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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAGgtactttaagttcttcagaagcctttttcatgatcggttcaatttctgtttttcctaagacatgctattgttcgaattccactcagcacattactaacaatacgtttgaccttacgtaccaatatatcatcaccacatctctttttacattgtgaattcacag

Basic information

species Zea mays
transcript GRMZM2G169089_T01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G169089_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os06g36800.1 (Oryza sativa), 5'ss of exon 13
GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAGgtactttaagttcttcagaagcctttttcatgatcggttc-aatttctgtttttcctaagacatgctattgttcgaattccactcagcacattactaacaatacgtttgaccttacgtaccaatatatcatcaccacatctctttttacattgtgaattcacag
||||| ||||| ||||||||||| ||||||||||||| ||| |||||||||     | |||||   |     ||      |||  ||| ||||||| ||   |       ||| | || ||  ||         |||  | | |    ||| || | |  |           || ||||   | | | ||  ||| ||              
GGTGTTGCTATCCTAATCTCGTTCCTGGTTTCAGCTGCATTTCATGAGgta-----aattctttccacatgcttagagctatcatttctaatttcttttcaccactccttatgattttattgaaaaatgctctggcatgtaatt--tcatatgtattattt-----------atttcattgtc-cttatcgatttgcag-------------
















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|18164197|gb|BM334036.1|BM334036
EST:     GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG                         ATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
genomic: GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAGgtactttaag ... gaattcacagATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
EST: gi|17930011|gb|BM266971.1|BM266971
EST:     GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG                         ATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
genomic: GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAGgtactttaag ... gaattcacagATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
EST: gi|18165097|gb|BM334936.1|BM334936
EST:     GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG                         ATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
genomic: GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAGgtactttaag ... gaattcacagATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
EST: gi|32929949|gb|CF034761.1|CF034761
EST:     GGTGTAGCTATTCTAATCTCGGTTCTGGTTTCAGCTGTATTCCATGAG                         ATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
genomic: GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAGgtactttaag ... gaattcacagATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
EST: gi|18172967|gb|BM348355.1|BM348355
EST:     GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG                         ATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
genomic: GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAGgtactttaag ... gaattcacagATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
EST: gi|113703224|gb|EE680728.1|EE680728
EST:     GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG                         ATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
genomic: GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAGgtactttaag ... gaattcacagATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
EST: gi|261490382|gb|GO359873.1|GO359873
EST:     GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG                         ATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
genomic: GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAGgtactttaag ... gaattcacagATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
EST: gi|18168645|gb|BM338485.1|BM338485
EST:     GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG                         ATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
genomic: GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAGgtactttaag ... gaattcacagATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
EST: gi|18171503|gb|BM341343.1|BM341343
EST:     GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG                         ATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
genomic: GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAGgtactttaag ... gaattcacagATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
EST: gi|18162243|gb|BM332082.1|BM332082
EST:     GTTTCAGCTGTATTCCATGAG                         ATATGTATTGCGGTGCCGTGCCACATTTTCAAATTATGGGCATTTTCTGGG
genomic: GTTTCAGCTGTATTCCATGAGgtactttaag ... gaattcacagATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
EST: gi|17929613|gb|BM266573.1|BM266573
EST:     CTCGTTTCTGGTNTCAGCTGTATTCCATGAG                         ATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
genomic: CTCGTTTCTGGTTTCAGCTGTATTCCATGAGgtactttaag ... gaattcacagATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
EST: gi|16921463|gb|BM075161.1|BM075161
EST:     GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG                         ATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
genomic: GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAGgtactttaag ... gaattcacagATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
EST: gi|18166090|gb|BM335929.1|BM335929
EST:     CAGCTGTATTCCATGAG                         ATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
genomic: CAGCTGTATTCCATGAGgtactttaag ... gaattcacagATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
EST: gi|17930787|gb|BM267747.1|BM267747
EST:     GGTGTAGCTAATCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG                         ATATGTATTGCGGTGCCGTGCCACATTTTCAAATTATGGGCATTTTCTGGG
genomic: GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAGgtactttaag ... gaattcacagATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
EST: gi|18166675|gb|BM336514.1|BM336514
EST:     GGTGTAGCTAATCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAG                         ATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG
genomic: GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAGgtactttaag ... gaattcacagATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGG

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: 44 (upstream exon), 45 (downstream exon)
Score: 13

GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAGgtactttaag ... gaattcacagATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGGATCATGTTTCAG


Block sizes: 44 (upstream exon), 44 (downstream exon)
Score: 32

GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAGgtactttaag ... gaattcacagATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGGATCATGTTTCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 50

GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAGgtactttaag ... gaattcacagATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGGATCATGTTTCAG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 35

GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAGgtactttaag ... gaattcacagATATGTATTGCGGTGCCGTGCCACATTTTCAAATTCTGGGCATTTTCTGGGATCATGTTTCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGTAGCTATTCTAATCTCGTTTCTGGTTTCAGCTGTATTCCATGAGgtactttaagttcttcagaagcctttttcatgatcggttcaatttctgtttttcctaagacatgctattgttcgaattccactcagcacattactaacaatacgtttgaccttacgtaccaatatatcatcaccacatctctttttacattgtgaattcacag

- - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - -  CAGCTG