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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTTTCCTCTTAAAGCAGAGCTGCTGAAACCTCAAGCAGAAATGGAGAGATTTATAACGGATTTGATAAAGAAAgtatgttgtctgttttcagtttttgaccatatgattgtttacatctttcaattctctagttatgttatgtgttgagcttgaacaaatgacattattcag

Basic information

species Zea mays
transcript GRMZM2G059039_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059039_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os02g20930.1 (Oryza sativa), 5'ss of exon 6
GTCTTTCCTCTTAAAGCAGAGCTGCTGAAACCTCAAGCAGAAATGGAGAGATTTATAACGGATTTGATAAAGAAAgtatgttgtc-tgttttcagtttttgaccatatgattgtttac---atctttcaattctctagttatgttatgtgttgagcttgaacaaa---tgacattattcag
||||| ||| ||||||||||||||||||||||||||||||||||||| |||| |||||| ||||||||||||||||||||   || |  |||||||||||| |  | ||||| |||      |  || || | || |  ||  || |||| ||| |||  ||||    ||  || ||||||
GTCTTCCCTGTTAAAGCAGAGCTGCTGAAACCTCAAGCAGAAATGGAAAGATATATAACTGATTTGATAAAGAAAgtatgccttcattatttcagtttttggctgtctgatttttttttcagtgatttaagtttccatgtacattgtgtgatgacctttgacaatggctgttataattcag
















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|211179438|gb|FL364366.1|FL364366
EST:     NAACCTCA-GCAGAAATGGAGAGATTTATAACGGGATT-GATNAAAGAAA                         -GTGTGCAAGATGTAACTGGGTCAGAA
genomic: AAACCTCAAGCAGAAATGGAGAGATTTATAACGG-ATTTGAT-AAAGAAAgtatgttgtc ... cattattcagAGTGTGCAAGATGTAACTGGTTCAGAA
EST: gi|148969036|gb|EE019749.2|EE019749
EST:     TGAAACCTCAAGCAGAAATGGAGAGATTTATAACGGATTTGATAAAGAAA                         AGTGTGCAAGATGTAACTGGTTCAGAATTCGAACTATTCATGGGGTTCTTG
genomic: TGAAACCTCAAGCAGAAATGGAGAGATTTATAACGGATTTGATAAAGAAAgtatgttgtc ... cattattcagAGTGTGCAAGATGTAACTGGTTCAGAATTCGAACTATTCATGGGGTTCTTG
EST: gi|71766575|gb|DR964512.1|DR964512
EST:     TGAAACCTCAAGCAGAAATGGAGAGATTTATAACGGATTTGATAAAGAAA                         AGTGTGCAAGATGTAACTGGTTCAGAATTCGAACTATTCATGGGGTTCTTG
genomic: TGAAACCTCAAGCAGAAATGGAGAGATTTATAACGGATTTGATAAAGAAAgtatgttgtc ... cattattcagAGTGTGCAAGATGTAACTGGTTCAGAATTCGAACTATTCATGGGGTTCTTG
EST: gi|60338080|gb|DN205053.1|DN205053
EST:     TGAAACCTCAAGCAGAAATGGAGAGATTTATAACGGATTTGATAAAGAAA                         AGTGTGCAAGATGTAACTGGTTCAGAATTCGAACTATTCATGGGGTTCTTG
genomic: TGAAACCTCAAGCAGAAATGGAGAGATTTATAACGGATTTGATAAAGAAAgtatgttgtc ... cattattcagAGTGTGCAAGATGTAACTGGTTCAGAATTCGAACTATTCATGGGGTTCTTG
EST: gi|148943964|gb|EC889044.2|EC889044
EST:     TGAAACCTCAAGCAGAAATGGAGAGATTTATAACGGATTTGATAAAGAAA                         AGTGTGCAAGATGTAACTGGTTCAGAATTCGAACTATTCATGGGGTTCTTG
genomic: TGAAACCTCAAGCAGAAATGGAGAGATTTATAACGGATTTGATAAAGAAAgtatgttgtc ... cattattcagAGTGTGCAAGATGTAACTGGTTCAGAATTCGAACTATTCATGGGGTTCTTG
EST: gi|211314239|gb|FL336753.1|FL336753
EST:     TGAAACCTCAAGCAGAAATGGAGAGATTTATAACGGATTTGATAAAGAAA                         AGTGTGCAAGATGTAACTGGTTCAGAATTCGGACTA
genomic: TGAAACCTCAAGCAGAAATGGAGAGATTTATAACGGATTTGATAAAGAAAgtatgttgtc ... cattattcagAGTGTGCAAGATGTAACTGGTTCAGAATTCGAACTA
EST: gi|76014976|gb|DT942146.1|DT942146
EST:     TGAAACCTCAAGCAGAAATGGAGAGATTTATAACGGATTTGATAAAGAAA                         AGTGTGCAAGATGTAACTGGTTCAGAATTCGAACTATTCATGGGGTTCTTG
genomic: TGAAACCTCAAGCAGAAATGGAGAGATTTATAACGGATTTGATAAAGAAAgtatgttgtc ... cattattcagAGTGTGCAAGATGTAACTGGTTCAGAATTCGAACTATTCATGGGGTTCTTG
EST: gi|211306674|gb|FL363564.1|FL363564
EST:     TGAAACCTCAAGCAGAAATGGAGAGATTTATAACGGATTTGATAAAGAAA                         AGTGTGCAAGATGTAACTGGTTCAGAATTCGAACTATTCATGGGGTTCTTG
genomic: TGAAACCTCAAGCAGAAATGGAGAGATTTATAACGGATTTGATAAAGAAAgtatgttgtc ... cattattcagAGTGTGCAAGATGTAACTGGTTCAGAATTCGAACTATTCATGGGGTTCTTG
EST: gi|31356580|gb|CD440937.1|CD440937
EST:     TGAAACCTCAAGCAGAAATGGAGAGATTTATAACGGATTTGATAAAGAAA                         AGTGTGCAAGATGTAACTGGTTCAGAATTCGAACTATTCATGGGGTTCTTG
genomic: TGAAACCTCAAGCAGAAATGGAGAGATTTATAACGGATTTGATAAAGAAAgtatgttgtc ... cattattcagAGTGTGCAAGATGTAACTGGTTCAGAATTCGAACTATTCATGGGGTTCTTG
EST: gi|89761569|gb|DY689527.1|DY689527
EST:     TGAAACCTCAAGCAGAAATGGAGAGATTTATAACGGATTTGATAAAGAAA                         AGTGTGCAAGATGTAACTGGTTCAGAATTCGAACTATTCATGGGGTTCTTG
genomic: TGAAACCTCAAGCAGAAATGGAGAGATTTATAACGGATTTGATAAAGAAAgtatgttgtc ... cattattcagAGTGTGCAAGATGTAACTGGTTCAGAATTCGAACTATTCATGGGGTTCTTG
EST: gi|149105666|gb|EE291222.2|EE291222
EST:     TGAAACCTCAAGCAGAAATGGAGAGATTTATAACGGATTTGATAAAGAAA                         AGTGTGCAAGATGTAACTGGTTCAGAATTCGAACTATTCATGGGGTTCTTG
genomic: TGAAACCTCAAGCAGAAATGGAGAGATTTATAACGGATTTGATAAAGAAAgtatgttgtc ... cattattcagAGTGTGCAAGATGTAACTGGTTCAGAATTCGAACTATTCATGGGGTTCTTG
EST: gi|31358588|gb|CD442945.1|CD442945
EST:     TGAAACCTCAAGCAGAAATGGAGAGATTTATAACGGATTTGATAAAGAAA                         AGTGTGCAAGATGTAACTGGTTCAGAATTCGAACTATTCATGGGGTTCTTG
genomic: TGAAACCTCAAGCAGAAATGGAGAGATTTATAACGGATTTGATAAAGAAAgtatgttgtc ... cattattcagAGTGTGCAAGATGTAACTGGTTCAGAATTCGAACTATTCATGGGGTTCTTG

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: 279

GTCTTTCCTCTTAAAGCAGAGCTGCTGAAACCTCAAGCAGAAATGGAGAGATTTATAACGGATTTGATAAAGAAAgtatgttgtc ... cattattcagAGTGTGCAAGATGTAACTGGTTCAGAATTCGAACTATTCATGGGGTTCTTGCGAAGCTTGAGCATATTTGGGGATTCTGCTCCTAGAGAGTCCTTTCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 88

GTCTTTCCTCTTAAAGCAGAGCTGCTGAAACCTCAAGCAGAAATGGAGAGATTTATAACGGATTTGATAAAGAAAgtatgttgtc ... cattattcagAGTGTGCAAGATGTAACTGGTTCAGAATTCGAACTATTCATGGGGTTCTTGCGAAGCTTGAGCATATTTGGGGATTCTGCTCCTAGAGAGTCCTTTCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 105

GTCTTTCCTCTTAAAGCAGAGCTGCTGAAACCTCAAGCAGAAATGGAGAGATTTATAACGGATTTGATAAAGAAAgtatgttgtc ... cattattcagAGTGTGCAAGATGTAACTGGTTCAGAATTCGAACTATTCATGGGGTTCTTGCGAAGCTTGAGCATATTTGGGGATTCTGCTCCTAGAGAGTCCTTTCAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 114

GTCTTTCCTCTTAAAGCAGAGCTGCTGAAACCTCAAGCAGAAATGGAGAGATTTATAACGGATTTGATAAAGAAAgtatgttgtc ... cattattcagAGTGTGCAAGATGTAACTGGTTCAGAATTCGAACTATTCATGGGGTTCTTGCGAAGCTTGAGCATATTTGGGGATTCTGCTCCTAGAGAGTCCTTTCAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCTTTCCTCTTAAAGCAGAGCTGCTGAAACCTCAAGCAGAAATGGAGAGATTTATAACGGATTTGATAAAGAAAgtatgttgtctgttttcagtttttgaccatatgattgtttacatctttcaattctctagttatgttatgtgttgagcttgaacaaatgacattattcag

- - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA