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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGTCAGTCCCATCTTACCTCCAACCAGACCAAGAACCTGAACTCAGCTTACCTGCTGCACCAACTGGCCATGCAGCAGTCCCGGCAAACCAGCAGCAGgtagtgaaactgttgtgagagaatgacgttagatgttgcgtactttttagtgttgcttttgtttatacccaacatcatggtagttatttggtttccttta...

Basic information

species Zea mays
transcript GRMZM2G092468_T01
intron # 6
splice site 5'
intron type U2

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|211056131|gb|FL465294.1|FL465294
EST:     TACCTGCTGCACCAACTGGCCATGCAGCAGTCCCAGCAAACCAGCAGCAG                         GAGGATGAGCTAGGATTGCCTACAGTGCCACAAGCATCCATTCGTACATAA
genomic: TACCTGCTGCACCAACTGGCCATGCAGCAGTCCCGGCAAACCAGCAGCAGgtagtgaaac ... ttggatgcagGAGGATGAGCTAGGATTGCCTACAGTGCCACAAGCATCCATTCGTACATAA
EST: gi|18165330|gb|BM335169.1|BM335169
EST:     TACCTGCTGCACCAACTGGCCATGCAGCAGTCCCAGCAAACCAGCAGCAG                         GAGGATGAGCTAGGATTGCCTACAGTGCCACAAGCATCCATTCGTACATAA
genomic: TACCTGCTGCACCAACTGGCCATGCAGCAGTCCCGGCAAACCAGCAGCAGgtagtgaaac ... ttggatgcagGAGGATGAGCTAGGATTGCCTACAGTGCCACAAGCATCCATTCGTACATAA
EST: gi|32843415|gb|CD983096.1|CD983096
EST:     TACCTGCTGCACCAACTGGCCATGCAGCAGTCCCAGCAAACCAGCAGCAG                         GAGGATGAGCTAGGATTGCCTACAGTGCCACAAGCATCCATTCGT
genomic: TACCTGCTGCACCAACTGGCCATGCAGCAGTCCCGGCAAACCAGCAGCAGgtagtgaaac ... ttggatgcagGAGGATGAGCTAGGATTGCCTACAGTGCCACAAGCATCCATTCGT
EST: gi|211056133|gb|FL465296.1|FL465296
EST:     TACCTGCTGCACCAACTGGCCATGCAGCAGTCCCAGCAAACCAGCAGCAG                         GAGGATGAGCTAGGATTGCCTACAGTGCCACAAGCATCCATTCGTACATAA
genomic: TACCTGCTGCACCAACTGGCCATGCAGCAGTCCCGGCAAACCAGCAGCAGgtagtgaaac ... ttggatgcagGAGGATGAGCTAGGATTGCCTACAGTGCCACAAGCATCCATTCGTACATAA
EST: gi|32850682|gb|CD990363.1|CD990363
EST:     TACCTGCTGCACCAACTGGCCATGCAGCAGTCCCAGCAAACCAGCAGCAG                         GAGGATGAGCTAGGATTGCCTACAGTGCCACAAGCATCCATTCGT
genomic: TACCTGCTGCACCAACTGGCCATGCAGCAGTCCCGGCAAACCAGCAGCAGgtagtgaaac ... ttggatgcagGAGGATGAGCTAGGATTGCCTACAGTGCCACAAGCATCCATTCGT
EST: gi|13557942|gb|BG549298.1|BG549298
EST:     TACCTGCTGCACCAACTGGCCATGCAGCAGTCCCGGCAAACCAGCAGCAG                         GAGGATGAGCTAGGATTGCCTACAGTGCCACAAGCATCCATTCGTACATAA
genomic: TACCTGCTGCACCAACTGGCCATGCAGCAGTCCCGGCAAACCAGCAGCAGgtagtgaaac ... ttggatgcagGAGGATGAGCTAGGATTGCCTACAGTGCCACAAGCATCCATTCGTACATAA
EST: gi|32844108|gb|CD983789.1|CD983789
EST:     TACCTGCTGCACCAACTGGCCATGCAGCAGTCCCAGCAAACCAGCAGCAG                         GAGGATGAGCTAGGATTGCCTACAGTGCCACAAGCATCCATTCGTA
genomic: TACCTGCTGCACCAACTGGCCATGCAGCAGTCCCGGCAAACCAGCAGCAGgtagtgaaac ... ttggatgcagGAGGATGAGCTAGGATTGCCTACAGTGCCACAAGCATCCATTCGTA
EST: gi|32843203|gb|CD982884.1|CD982884
EST:     TACCTGCTGCACCAACTGGCCATGCAGCAGTCCCAGCAAACCAGCAGCAG                         GAGGATGAGCTAGGATTGCCTACAGTACCACAAGCATCCATTCGTAC
genomic: TACCTGCTGCACCAACTGGCCATGCAGCAGTCCCGGCAAACCAGCAGCAGgtagtgaaac ... ttggatgcagGAGGATGAGCTAGGATTGCCTACAGTGCCACAAGCATCCATTCGTAC
EST: gi|87151661|gb|DY396450.1|DY396450
EST:     TACCTGCTGCACCAACTGGCCATGCAGCAGTCCCAGCAAACCAGCAGCAG                         GAGGATGAGCTAGGATTGCC
genomic: TACCTGCTGCACCAACTGGCCATGCAGCAGTCCCGGCAAACCAGCAGCAGgtagtgaaac ... ttggatgcagGAGGATGAGCTAGGATTGCC
EST: gi|116828810|gb|EC861202.1|EC861202
EST:     TACCTGCTGCACCAACTGGCCATGCAGCAGTCCCAGCAAACCAGCAGCAG                         GAGGATGAGCTAGGATTGCCTACAGTGCCACAAGCATCCATTCGTACATAA
genomic: TACCTGCTGCACCAACTGGCCATGCAGCAGTCCCGGCAAACCAGCAGCAGgtagtgaaac ... ttggatgcagGAGGATGAGCTAGGATTGCCTACAGTGCCACAAGCATCCATTCGTACATAA
EST: gi|32844472|gb|CD984153.1|CD984153
EST:     TACCTGCTGCACCAACTGGCCATGCAGCAGTCCCAGCAAACCAGCAGCAG                         GAGGATGAGCTAGGATTGCCTACAGTGCCACAAGCATCCATTCGT
genomic: TACCTGCTGCACCAACTGGCCATGCAGCAGTCCCGGCAAACCAGCAGCAGgtagtgaaac ... ttggatgcagGAGGATGAGCTAGGATTGCCTACAGTGCCACAAGCATCCATTCGT
EST: gi|24934372|gb|CA452590.1|CA452590
EST:     TACCTGCTGCACCAACTGGCCATGCAGCAGTCCCGGCAAACCAGCAGCAG                         GAGGATGAGCTAGGATTGCCTACAGTGCCACAAGCATCCATTCGT
genomic: TACCTGCTGCACCAACTGGCCATGCAGCAGTCCCGGCAAACCAGCAGCAGgtagtgaaac ... ttggatgcagGAGGATGAGCTAGGATTGCCTACAGTGCCACAAGCATCCATTCGT
EST: gi|32830794|gb|CD970472.1|CD970472
EST:     TACCTGCTGCACCAACTGGCCATGCAGCAGTCCCAGCAAACCAGCAGCAG                         GAGGATGAGCTAGGATTGCCTACAGTGCCACAAGCATCCATTCGTA
genomic: TACCTGCTGCACCAACTGGCCATGCAGCAGTCCCGGCAAACCAGCAGCAGgtagtgaaac ... ttggatgcagGAGGATGAGCTAGGATTGCCTACAGTGCCACAAGCATCCATTCGTA
EST: gi|211406647|gb|FL439010.1|FL439010
EST:     TACCTGCTGCACCAACTGGCCATGCAGCAGTCCCGGCAAACCAGCAGCAG                         GAGGATGAGCTAGGATTGCCTACAGTGCCACAAGCATCCATTCGTACATAA
genomic: TACCTGCTGCACCAACTGGCCATGCAGCAGTCCCGGCAAACCAGCAGCAGgtagtgaaac ... ttggatgcagGAGGATGAGCTAGGATTGCCTACAGTGCCACAAGCATCCATTCGTACATAA
EST: gi|211406648|gb|FL439011.1|FL439011
EST:     TACCTGCTGCACCAACTGGCCATGCAGCAGTCCCGGCAAACCAGCAGCAG                         GAGGATGAGCTAGGATTGCCTACAGTGCCACAAGCATCCATTTGTACATAA
genomic: TACCTGCTGCACCAACTGGCCATGCAGCAGTCCCGGCAAACCAGCAGCAGgtagtgaaac ... ttggatgcagGAGGATGAGCTAGGATTGCCTACAGTGCCACAAGCATCCATTCGTACATAA
EST: gi|32843530|gb|CD983211.1|CD983211
EST:     TACCTGCTGCACCAACTGGCCAT-CAGCAGTCCCAGCAAACCAGCAGCAG                         GAGGATGAGCTAGGATTGCCTACAGT-CCACAAGCATCCATTCGTAC
genomic: TACCTGCTGCACCAACTGGCCATGCAGCAGTCCCGGCAAACCAGCAGCAGgtagtgaaac ... ttggatgcagGAGGATGAGCTAGGATTGCCTACAGTGCCACAAGCATCCATTCGTAC
EST: gi|71437048|gb|DR818098.1|DR818098
EST:     TACCTGCTGCACCAACTGGCCATGCAGCAGTCCCGGCAAACCAGCAGCAG                         GAGGATGAGCTAGGATTGCCTACAGTGGCACAAGCATCCATTCGTACATAA
genomic: TACCTGCTGCACCAACTGGCCATGCAGCAGTCCCGGCAAACCAGCAGCAGgtagtgaaac ... ttggatgcagGAGGATGAGCTAGGATTGCCTACAGTGCCACAAGCATCCATTCGTACATAA
EST: gi|18168644|gb|BM338484.1|BM338484
EST:     TACCTGCTGCACCAACTGGCCATGCAGCAGTCCCGGCAAACCAGCAGCAG                         GAGGATGAGCTAGGATTGCCTACAGTGCCACAAGCATCCATTCGTACATAA
genomic: TACCTGCTGCACCAACTGGCCATGCAGCAGTCCCGGCAAACCAGCAGCAGgtagtgaaac ... ttggatgcagGAGGATGAGCTAGGATTGCCTACAGTGCCACAAGCATCCATTCGTACATAA
EST: gi|211019544|gb|FL384186.1|FL384186
EST:     TACCTGCTGCACCAACTGGCCATGCAGCAGTCCCGGCAAACCAGCAGCAG                         GAGGATGAGCTAGGATTGCCTACAGTGCCACAAGCATCCATTCGTACATAA
genomic: TACCTGCTGCACCAACTGGCCATGCAGCAGTCCCGGCAAACCAGCAGCAGgtagtgaaac ... ttggatgcagGAGGATGAGCTAGGATTGCCTACAGTGCCACAAGCATCCATTCGTACATAA
EST: gi|211394823|gb|FL369347.1|FL369347
EST:     ACCTGCTGCACCAAACTGGCCATGCAGCAGTCCCGGCAAAC-AGCAGCAG                         GAGGATGAGCTAGGATTTGCCTACAGTGC-ACAAGCATCCATTC
genomic: ACCTGCTGCACCAA-CTGGCCATGCAGCAGTCCCGGCAAACCAGCAGCAGgtagtgaaac ... ttggatgcagGAGGATGAGCTAGGATT-GCCTACAGTGCCACAAGCATCCATTC
EST: gi|161585881|gb|EY956853.1|EY956853
EST:     CGGCAAACCAGCAGCAG                         GAGGATGAGCTAGGATTGCCTACAGTGCCACAAGCATCCATTCGTACATAA
genomic: CGGCAAACCAGCAGCAGgtagtgaaac ... ttggatgcagGAGGATGAGCTAGGATTGCCTACAGTGCCACAAGCATCCATTCGTACATAA
EST: gi|32831503|gb|CD971181.1|CD971181
EST:     TACCTGCTGCACCAACTGGCCATGCAGCAGTCCCAGCAAACCAGCAGCAG                         GAGGATGAGCTAGGATTGCCTACAGTGCCACAAGCATCCATTCGT
genomic: TACCTGCTGCACCAACTGGCCATGCAGCAGTCCCGGCAAACCAGCAGCAGgtagtgaaac ... ttggatgcagGAGGATGAGCTAGGATTGCCTACAGTGCCACAAGCATCCATTCGT
EST: gi|32843863|gb|CD983544.1|CD983544
EST:     TACCTGCTGCACCAACTGGCCATGCAGCAGTCCCAGCAAACCAGCAGCAG                         GAGGATGAGCTAGGATTGCCTACAGTGCCACAAGCATCCATTCGT
genomic: TACCTGCTGCACCAACTGGCCATGCAGCAGTCCCGGCAAACCAGCAGCAGgtagtgaaac ... ttggatgcagGAGGATGAGCTAGGATTGCCTACAGTGCCACAAGCATCCATTCGT
EST: gi|32843474|gb|CD983155.1|CD983155
EST:     TACCTGCTGCACCAACTGGCCATGCAGCAGTCCCAGCAAACCAGCAGCAG                         GAGGATGAGCTAGGATTGCCTACAGTGCCACAAGCATCCATTCGT
genomic: TACCTGCTGCACCAACTGGCCATGCAGCAGTCCCGGCAAACCAGCAGCAGgtagtgaaac ... ttggatgcagGAGGATGAGCTAGGATTGCCTACAGTGCCACAAGCATCCATTCGT

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), 48 (downstream exon)
Score: 60

AGAGTCAGTCCCATCTTACCTCCAACCAGACCAAGAACCTGAACTCAGCTTACCTGCTGCACCAACTGGCCATGCAGCAGTCCCGGCAAACCAGCAGCAGgtagtgaaac ... ttggatgcagGAGGATGAGCTAGGATTGCCTACAGTGCCACAAGCATCCATTCGTACATAATCAAGCAGAATCACGTTTCTTGCAGTCAACGATATAAAGGAAGTCGTAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 277

AGAGTCAGTCCCATCTTACCTCCAACCAGACCAAGAACCTGAACTCAGCTTACCTGCTGCACCAACTGGCCATGCAGCAGTCCCGGCAAACCAGCAGCAGgtagtgaaac ... ttggatgcagGAGGATGAGCTAGGATTGCCTACAGTGCCACAAGCATCCATTCGTACATAATCAAGCAGAATCACGTTTCTTGCAGTCAACGATATAAAGGAAGTCGTAT


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

AGAGTCAGTCCCATCTTACCTCCAACCAGACCAAGAACCTGAACTCAGCTTACCTGCTGCACCAACTGGCCATGCAGCAGTCCCGGCAAACCAGCAGCAGgtagtgaaac ... ttggatgcagGAGGATGAGCTAGGATTGCCTACAGTGCCACAAGCATCCATTCGTACATAATCAAGCAGAATCACGTTTCTTGCAGTCAACGATATAAAGGAAGTCGTAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 222

AGAGTCAGTCCCATCTTACCTCCAACCAGACCAAGAACCTGAACTCAGCTTACCTGCTGCACCAACTGGCCATGCAGCAGTCCCGGCAAACCAGCAGCAGgtagtgaaac ... ttggatgcagGAGGATGAGCTAGGATTGCCTACAGTGCCACAAGCATCCATTCGTACATAATCAAGCAGAATCACGTTTCTTGCAGTCAACGATATAAAGGAAGTCGTAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGTCAGTCCCATCTTACCTCCAACCAGACCAAGAACCTGAACTCAGCTTACCTGCTGCACCAACTGGCCATGCAGCAGTCCCGGCAAACCAGCAGCAGgtagtgaaactgttgtgagagaatgacgttagatgttgcgtactttttagtgttgcttttgtttatacccaacatcatggtagttatttggtttccttta

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