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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTGgtaaaaattacaactaaaactcagcttgtaaattgttttatatgttcattctatcaccctttttgttgataccaagcggttatatcaagcgccataaactgcaccagtactgattcaatagtatctttcatttgtctgtatatag

Basic information

species Zea mays
transcript GRMZM2G074386_T06
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074386_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os09g32800.2 (Oryza sativa), 5'ss of exon 3
GGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTGgtaaaaattacaactaaaactcagcttgta-aattgttttatatgttcattctatcaccctttttgttgataccaagcggttatatcaagcgccataaactgcaccagtactgattcaatagtatctttcatttgtctgtatatag
 || |||||||| | |||||||||||| ||||| || |||||||| |||||||||||||||||| | |||||||||||||||||||       | | | ||||   |   |  ||  |  || ||  ||| ||     ||| ||| |  | ||| |||      | || |   |   |  | ||                                            
AGCGGACAAATGCGCACTAGCATCTTCCGGCTTCCAAGGTGATATCAAAGCTCTGCACAAGAACTTGGCTGCCAGAGAATTGgtaagttcccgagccataacttctccactgtaacagggttgtactttcgtttag--accttttgttgttatatcaatacaagaaatgata-gttgtttattgt-------------------------------------------
















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|211293899|gb|FL244459.1|FL244459
EST:     TTCAGGGTGATATTAAGGCTCTGCACAAGAACCTAGCTGCCAGAGAATTG                         CTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
genomic: TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTGgtaaaaatta ... ctgtatatagCTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
EST: gi|211423761|gb|FL057574.1|FL057574
EST:     TTCAGGGTGATATTAAGGCTCTGCACAAGAACCTAGCTGCCAGAGAATTG                         CTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
genomic: TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTGgtaaaaatta ... ctgtatatagCTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
EST: gi|211304832|gb|FL260605.1|FL260605
EST:     TTCAGGGTGATATTAAGGCTCTGCACAAGAACCTAGCTGCCAGAGAATTG                         CTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
genomic: TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTGgtaaaaatta ... ctgtatatagCTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
EST: gi|211293903|gb|FL244463.1|FL244463
EST:     TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTG                         CTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCT-CCATGGCACAG
genomic: TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTGgtaaaaatta ... ctgtatatagCTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
EST: gi|211151431|gb|FL260598.1|FL260598
EST:     TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTG                         CTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
genomic: TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTGgtaaaaatta ... ctgtatatagCTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
EST: gi|211304831|gb|FL260604.1|FL260604
EST:     TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTG                         CTATACCAACACCAGCATAAC
genomic: TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTGgtaaaaatta ... ctgtatatagCTATACCAACACCAGCATAAC
EST: gi|211399896|gb|FL244532.1|FL244532
EST:     TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTG                         CTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
genomic: TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTGgtaaaaatta ... ctgtatatagCTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
EST: gi|211300322|gb|FL244507.1|FL244507
EST:     TTCAGGGTGATATTAAGGCTCTGCACAAGAACCTAGCTGCCAGAGAATTG                         CTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
genomic: TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTGgtaaaaatta ... ctgtatatagCTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
EST: gi|211149988|gb|FL260580.1|FL260580
EST:     TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTG                         CTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
genomic: TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTGgtaaaaatta ... ctgtatatagCTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
EST: gi|211151434|gb|FL260601.1|FL260601
EST:     TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCYGCCAGAGAATYG                         CYATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
genomic: TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTGgtaaaaatta ... ctgtatatagCTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
EST: gi|211302466|gb|FL244528.1|FL244528
EST:     TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTG                         CTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
genomic: TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTGgtaaaaatta ... ctgtatatagCTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
EST: gi|211151420|gb|FL260587.1|FL260587
EST:     TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTG                         CTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
genomic: TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTGgtaaaaatta ... ctgtatatagCTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
EST: gi|211151421|gb|FL260588.1|FL260588
EST:     TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTG                         CTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
genomic: TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTGgtaaaaatta ... ctgtatatagCTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
EST: gi|211289625|gb|FL244438.1|FL244438
EST:     TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTG                         CTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
genomic: TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTGgtaaaaatta ... ctgtatatagCTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
EST: gi|211293906|gb|FL244466.1|FL244466
EST:     TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTG                         CTATACCGACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
genomic: TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTGgtaaaaatta ... ctgtatatagCTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
EST: gi|211302460|gb|FL244522.1|FL244522
EST:     TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTG                         CTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
genomic: TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTGgtaaaaatta ... ctgtatatagCTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
EST: gi|211151427|gb|FL260594.1|FL260594
EST:     TTCAGGGTGATATTAAGGCTCTGCACAAGAACCTAGCTGCCAGAGAATTG                         CTATACCNACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
genomic: TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTGgtaaaaatta ... ctgtatatagCTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
EST: gi|211149990|gb|FL260582.1|FL260582
EST:     TTCAGGGTGATATTAAGGCTCTGCACAAGAACCTAGCTGCCAGAGAATTG                         CTATACCAACACCCGCCTAACAAAAGGATGAGCTGCCCTTGC-ATGGCACA
genomic: TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTGgtaaaaatta ... ctgtatatagCTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCT-GCCATGGCACA
EST: gi|211149983|gb|FL260575.1|FL260575
EST:     TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTG                         CTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
genomic: TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTGgtaaaaatta ... ctgtatatagCTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
EST: gi|211151422|gb|FL260589.1|FL260589
EST:     TCAGGGTGATATTAAAGGNTCTGCACAAGAACCTAGCTGCCAGAGAATTG                         CTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
genomic: TCAGGGTGATATTAAAGC-TCTGCACAAGAACCTAGCTGCCAGAGAATTGgtaaaaatta ... ctgtatatagCTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
EST: gi|211300327|gb|FL244512.1|FL244512
EST:     TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTG                         CTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
genomic: TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTGgtaaaaatta ... ctgtatatagCTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
EST: gi|19436693|gb|BM953103.1|BM953103
EST:     ATTAAGGCTCTGCACAAGAACCTAGCTGCCAGAGAATTG                         CTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
genomic: ATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTGgtaaaaatta ... ctgtatatagCTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
EST: gi|116819555|gb|EC862690.1|EC862690
EST:     TTCAGGGTGATATTAAGGCTCTGCACAAGAACCTAGCTGCCAGAGAATTG                         CTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
genomic: TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTGgtaaaaatta ... ctgtatatagCTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
EST: gi|211151428|gb|FL260595.1|FL260595
EST:     TTCAGGGTGATATTAAGGCTCTGCACAAGAACCTAGCTGCCAGAGAATTG                         CTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
genomic: TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTGgtaaaaatta ... ctgtatatagCTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
EST: gi|32910464|gb|CF015276.1|CF015276
EST:     TTCAGGGTGATATTAAGGCTCTGCACAAGAACCTAGCTGCCAGAGAATTG                         CTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
genomic: TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTGgtaaaaatta ... ctgtatatagCTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
EST: gi|211149994|gb|FL260586.1|FL260586
EST:     TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTG                         CTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG
genomic: TTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTGgtaaaaatta ... ctgtatatagCTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAG

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: 213

GGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTGgtaaaaatta ... ctgtatatagCTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAGCTCCTCTCCAATACCCTGTACTACAAGCGCTTCTTCCCATATTACGCCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 209

GGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTGgtaaaaatta ... ctgtatatagCTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAGCTCCTCTCCAATACCCTGTACTACAAGCGCTTCTTCCCATATTACGCCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 238

GGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTGgtaaaaatta ... ctgtatatagCTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAGCTCCTCTCCAATACCCTGTACTACAAGCGCTTCTTCCCATATTACGCCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 158

GGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTGgtaaaaatta ... ctgtatatagCTATACCAACACCAGCATAACAAAAGGATGAGCTGCCCTGCCATGGCACAGCTCCTCTCCAATACCCTGTACTACAAGCGCTTCTTCCCATATTACGCCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCTGACAAATGTGTACTAGCATCTTCTGGCTTTCAGGGTGATATTAAAGCTCTGCACAAGAACCTAGCTGCCAGAGAATTGgtaaaaattacaactaaaactcagcttgtaaattgttttatatgttcattctatcaccctttttgttgataccaagcggttatatcaagcgccataaactgcaccagtactgattcaatagtatctttcatttgtctgtatatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC