAA
genomic: GCTTGAGGCAGCATTTTGCAGCTGAAAGGAAATGGGCCCTTGGTCTTCAGgtaattttct ... tgtctaacagTCTCGAGCACATCCACGAGAAATAATAAGTGAAGTGCTTAAAGCTCTGCAA
EST: gi|76933421|gb|DV173441.1|DV173441
EST:     GCTTGAGGCAGCATTTTGCAGCTGAAAGGAAATGGGCCCTTGGTCTTCAG                         TCTCGAGCACATCCACGAGAAATAATAAGTGAAGTGCTTAAAGCTCTGCAA
genomic: GCTTGAGGCAGCATTTTGCAGCTGAAAGGAAATGGGCCCTTGGTCTTCAGgtaattttct ... tgtctaacagTCTCGAGCACATCCACGAGAAATAATAAGTGAAGTGCTTAAAGCTCTGCAA
EST: gi|15312951|gb|BI478479.1|BI478479
EST:     GCTTGAGGCAGCATTTTGCAGCTGAAAGGAAATGGGCCCTTGGTCTTCAG                         TCTCGAGCACATCCACGAGAAATAATAAGTGAAGTGCTTAAAGCTCTGCAA
genomic: GCTTGAGGCAGCATTTTGCAGCTGAAAGGAAATGGGCCCTTGGTCTTCAGgtaattttct ... tgtctaacagTCTCGAGCACATCCACGAGAAATAATAAGTGAAGTGCTTAAAGCTCTGCAA
EST: gi|67028292|gb|CO457041.1|CO457041
EST:     GCTTGAGGCAGCATTTTGCAGCTGAAAGGAAATGGGCCCTTGGTCTTCAG                         TCTCGAGCACATCCACGAGAAATAATAAGTGAAGTGCTTAAAGCTCTGCAA
genomic: GCTTGAGGCAGCATTTTGCAGCTGAAAGGAAATGGGCCCTTGGTCTTCAGgtaattttct ... tgtctaacagTCTCGAGCACATCCACGAGAAATAATAAGTGAAGTGCTTAAAGCTCTGCAA
EST: gi|211429825|gb|FL327475.1|FL327475
EST:     GCTTGAGGCAGCATTTTGCAGCTGAAAGGAAATGGGCCCTTGGTCTTCAG                         TCTCGAGCACATCCCCGAGAAATAATAAGTGAAGTGCTTAAAGCTCTGCAA
genomic: GCTTGAGGCAGCATTTTGCAGCTGAAAGGAAATGGGCCCTTGGTCTTCAGgtaattttct ... tgtctaacagTCTCGAGCACATCCACGAGAAATAATAAGTGAAGTGCTTAAAGCTCTGCAA
EST: gi|76012619|gb|DT939789.1|DT939789
EST:     GCTTGAGGCAGCATTTTGCAGCTGAAAGGAAATGGGCCCTTGGTCTTCAG                         TCTCGAGCACATCCACGAGAAATAATAAGTGAAGTGCTTAAAGCTCTGCAA
genomic: GCTTGAGGCAGCATTTTGCAGCTGAAAGGAAATGGGCCCTTGGTCTTCAGgtaattttct ... tgtctaacagTCTCGAGCACATCCACGAGAAATAATAAGTGAAGTGCTTAAAGCTCTGCAA
EST: gi|32835075|gb|CD974753.1|CD974753
EST:     GCTTGAGGCAGCATTTTGCAGCTGAAAGGAAATGGGCCCTTGGTCTTCAG                         TCTCGAGCACATCCACGAGAAATAATAAGTGAAGTGCTTAAAGCTCTGCAA
genomic: GCTTGAGGCAGCATTTTGCAGCTGAAAGGAAATGGGCCCTTGGTCTTCAGgtaattttct ... tgtctaacagTCTCGAGCACATCCACGAGAAATAATAAGTGAAGTGCTTAAAGCTCTGCAA
EST: gi|78108755|gb|DV527172.1|DV527172
EST:     GCTTGAGGCAGCATTTTGCAGCTGAAAGGAAATGGGCCCTTGGTCTTCAG                         TCTCGAGCACATCCACGAGAAATAATAAGTGAAGTGCTTAAAGCTCTGCAA
genomic: GCTTGAGGCAGCATTTTGCAGCTGAAAGGAAATGGGCCCTTGGTCTTCAGgtaattttct ... tgtctaacagTCTCGAGCACATCCACGAGAAATAATAAGTGAAGTGCTTAAAGCTCTGCAA
EST: gi|6223810|gb|AW154941.1|AW154941
EST:     GCTTGAGGCAGCATTTTGCAGCTGAAAGGAAATGGGCCCTTGGTCTTCAG                         TCTCGAGCACATCCACGAGAAATAATAAGTGAAGTGCTTAAAGCTCTGCAA
genomic: GCTTGAGGCAGCATTTTGCAGCTGAAAGGAAATGGGCCCTTGGTCTTCAGgtaattttct ... tgtctaacagTCTCGAGCACATCCACGAGAAATAATAAGTGAAGTGCTTAAAGCTCTGCAA
EST: gi|60395300|gb|DN228169.1|DN228169
EST:     GCTTGAGGCAGCATTTTGCAGCTGAAAGGAAATGGGCCCTTGGTCTTCAG                         TCTCGAGCACATCCACGAGAAATAATAAGTGAAGTGCTTAAAGCTCTGCAA
genomic: GCTTGAGGCAGCATTTTGCAGCTGAAAGGAAATGGGCCCTTGGTCTTCAGgtaattttct ... tgtctaacagTCTCGAGCACATCCACGAGAAATAATAAGTGAAGTGCTTAAAGCTCTGCAA

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), 48 (downstream exon)
Score: 213

TTCAGCAACTGAACTTCGTCAGCATGGGTTTTCAGAATCTCCAGGTTCTGGCTTGAGGCAGCATTTTGCAGCTGAAAGGAAATGGGCCCTTGGTCTTCAGgtaattttct ... tgtctaacagTCTCGAGCACATCCACGAGAAATAATAAGTGAAGTGCTTAAAGCTCTGCAAGAACTGAATGTTTACTGGAAAAAGATTGGACACTACAACATGAAATGCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 141

TTCAGCAACTGAACTTCGTCAGCATGGGTTTTCAGAATCTCCAGGTTCTGGCTTGAGGCAGCATTTTGCAGCTGAAAGGAAATGGGCCCTTGGTCTTCAGgtaattttct ... tgtctaacagTCTCGAGCACATCCACGAGAAATAATAAGTGAAGTGCTTAAAGCTCTGCAAGAACTGAATGTTTACTGGAAAAAGATTGGACACTACAACATGAAATGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 270

TTCAGCAACTGAACTTCGTCAGCATGGGTTTTCAGAATCTCCAGGTTCTGGCTTGAGGCAGCATTTTGCAGCTGAAAGGAAATGGGCCCTTGGTCTTCAGgtaattttct ... tgtctaacagTCTCGAGCACATCCACGAGAAATAATAAGTGAAGTGCTTAAAGCTCTGCAAGAACTGAATGTTTACTGGAAAAAGATTGGACACTACAACATGAAATGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 115

TTCAGCAACTGAACTTCGTCAGCATGGGTTTTCAGAATCTCCAGGTTCTGGCTTGAGGCAGCATTTTGCAGCTGAAAGGAAATGGGCCCTTGGTCTTCAGgtaattttct ... tgtctaacagTCTCGAGCACATCCACGAGAAATAATAAGTGAAGTGCTTAAAGCTCTGCAAGAACTGAATGTTTACTGGAAAAAGATTGGACACTACAACATGAAATGCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCAGCAACTGAACTTCGTCAGCATGGGTTTTCAGAATCTCCAGGTTCTGGCTTGAGGCAGCATTTTGCAGCTGAAAGGAAATGGGCCCTTGGTCTTCAGgtaattttcttgttaagtacatcttatgatgtgtttcatgaattattccgaattccgattcatttatctgtaattgtctaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA