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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAACAAGATCACCACACAGACTGGAATTGGCACTTCCATTGCTGTTTCTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAGgtatgcctttgtcctcatttattactaggatgttctattgagttccagtttagaatcttttctaaaaaacaggacctctcttctcttaggggttatttga...

Basic information

species Zea mays
transcript GRMZM2G083344_T02
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G083344_T02 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os05g15160.1 (Oryza sativa), 5'ss of exon 11
GCAACAAGATCACCACACAGACTGGAATTGGCACTTCCATTGCTGTTTCTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGA---GAAAAAGgtatgcctttgtcct-catttattactaggatgttctattgagttccagtttagaat--cttttctaaaaaacaggacctctcttctcttaggggttatttga
 |||||||||||||||||| || ||||||||||||| ||||||  |  |||||||||| ||||| || | ||| |||||||||||||| ||   ||||| ||||||  | | | ||  ||  |||   |   |      |||   | ||   ||   |  ||| | |     | |||| |  | | |   |    || |  |  
-CAACAAGATCACCACACAAACAGGAATTGGCACTTGCATTGCCATAGCTGGTGTTGCACTCTATTCTTATATCAAGGCTAAGATTGAAGAAGAGAAAACGgtatgtgtgtatactatatacattctaaatctcaatatttgcaatgcaccctaacgttacttcttttttttagaggaaccat-tgcaactgaaagtaacat--
















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|8665718|gb|BE186534.1|BE186534
EST:     CTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAG                         CAAATAAAGAGTGCATAAGGTGTTGGCTGATGTGGATGCGGTTGGTTTGTC
genomic: CTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAGgtatgccttt ... ctaaatgcagCAAATAAAGAGTGCATAAGGTGTTGGCTGATGTGGATGCGGTTGGTTTGTC
EST: gi|211430251|gb|FL453372.1|FL453372
EST:     CTGGTGTTGCCCTCTACTCATTTATAAAGGNTAAGATTGAGGAGAAAAAG                         CAAATAAAGAGTGCATAAGGTGTTGGCTGATGTGGATSCGGTTGGTTTGTC
genomic: CTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAGgtatgccttt ... ctaaatgcagCAAATAAAGAGTGCATAAGGTGTTGGCTGATGTGGATGCGGTTGGTTTGTC
EST: gi|211525667|gb|FL445646.1|FL445646
EST:     CTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAG                         CAAATAAAGAGTGCATAAGGTGTTGGCTGATGTGGATGCGGTTGGTTTGTC
genomic: CTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAGgtatgccttt ... ctaaatgcagCAAATAAAGAGTGCATAAGGTGTTGGCTGATGTGGATGCGGTTGGTTTGTC
EST: gi|33096626|gb|CF056620.1|CF056620
EST:     GCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAG                         CAAATAAAGAGTGCATAAGGTGTTGGCTGATGTGGATGCGGTTGGTTTGTC
genomic: GCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAGgtatgccttt ... ctaaatgcagCAAATAAAGAGTGCATAAGGTGTTGGCTGATGTGGATGCGGTTGGTTTGTC
EST: gi|9731654|gb|BE510406.1|BE510406
EST:     CTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAG                         C-AATAAAGAGTGCATAAGGTGTTGGCTGATGTGGATGCGGTTGGTTTGTC
genomic: CTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAGgtatgccttt ... ctaaatgcagCAAATAAAGAGTGCATAAGGTGTTGGCTGATGTGGATGCGGTTGGTTTGTC
EST: gi|71760100|gb|DR958037.1|DR958037
EST:     CTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAG                         CAAATAAAGAGTGCATAAGGTGTTGGCTGATGTGGATGCGGTTGGTTTGTC
genomic: CTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAGgtatgccttt ... ctaaatgcagCAAATAAAGAGTGCATAAGGTGTTGGCTGATGTGGATGCGGTTGGTTTGTC
EST: gi|32928246|gb|CF033058.1|CF033058
EST:     CTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAG                         CAAATAAAGAGTGCATAAGGTGTTGGCTGATGTGGATGCGGTTGGTTTGTC
genomic: CTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAGgtatgccttt ... ctaaatgcagCAAATAAAGAGTGCATAAGGTGTTGGCTGATGTGGATGCGGTTGGTTTGTC
EST: gi|5018389|gb|AI714582.1|AI714582
EST:     CTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAG                         CAAATAAAGAGTGCATAAGGTGTTGG
genomic: CTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAGgtatgccttt ... ctaaatgcagCAAATAAAGAGTGCATAAGGTGTTGG
EST: gi|32165070|gb|CD670388.1|CD670388
EST:     CTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAG                         CAAATAAAGAGTGCATAAGGTGTTGGCTGATGTGGATGCGGTTGGTTTGTC
genomic: CTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAGgtatgccttt ... ctaaatgcagCAAATAAAGAGTGCATAAGGTGTTGGCTGATGTGGATGCGGTTGGTTTGTC
EST: gi|37381423|gb|CF627595.1|CF627595
EST:     CTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAG                         CAAATAAAGAGTGCATAAGGTGTTGGCTGATGTGGATGCGGTTGGTTTGTC
genomic: CTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAGgtatgccttt ... ctaaatgcagCAAATAAAGAGTGCATAAGGTGTTGGCTGATGTGGATGCGGTTGGTTTGTC
EST: gi|71328475|gb|DR800887.1|DR800887
EST:     CTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAG                         CAAATAAAGAGTGCATAAGGTGTTGGCTGATGTGGATGCGGTTGGTTTGTC
genomic: CTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAGgtatgccttt ... ctaaatgcagCAAATAAAGAGTGCATAAGGTGTTGGCTGATGTGGATGCGGTTGGTTTGTC
EST: gi|76930049|gb|DV172255.1|DV172255
EST:     CTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAG                         CAAATAAAGAGTGCATAAGGTGTTGGCTGATGTGGATGCGGTTGGTTTGTC
genomic: CTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAGgtatgccttt ... ctaaatgcagCAAATAAAGAGTGCATAAGGTGTTGGCTGATGTGGATGCGGTTGGTTTGTC
EST: gi|71768355|gb|DR966292.1|DR966292
EST:     CTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAG                         CAAATAAAGAGTGCATAAGGTGTTGGCTGATGTGGATGCGGTTGGTTTGTC
genomic: CTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAGgtatgccttt ... ctaaatgcagCAAATAAAGAGTGCATAAGGTGTTGGCTGATGTGGATGCGGTTGGTTTGTC
EST: gi|32935156|gb|CF039968.1|CF039968
EST:     CTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAG                         CAAATAAAGAGTGCATAAGGTGTTGGCTGATGTGGATGCGGTTGGTTTGTC
genomic: CTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAGgtatgccttt ... ctaaatgcagCAAATAAAGAGTGCATAAGGTGTTGGCTGATGTGGATGCGGTTGGTTTGTC
EST: gi|32862760|gb|CF002442.1|CF002442
EST:     CTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAG                         CAAATAAAGAGTGCATAAGGTGTTGGCTGATGTGGATGCGGTTGGTTTGTC
genomic: CTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAGgtatgccttt ... ctaaatgcagCAAATAAAGAGTGCATAAGGTGTTGGCTGATGTGGATGCGGTTGGTTTGTC
EST: gi|211083989|gb|FL462610.1|FL462610
EST:     CTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAG                         CAMATAAAGAGTGCATAAGGTGTTGGCTGATGTGGATGCGGTTGGTTTGTC
genomic: CTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAGgtatgccttt ... ctaaatgcagCAAATAAAGAGTGCATAAGGTGTTGGCTGATGTGGATGCGGTTGGTTTGTC
EST: gi|113703585|gb|EE681089.1|EE681089
EST:     CTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAG                         CAAATAAAGAGTGCATAAGGTGTTGGCTGATGTGGATGCGGTTGGTTTGTC
genomic: CTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAGgtatgccttt ... ctaaatgcagCAAATAAAGAGTGCATAAGGTGTTGGCTGATGTGGATGCGGTTGGTTTGTC
EST: gi|50328059|gb|CO523185.1|CO523185
EST:     CTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAG                         CAAATAAAGAGTGCATAAGGTGTTGGCTGATGTGGATGCGGTTGGTTTGTC
genomic: CTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAGgtatgccttt ... ctaaatgcagCAAATAAAGAGTGCATAAGGTGTTGGCTGATGTGGATGCGGTTGGTTTGTC
EST: gi|9731653|gb|BE510405.1|BE510405
EST:     CTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAG                         C-AATAAAGAGTGCATAAGGTGTTGGCTGATGTGGATGCGGTTGGTTTGTC
genomic: CTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAGgtatgccttt ... ctaaatgcagCAAATAAAGAGTGCATAAGGTGTTGGCTGATGTGGATGCGGTTGGTTTGTC
EST: gi|78104082|gb|DV522500.1|DV522500
EST:     CTGGTGTTGCCCTCTACTCATTTATAAAGGTTAAGATGGAGGAGAAAAAG                         CAAATAAAGAGTGCATAAGGTGTTGGCTGATGTGGATGCGGTTGGTTTGTC
genomic: CTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAGgtatgccttt ... ctaaatgcagCAAATAAAGAGTGCATAAGGTGTTGGCTGATGTGGATGCGGTTGGTTTGTC
EST: gi|32837170|gb|CD976848.1|CD976848
EST:     CTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAG                         CAAATAAAGAGTGCATAAGGTGTTGGCTGATGTGGATGCGGNTGGTTTGTC
genomic: CTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAGgtatgccttt ... ctaaatgcagCAAATAAAGAGTGCATAAGGTGTTGGCTGATGTGGATGCGGTTGGTTTGTC

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: 190

GCAACAAGATCACCACACAGACTGGAATTGGCACTTCCATTGCTGTTTCTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAGgtatgccttt ... ctaaatgcagCAAATAAAGAGTGCATAAGGTGTTGGCTGATGTGGATGCGGTTGGTTTGTCGCTTTGATGGACCTCTATTCTCTCGGTGAACGAACAAACTTGCAAGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 83

GCAACAAGATCACCACACAGACTGGAATTGGCACTTCCATTGCTGTTTCTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAGgtatgccttt ... ctaaatgcagCAAATAAAGAGTGCATAAGGTGTTGGCTGATGTGGATGCGGTTGGTTTGTCGCTTTGATGGACCTCTATTCTCTCGGTGAACGAACAAACTTGCAAGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 60

GCAACAAGATCACCACACAGACTGGAATTGGCACTTCCATTGCTGTTTCTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAGgtatgccttt ... ctaaatgcagCAAATAAAGAGTGCATAAGGTGTTGGCTGATGTGGATGCGGTTGGTTTGTCGCTTTGATGGACCTCTATTCTCTCGGTGAACGAACAAACTTGCAAGATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 39

GCAACAAGATCACCACACAGACTGGAATTGGCACTTCCATTGCTGTTTCTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAGgtatgccttt ... ctaaatgcagCAAATAAAGAGTGCATAAGGTGTTGGCTGATGTGGATGCGGTTGGTTTGTCGCTTTGATGGACCTCTATTCTCTCGGTGAACGAACAAACTTGCAAGATG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAACAAGATCACCACACAGACTGGAATTGGCACTTCCATTGCTGTTTCTGGTGTTGCCCTCTACTCATTTATAAAGGCTAAGATTGAGGAGAAAAAGgtatgcctttgtcctcatttattactaggatgttctattgagttccagtttagaatcttttctaaaaaacaggacctctcttctcttaggggttatttga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA