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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTGGTCTTCTAGTGGTCTGCTTGAGAAAATGAAGAAACTTTCTGAAAGAAGGAAGCTTGAAGATTTAACAATTGGTCCAGTCCTTACAgtaagtcaggggcggagccagcccttttttgggggtcagctgaccccggtaaatttctgaatatctaatagaaaatggtgttaataacaatagttctata...

Basic information

species Zea mays
transcript GRMZM2G090087_T03
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G090087_T03 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os05g45960.1 (Oryza sativa), 5'ss of exon 11
AATTGGTCTTCTAGTGGTCTGCTTGAGAAAATGAAGAAACTTTCTGAAAGAAGGAAGCTTGAAGATTTAACAATTGGTCCAGTCCTTACAgtaagtcaggggc----ggagccagcccttttttgggggtca-gctgaccccggtaaatttctgaatatctaataga--aaatggtgtt-aataacaatagttctata
|||||||| |||||||| || ||||| |||||||| |  |||||||||||||||||||||||||| || || ||||| ||||||||||| || ||| |    |        | |||| ||||   |   | |  ||       || | | | |||| || |  | |   ||| | |||| || ||||| |        
AATTGGTCGTCTAGTGGGCTTCTTGATAAAATGAAAAGTCTTTCTGAAAGAAGGAAGCTTGAAGACTTGACCATTGGCCCAGTCCTTACTgtgagtgatcaactctaatcactagccattttcatgtattaatactattttttgttagtatttgaacattttgtggttcaaaagttgttgaaaaacaaaa--------
















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|211226663|gb|FL216925.1|FL216925
EST:     TGTCTGAAAGAAGGAAGCTTGAAGATTTAACAATTGGTCCAGTCCTTACA                         GTTACTACAGAAGCCATGATAGAGCACATGAAC
genomic: T-TCTGAAAGAAGGAAGCTTGAAGATTTAACAATTGGTCCAGTCCTTACAgtaagtcagg ... tctgatccagGTTACTACAGAAGCCATGATAGAGCACATGAAC
EST: gi|67019711|gb|CO448460.1|CO448460
EST:     TTTCTGAAAGAAGGAAGCTTGAAGATTTAACAATTGGTCCAGTCCTTACA                         GTTACTACAGAAGCCATGATAGAGCACATGAACAACCTTCTCAAAATAAGA
genomic: TTTCTGAAAGAAGGAAGCTTGAAGATTTAACAATTGGTCCAGTCCTTACAgtaagtcagg ... tctgatccagGTTACTACAGAAGCCATGATAGAGCACATGAACAACCTTCTCAAAATAAGA
EST: gi|211120257|gb|FL200678.1|FL200678
EST:     AAGATTTAACAATTGGTCCAGTCCTTACA                         GTTACTACAGAAGCCATGATAGAGCACATGAACAACCTTCTCAAAATAAGA
genomic: AAGATTTAACAATTGGTCCAGTCCTTACAgtaagtcagg ... tctgatccagGTTACTACAGAAGCCATGATAGAGCACATGAACAACCTTCTCAAAATAAGA
EST: gi|67020094|gb|CO448843.1|CO448843
EST:     TTTCTGAAAGAA-GAAGCTTGAAGATTTAACAATTGGTCCAGTCCTTACA                         GTTACTACAGAAGCCATGATAGAGCACATGAACAACCTTCTCAAAATAAGA
genomic: TTTCTGAAAGAAGGAAGCTTGAAGATTTAACAATTGGTCCAGTCCTTACAgtaagtcagg ... tctgatccagGTTACTACAGAAGCCATGATAGAGCACATGAACAACCTTCTCAAAATAAGA
EST: gi|33101148|gb|CF061108.1|CF061108
EST:     TTTCTGAAAGAAGGAAGCTTGAAGATTTAACAATTGGTCCAGTCCTTACA                         GTTACTACAGAAGCCATGATAGAGCACATGAACAACCTTCTCAAAATAAG
genomic: TTTCTGAAAGAAGGAAGCTTGAAGATTTAACAATTGGTCCAGTCCTTACAgtaagtcagg ... tctgatccagGTTACTACAGAAGCCATGATAGAGCACATGAACAACCTTCTCAAAATAAG
EST: gi|18659076|gb|BM500142.1|BM500142
EST:     TGAAGATTTAACAATTGGTCCAGTCCTTACA                         GTTACTACAGAAGCCATGATAGAGCACATGAACAACCTTCTCAAAATAAGA
genomic: TGAAGATTTAACAATTGGTCCAGTCCTTACAgtaagtcagg ... tctgatccagGTTACTACAGAAGCCATGATAGAGCACATGAACAACCTTCTCAAAATAAGA
EST: gi|67026280|gb|CO455029.1|CO455029
EST:     TTCTGAAAGAAG-AAGCTTGNNAGATT-A-CAATTGGTCCAGTCCTTACA                         GTTACTACAGAAGCCATGATAGAGCACATGA
genomic: TTCTGAAAGAAGGAAGCTTGA-AGATTTAACAATTGGTCCAGTCCTTACAgtaagtcagg ... tctgatccagGTTACTACAGAAGCCATGATAGAGCACATGA
EST: gi|67024223|gb|CO452972.1|CO452972
EST:     TTTCTGAAAGAAGGAAGCTTGAAGATTTAACAATTGGTCCAGTCCTTACA                         GTTACTACAGAAGCCATGATAGAGCACATGAACAACCTTCTCAAAATAAGA
genomic: TTTCTGAAAGAAGGAAGCTTGAAGATTTAACAATTGGTCCAGTCCTTACAgtaagtcagg ... tctgatccagGTTACTACAGAAGCCATGATAGAGCACATGAACAACCTTCTCAAAATAAGA
EST: gi|24773212|gb|CA408466.1|CA408466
EST:     TTTCTGAAAGAAGGAAGCTTGAAGATTTAACAATTGGTCCAGTCCTTACA                         GTTACTACAGAAGCCATGATAGAGCACATGAACAACCTTCTCAAAATAAGA
genomic: TTTCTGAAAGAAGGAAGCTTGAAGATTTAACAATTGGTCCAGTCCTTACAgtaagtcagg ... tctgatccagGTTACTACAGAAGCCATGATAGAGCACATGAACAACCTTCTCAAAATAAGA
EST: gi|67023454|gb|CO452203.1|CO452203
EST:     TTTCTGAAAGAAGGAAGCTTGAAGATTTAACAATTGGTCCAGTCCTTACA                         GGTACTACAGAAGCCATGATAGAGCACATGAACAACCTTCTCAAAATAAGA
genomic: TTTCTGAAAGAAGGAAGCTTGAAGATTTAACAATTGGTCCAGTCCTTACAgtaagtcagg ... tctgatccagGTTACTACAGAAGCCATGATAGAGCACATGAACAACCTTCTCAAAATAAGA
EST: gi|32846970|gb|CD986651.1|CD986651
EST:     TTTCTGAAAGAAGGAAGCTTGAAGATTTAACAATTGGTCCAGTCCTTACA                         GTTACTACAGAAGCCATGATAGAGCACATGAACAACCTTCTAAAAATACGA
genomic: TTTCTGAAAGAAGGAAGCTTGAAGATTTAACAATTGGTCCAGTCCTTACAgtaagtcagg ... tctgatccagGTTACTACAGAAGCCATGATAGAGCACATGAACAACCTTCTCAAAATAAGA
EST: gi|33102441|gb|CF062401.1|CF062401
EST:     ATTTAACAATTGGTCCAGTCCTTACA                         GTTACTACAGAAGCCATGATAGAGCACATGAACAACCTTCTCAAAATAAGA
genomic: ATTTAACAATTGGTCCAGTCCTTACAgtaagtcagg ... tctgatccagGTTACTACAGAAGCCATGATAGAGCACATGAACAACCTTCTCAAAATAAGA
EST: gi|211120258|gb|FL200679.1|FL200679
EST:     TTTCTGAAAGAAGGAAGCTTGAAGATTTAACAATTGGTCCAGTCCTTACA                         GTTACTACAGAAGCCATGATAGAGCACATGAACAACCTTCTCAAAATAAGA
genomic: TTTCTGAAAGAAGGAAGCTTGAAGATTTAACAATTGGTCCAGTCCTTACAgtaagtcagg ... tctgatccagGTTACTACAGAAGCCATGATAGAGCACATGAACAACCTTCTCAAAATAAGA
EST: gi|32847832|gb|CD987513.1|CD987513
EST:     TTTCTGAAAGAAGGAAGCTTGAAGATTTAACAATTGGTCCAGTCCTTACA                         GTTACTACAGAAGCCATGATAGAGCACATGAACAACCTTCTAAAAATACGA
genomic: TTTCTGAAAGAAGGAAGCTTGAAGATTTAACAATTGGTCCAGTCCTTACAgtaagtcagg ... tctgatccagGTTACTACAGAAGCCATGATAGAGCACATGAACAACCTTCTCAAAATAAGA
EST: gi|211120256|gb|FL200677.1|FL200677
EST:     AAGATTTAACAATTGGTCCAGTCCTTACA                         GTTACTACAGAAGCCATGATAGAGCACATGAACAACCCTTCTCAAAATAAG
genomic: AAGATTTAACAATTGGTCCAGTCCTTACAgtaagtcagg ... tctgatccagGTTACTACAGAAGCCATGATAGAGCACATGAACAA-CCTTCTCAAAATAAG
EST: gi|211228712|gb|FL216930.1|FL216930
EST:     TCTGAAAAGAAGGAAGCTTGAAGATTTAACAATTGGTCCAGTCCTTTACA                         GTTACTACAGAAGCCATGATAGAGCA
genomic: TCTGAAA-GAAGGAAGCTTGAAGATTTAACAATTGGTCCAGTCCTT-ACAgtaagtcagg ... tctgatccagGTTACTACAGAAGCCATGATAGAGCA

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: 30

AATTGGTCTTCTAGTGGTCTGCTTGAGAAAATGAAGAAACTTTCTGAAAGAAGGAAGCTTGAAGATTTAACAATTGGTCCAGTCCTTACAgtaagtcagg ... tctgatccagGTTACTACAGAAGCCATGATAGAGCACATGAACAACCTTCTCAAAATAAGAGGATCAAAGGTTCTGTTTGGTGGTGAACCGTTAGCGAATCACTCAATTC


Block sizes: 44 (upstream exon), 39 (downstream exon)
Score: 4

AATTGGTCTTCTAGTGGTCTGCTTGAGAAAATGAAGAAACTTTCTGAAAGAAGGAAGCTTGAAGATTTAACAATTGGTCCAGTCCTTACAgtaagtcagg ... tctgatccagGTTACTACAGAAGCCATGATAGAGCACATGAACAACCTTCTCAAAATAAGAGGATCAAAGGTTCTGTTTGGTGGTGAACCGTTAGCGAATCACTCAATTC


Block sizes: 45 (upstream exon), 35 (downstream exon)
Score: 5

AATTGGTCTTCTAGTGGTCTGCTTGAGAAAATGAAGAAACTTTCTGAAAGAAGGAAGCTTGAAGATTTAACAATTGGTCCAGTCCTTACAgtaagtcagg ... tctgatccagGTTACTACAGAAGCCATGATAGAGCACATGAACAACCTTCTCAAAATAAGAGGATCAAAGGTTCTGTTTGGTGGTGAACCGTTAGCGAATCACTCAATTC


Block sizes: 8 (upstream exon), 42 (downstream exon)
Score: 1

AATTGGTCTTCTAGTGGTCTGCTTGAGAAAATGAAGAAACTTTCTGAAAGAAGGAAGCTTGAAGATTTAACAATTGGTCCAGTCCTTACAgtaagtcagg ... tctgatccagGTTACTACAGAAGCCATGATAGAGCACATGAACAACCTTCTCAAAATAAGAGGATCAAAGGTTCTGTTTGGTGGTGAACCGTTAGCGAATCACTCAATTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATTGGTCTTCTAGTGGTCTGCTTGAGAAAATGAAGAAACTTTCTGAAAGAAGGAAGCTTGAAGATTTAACAATTGGTCCAGTCCTTACAgtaagtcaggggcggagccagcccttttttgggggtcagctgaccccggtaaatttctgaatatctaatagaaaatggtgttaataacaatagttctata

- - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aataacaa