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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacttttccattctccctgagctgtaaaaaagctaaaaacatttactgacgcttaacttttcaagATATGGGAGAACTATGTCGAGGGTGAAAATGCTTCCAATGGATCCACACCTGAATCTAAACAAAAGCAAATTCTCAAG

Basic information

species Zea mays
transcript AC207890.3_FGT002
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC207890.3_FGT002 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os02g32350.1 (Oryza sativa), 3'ss of exon 12
gtaacttttccattctccctgagctgtaaaaaagctaaaaacatttactgacgcttaacttttcaagATATGGGAGAACTATGTCGAGGGTGAAAATGCTTCCAATGGATCCACACCTGAATCTAAACAAAAGCAAATTCTCAAG
|||||   | |  | | | ||| ||  | ||     ||| |   | ||   |  ||   |||||||||| |||||||| ||||| ||||||||| | | ||||||||||||  || ||||||| ||||||||| |||||||||||
gtaaccacttc--tattcttgaactacacaaggagaaaacatgctgac-atccttttctttttcaagATCTGGGAGAATTATGTAGAGGGTGAAGAAGTTTCCAATGGATCTGCATCTGAATCCAAACAAAAGGAAATTCTCAAG
















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|211005286|gb|FL363346.1|FL363346
EST:     CTTATATCCTAACAAGAGCYGAACAGTCTGCGAAGCAACAGAAGATTTAG                         ATATGGGAGAACT
genomic: CTTATATCCTAACAAGAGCTGAACAGTCTGCGAAGCAACAGAAGATTAAGgtaacttttc ... acttttcaagATATGGGAGAACT
EST: gi|9028579|gb|BE238619.1|BE238619
EST:     CTTATATCCTAACAAGAGCTGAACAGTCTGCGAAGCAACAGAAGATTAAG                         ATATGGGAGAACTATGTCGAGGGTGAAAATGCTTCCAATGGATCCACACCT
genomic: CTTATATCCTAACAAGAGCTGAACAGTCTGCGAAGCAACAGAAGATTAAGgtaacttttc ... acttttcaagATATGGGAGAACTATGTCGAGGGTGAAAATGCTTCCAATGGATCCACACCT
EST: gi|31352747|gb|CD437104.1|CD437104
EST:     CTTATATCCTAACAAGAGCTGAACAGTCTGCGAAGCAACAGAAGATTAAG                         ATATGGGAGAACTATGTCGAGGGTGAAAATGCTTCCAATGGATCCACACCT
genomic: CTTATATCCTAACAAGAGCTGAACAGTCTGCGAAGCAACAGAAGATTAAGgtaacttttc ... acttttcaagATATGGGAGAACTATGTCGAGGGTGAAAATGCTTCCAATGGATCCACACCT
EST: gi|213184087|gb|FM191543.1|FM191543
EST:     CTTATATCCTAACAAGAGCTGAACAGTCTGCGAAGCAACAGAAGATTAAG                         ATATGGGAGAACTATGTCGAGGGTGAAAATGCTTCCAATGGATCCACACCT
genomic: CTTATATCCTAACAAGAGCTGAACAGTCTGCGAAGCAACAGAAGATTAAGgtaacttttc ... acttttcaagATATGGGAGAACTATGTCGAGGGTGAAAATGCTTCCAATGGATCCACACCT
EST: gi|32865345|gb|CF005027.1|CF005027
EST:     CTTATATCCTAACAAGAGCTGAACAGTCTGCGAAGCAACAGAAGATTAAG                         ATATGGGAGAACTATGTCGAGGGTGAAAATGCTTCCAATGGATCCACACCT
genomic: CTTATATCCTAACAAGAGCTGAACAGTCTGCGAAGCAACAGAAGATTAAGgtaacttttc ... acttttcaagATATGGGAGAACTATGTCGAGGGTGAAAATGCTTCCAATGGATCCACACCT
EST: gi|213191810|gb|FM182159.1|FM182159
EST:     CTTATATCCTAACAAGAGCTGAACAGTCTGCGAAGCAACAGAAGATTAAG                         ATATGGGAGAACTATGTCGAGGGTGAAAATGCTTCCAATGGATCCACACCT
genomic: CTTATATCCTAACAAGAGCTGAACAGTCTGCGAAGCAACAGAAGATTAAGgtaacttttc ... acttttcaagATATGGGAGAACTATGTCGAGGGTGAAAATGCTTCCAATGGATCCACACCT

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: 168

AGCTGGACTTGCCAAGCTGAGTTCATTTGGCTTGGATAGGACCTCAGATGCTTATATCCTAACAAGAGCTGAACAGTCTGCGAAGCAACAGAAGATTAAGgtaacttttc ... acttttcaagATATGGGAGAACTATGTCGAGGGTGAAAATGCTTCCAATGGATCCACACCTGAATCTAAACAAAAGCAAATTCTCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 199

AGCTGGACTTGCCAAGCTGAGTTCATTTGGCTTGGATAGGACCTCAGATGCTTATATCCTAACAAGAGCTGAACAGTCTGCGAAGCAACAGAAGATTAAGgtaacttttc ... acttttcaagATATGGGAGAACTATGTCGAGGGTGAAAATGCTTCCAATGGATCCACACCTGAATCTAAACAAAAGCAAATTCTCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 270

AGCTGGACTTGCCAAGCTGAGTTCATTTGGCTTGGATAGGACCTCAGATGCTTATATCCTAACAAGAGCTGAACAGTCTGCGAAGCAACAGAAGATTAAGgtaacttttc ... acttttcaagATATGGGAGAACTATGTCGAGGGTGAAAATGCTTCCAATGGATCCACACCTGAATCTAAACAAAAGCAAATTCTCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 273

AGCTGGACTTGCCAAGCTGAGTTCATTTGGCTTGGATAGGACCTCAGATGCTTATATCCTAACAAGAGCTGAACAGTCTGCGAAGCAACAGAAGATTAAGgtaacttttc ... acttttcaagATATGGGAGAACTATGTCGAGGGTGAAAATGCTTCCAATGGATCCACACCTGAATCTAAACAAAAGCAAATTCTCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctccctgagctgtaaaaaagctaaaaacatttactgacgcttaacttttcaagATATGGGAGAACTATGTCGAGGGTGAAAATGCTTCCAATGGATCCACACCTGAATCTAAACAAAAGCAAATTCTCAAG
                                              cttttc  CT-rich tract
              taaaaaagctaaaaac  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacttttccattctccctgagctgtaaaaaagctaaaaacatttactgacgcttaacttttcaagATATGGGAGAACTATGTCGAGGGTGAAAATGCTTCCAATGGATCCACACCTGAATCTAAACAAAAGCAAATTCTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA