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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAGgtcattcttctatctggctccaagtttcctgctattgacagttttaaagatttcgtttgcactcacttcaattgattcaatttctag

Basic information

species Zea mays
transcript GRMZM5G813909_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G813909_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os02g45650.1 (Oryza sativa), 5'ss of exon 12
CACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAGgt-cattcttctatctggctccaagtttcctgctattgacagttttaaagatttcgtttgcactcacttcaattgattcaatttctag
||||| ||||||||  |||| ||||||||||| ||||| ||||||||||||||  | ||||||||||||||||| |||| |||||| |  || |||  || |||||| || | | |||| |  ||||  ||||||| || |    ||||  |||||||||
CACACTATAATACCTGTCCAGCACCTTCTGAGTTTTTGTCTGAACCTTGTCAGTCGGGCATTTGAATTTCAGgttcatttttctatttcccttcaaagtttctgctactg-ctgctttataactttcagttgcacttacct----tgatataatttctag

upper sequence: GRMZM5G813909_T01 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA18G47190.1 (Glycine max), 5'ss of exon 11
CACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAGgtcattcttctatctggctccaa--gtttcctgctattgacagttttaaagatttcgt------ttgcactcacttcaattgattcaat-ttctag------
 | ||  |||| ||  | || ||  |  | |||||| | ||||||||||||||| || |||||||||||||||| | | | || |    ||||     | || |  | |||  |||    | |  |||||      | ||| |   |||  || |  || | |||| |      
-ATACTGTAATCCCACTTCAGCAATTGGTCAGCTTTGGTCTGAACCTTGTCAGCCGATCATTTGAATTTCAGGttactttccttttcttctcctttcatctctttttgttgg-agtgaagatggattcgtggaaaatagcaatgtattctgtttacacattattctggccaaat
















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|32909801|gb|CF014613.1|CF014613
EST:     ACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAG                         GCTGATGCCTTTGCCAAGAACCTTGGATATGCCCCTCAGCTCCGAGCAGCC
genomic: ACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAGgtcattcttc ... caatttctagGCTGATGCCTTTGCCAAGAACCTTGGATATGCCCCTCAGCTCCGAGCAGCC
EST: gi|18165861|gb|BM335700.1|BM335700
EST:     ACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAG                         GCTGATGCCTTTGCCAAGAACCTTGGATATGCCCCTCAGCTCCGAGCAGCC
genomic: ACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAGgtcattcttc ... caatttctagGCTGATGCCTTTGCCAAGAACCTTGGATATGCCCCTCAGCTCCGAGCAGCC
EST: gi|32935179|gb|CF039991.1|CF039991
EST:     CATTTGAATTTCAG                         GCTGATGCCTTTGCCAAGAACCTTGGATATGCCCCTCAGCTCCGAGCAGCC
genomic: CATTTGAATTTCAGgtcattcttc ... caatttctagGCTGATGCCTTTGCCAAGAACCTTGGATATGCCCCTCAGCTCCGAGCAGCC
EST: gi|76293280|gb|DV032848.1|DV032848
EST:     ACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAG                         GCTGATGCCTTTGCCAAGAACCTTGGATATGCCCCTCAGCTCCGAGCAGCC
genomic: ACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAGgtcattcttc ... caatttctagGCTGATGCCTTTGCCAAGAACCTTGGATATGCCCCTCAGCTCCGAGCAGCC
EST: gi|32914225|gb|CF019037.1|CF019037
EST:     ACCTTCTGAGCTTTTGTTTTTACCTTGTCAGCAGAGCGTTTGAATTTCAG                         GCTGATGCCTTTGCCAAGAACCTTGGATATGCCCCTCAGCTCCGAGCAGCC
genomic: ACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAGgtcattcttc ... caatttctagGCTGATGCCTTTGCCAAGAACCTTGGATATGCCCCTCAGCTCCGAGCAGCC
EST: gi|32914224|gb|CF019036.1|CF019036
EST:     ACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAG                         GCTGATGCCTTTGCCAAGAACCTTGGATATGCCCCTCAGCTCCGAGCAGCC
genomic: ACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAGgtcattcttc ... caatttctagGCTGATGCCTTTGCCAAGAACCTTGGATATGCCCCTCAGCTCCGAGCAGCC
EST: gi|71761327|gb|DR959264.1|DR959264
EST:     ACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAG                         GCTGATGCCTTTGCCAAGAACCTTGGATATGCCCCTCAGCTCCGAGCAGCC
genomic: ACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAGgtcattcttc ... caatttctagGCTGATGCCTTTGCCAAGAACCTTGGATATGCCCCTCAGCTCCGAGCAGCC
EST: gi|32806461|gb|CD958695.1|CD958695
EST:     ACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAG                         GCTGATGCCTTTGCCAAGAACCTTGGATATGCCCCTCAGCTCCGAGCAGCC
genomic: ACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAGgtcattcttc ... caatttctagGCTGATGCCTTTGCCAAGAACCTTGGATATGCCCCTCAGCTCCGAGCAGCC
EST: gi|32909800|gb|CF014612.1|CF014612
EST:     ACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAG                         GCTGATGCCTTTGCCAAGAACCTTGGATATGCCCCTCAGCTCCGAGCAGCC
genomic: ACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAGgtcattcttc ... caatttctagGCTGATGCCTTTGCCAAGAACCTTGGATATGCCCCTCAGCTCCGAGCAGCC
EST: gi|32791671|gb|CD943907.1|CD943907
EST:     ACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAG                         GCTGATGCCTTTGCCAAGAACCTTGGATATGCCCCTCAGCTCCGAGCAGCC
genomic: ACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAGgtcattcttc ... caatttctagGCTGATGCCTTTGCCAAGAACCTTGGATATGCCCCTCAGCTCCGAGCAGCC
EST: gi|32806368|gb|CD958602.1|CD958602
EST:     ACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAG                         GCTGATGCCTTTGCCAAGAACCTTGGATATGCCCCTCAGCTCCGAGCAGCC
genomic: ACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAGgtcattcttc ... caatttctagGCTGATGCCTTTGCCAAGAACCTTGGATATGCCCCTCAGCTCCGAGCAGCC
EST: gi|211004566|gb|FL452982.1|FL452982
EST:     GAACCTTGTCAGCAGAGCATTTGAATTTCAG                         GCTGATGCCTTTGCCAAGAACCTTGGATATGCCCCTCAGCTCCGAGCAGCC
genomic: GAACCTTGTCAGCAGAGCATTTGAATTTCAGgtcattcttc ... caatttctagGCTGATGCCTTTGCCAAGAACCTTGGATATGCCCCTCAGCTCCGAGCAGCC
EST: gi|71767567|gb|DR965504.1|DR965504
EST:     ACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAG                         GCTGATGCCTTTGCCAAGAACCTTGGATATGCCCCTCAGCTCCGAGCAGCC
genomic: ACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAGgtcattcttc ... caatttctagGCTGATGCCTTTGCCAAGAACCTTGGATATGCCCCTCAGCTCCGAGCAGCC
EST: gi|78114997|gb|DV533385.1|DV533385
EST:     ACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAG                         GCTGATGCCTTTGCCAAGAACCTTGGATATGCCCCTCAGCTCCGAGCAGCC
genomic: ACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAGgtcattcttc ... caatttctagGCTGATGCCTTTGCCAAGAACCTTGGATATGCCCCTCAGCTCCGAGCAGCC
EST: gi|71758092|gb|DR956029.1|DR956029
EST:     ACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAG                         GCTGATGCCTTTGCCAAGAACCTTGGATATGCCCCTCAGCTCCGAGCAGCC
genomic: ACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAGgtcattcttc ... caatttctagGCTGATGCCTTTGCCAAGAACCTTGGATATGCCCCTCAGCTCCGAGCAGCC
EST: gi|6095666|gb|AW120333.1|AW120333
EST:     ACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAG                         GCTGATGCCTTTGCCAAGAACCTTGGATATGCCCCTCAGCTCCGAGCAGCC
genomic: ACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAGgtcattcttc ... caatttctagGCTGATGCCTTTGCCAAGAACCTTGGATATGCCCCTCAGCTCCGAGCAGCC
EST: gi|50322420|gb|CO517546.1|CO517546
EST:     ACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAG                         GCTGATGCCTTTGCCAAGAACCTTGGATATGCCCCTCAGCTCCGAGCAGCC
genomic: ACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAGgtcattcttc ... caatttctagGCTGATGCCTTTGCCAAGAACCTTGGATATGCCCCTCAGCTCCGAGCAGCC

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: 48 (upstream exon), 49 (downstream exon)
Score: 116

CACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAGgtcattcttc ... caatttctagGCTGATGCCTTTGCCAAGAACCTTGGATATGCCCCTCAGCTCCGAGCAGCCCTTGTTAAACTACAG


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

CACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAGgtcattcttc ... caatttctagGCTGATGCCTTTGCCAAGAACCTTGGATATGCCCCTCAGCTCCGAGCAGCCCTTGTTAAACTACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 110

CACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAGgtcattcttc ... caatttctagGCTGATGCCTTTGCCAAGAACCTTGGATATGCCCCTCAGCTCCGAGCAGCCCTTGTTAAACTACAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 97

CACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAGgtcattcttc ... caatttctagGCTGATGCCTTTGCCAAGAACCTTGGATATGCCCCTCAGCTCCGAGCAGCCCTTGTTAAACTACAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACACCATAATACCCATCCAACACCTTCTGAGCTTTTGCCTGAACCTTGTCAGCAGAGCATTTGAATTTCAGgtcattcttctatctggctccaagtttcctgctattgacagttttaaagatttcgtttgcactcacttcaattgattcaatttctag

- - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA