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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTGTGTGAGGAAGGTGCGGAATAAAGTGGTTGGGCAAATAGGAGATGCTTTCCTGACATATGACCGgtgtgttttttatgctctatattgaagtttttgtcattggctttgattctatatttaccaacatttctttacccagtcttggtgaatcatcaaatttaacctttgttttcctacag

Basic information

species Zea mays
transcript GRMZM2G164835_T01
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164835_T01 (Zea mays), 5'ss of exon 20
lower sequence: LOC_Os06g45980.1 (Oryza sativa), 5'ss of exon 20
GTTTGTGTGAGGAAGGTGCGGAATAAAGTGGTTGGGCAAATAGGAGATGCTTTCCTGACATATGACCGgtgtgttt-tttatgctctatattgaagtttttgtcattggctttgattctatatttaccaacatttct-ttacccagtcttggtgaatcatcaaatttaacctttgttttcctacag----------------------------------------------
|||||||||||||||||||| || |||||| |||| |||||||||||||||||| || ||||||| |||| ||| | ||||||    ||  |    |     |        |   || | | | |||     | | | | ||      |  ||     ||| | || |   ||       || ||                                               
GTTTGTGTGAGGAAGGTGCGCAACAAAGTGATTGGACAAATAGGAGATGCTTTCTTGTCATATGAACGgtatgtctgtttatggagcatgcttttataaccattccatatgtcagttttctgtctacttttgtatgtatcactgtaaataagtactatatctagttcatatttaccaagtcttcaagctgcttgctaactaaatcaccaaatcaatcgttttgcccccacag
















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|60354350|gb|DN221323.1|DN221323
EST:     CGGAATAAAGTGGTTGGGCAAATAGGAGATGCTTTCCTGACATATGACCG                         GGTTACTGGTGAATTCAAGGATGCTGGTAAGGCCACTACAGCACCCAGTGC
genomic: CGGAATAAAGTGGTTGGGCAAATAGGAGATGCTTTCCTGACATATGACCGgtgtgttttt ... tttcctacagGGTTACTGGTGAATTCAAGGATGCTGGTAAGGCCACTACAGCACCCAGTGC
EST: gi|83279351|gb|DV943359.1|DV943359
EST:     AAAGTGGTTGGGCAAATTGGAGATGCTTTCCTGACATATGACCG                         GGTTACTGGTGAATTCAAGGATGCTGGTAAGGCCATTACAGCACCCAGTGC
genomic: AAAGTGGTTGGGCAAATAGGAGATGCTTTCCTGACATATGACCGgtgtgttttt ... tttcctacagGGTTACTGGTGAATTCAAGGATGCTGGTAAGGCCACTACAGCACCCAGTGC
EST: gi|76917406|gb|DV166826.1|DV166826
EST:     CGGAATAAAGTGGTTGGGCAAATAGGAGATGCTTTCCTGACATATGACCG                         GGTTACTGGTGAATTCAAGGATGCTGGTAAGGCCACTACAGCACCCAGTGC
genomic: CGGAATAAAGTGGTTGGGCAAATAGGAGATGCTTTCCTGACATATGACCGgtgtgttttt ... tttcctacagGGTTACTGGTGAATTCAAGGATGCTGGTAAGGCCACTACAGCACCCAGTGC
EST: gi|211007209|gb|FL448362.1|FL448362
EST:     CGGAATAAAGTGGTTGGGCAAATAGGAGATGCTTTCCTGACATATGACCG                         GGTTACTGGTGAATTCAAGGATGCTGGTAAGGCCACTACAGCACCCAGTGC
genomic: CGGAATAAAGTGGTTGGGCAAATAGGAGATGCTTTCCTGACATATGACCGgtgtgttttt ... tttcctacagGGTTACTGGTGAATTCAAGGATGCTGGTAAGGCCACTACAGCACCCAGTGC
EST: gi|148950506|gb|EC896079.2|EC896079
EST:     CGGAATAAAGTGGTTGGGCAAATAGGAGATGCTTTCCTGACATATGACCG                         GGTTACTGGTGAATTCAAGGATGCTGGTAAGGCCACTACAGCACCCAGTGC
genomic: CGGAATAAAGTGGTTGGGCAAATAGGAGATGCTTTCCTGACATATGACCGgtgtgttttt ... tttcctacagGGTTACTGGTGAATTCAAGGATGCTGGTAAGGCCACTACAGCACCCAGTGC
EST: gi|94472504|gb|EB701462.1|EB701462
EST:     CGGAATAAAGTGGTTGGGCAAATAGGAGATGCTTTCCTGACATATGACCG                         GGTTACTGGTGAATTCAAGGATGCTGGTAAGGCCACTACAGCACCCAGTGC
genomic: CGGAATAAAGTGGTTGGGCAAATAGGAGATGCTTTCCTGACATATGACCGgtgtgttttt ... tttcctacagGGTTACTGGTGAATTCAAGGATGCTGGTAAGGCCACTACAGCACCCAGTGC
EST: gi|89760436|gb|DY688849.1|DY688849
EST:     CGGAATAAAGTGGTTGGGCAAATAGGAGATGCTTTCCTGACATATGACCG                         GGTTACTGGTGAATTCAAGGATGCTGGTAAGGCCACTACAGCACCCAGTGC
genomic: CGGAATAAAGTGGTTGGGCAAATAGGAGATGCTTTCCTGACATATGACCGgtgtgttttt ... tttcctacagGGTTACTGGTGAATTCAAGGATGCTGGTAAGGCCACTACAGCACCCAGTGC

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), 48 (downstream exon)
Score: 134

GTTTGTGTGAGGAAGGTGCGGAATAAAGTGGTTGGGCAAATAGGAGATGCTTTCCTGACATATGACCGgtgtgttttt ... tttcctacagGGTTACTGGTGAATTCAAGGATGCTGGTAAGGCCACTACAGCACCCAGTGCAAAAGCGGCAAAACAGTCACGCAAAGAGGCATATAAGATGCCATTTCAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 35

GTTTGTGTGAGGAAGGTGCGGAATAAAGTGGTTGGGCAAATAGGAGATGCTTTCCTGACATATGACCGgtgtgttttt ... tttcctacagGGTTACTGGTGAATTCAAGGATGCTGGTAAGGCCACTACAGCACCCAGTGCAAAAGCGGCAAAACAGTCACGCAAAGAGGCATATAAGATGCCATTTCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 63

GTTTGTGTGAGGAAGGTGCGGAATAAAGTGGTTGGGCAAATAGGAGATGCTTTCCTGACATATGACCGgtgtgttttt ... tttcctacagGGTTACTGGTGAATTCAAGGATGCTGGTAAGGCCACTACAGCACCCAGTGCAAAAGCGGCAAAACAGTCACGCAAAGAGGCATATAAGATGCCATTTCAA


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 19

GTTTGTGTGAGGAAGGTGCGGAATAAAGTGGTTGGGCAAATAGGAGATGCTTTCCTGACATATGACCGgtgtgttttt ... tttcctacagGGTTACTGGTGAATTCAAGGATGCTGGTAAGGCCACTACAGCACCCAGTGCAAAAGCGGCAAAACAGTCACGCAAAGAGGCATATAAGATGCCATTTCAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTGTGTGAGGAAGGTGCGGAATAAAGTGGTTGGGCAAATAGGAGATGCTTTCCTGACATATGACCGgtgtgttttttatgctctatattgaagtttttgtcattggctttgattctatatttaccaacatttctttacccagtcttggtgaatcatcaaatttaacctttgttttcctacag

- - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - -  GAGATG