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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTCTGTCTTTTATGTATGATGGTGTACCTCTTCTAGCTATGTTGGATGAGTATGTTATGCTCAGGCAGGAAAGGGAAGAAGAGAAGAAAAGAACGCGGgtaagtgtgatatgctctttaaatctagaatccattatcacctggatgccaattcatttattgtccattgagttctgtttggacctatgctggagtctgg...

Basic information

species Zea mays
transcript GRMZM2G465169_T02
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G465169_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os06g20370.1 (Oryza sativa), 5'ss of exon 9
TGGTCTGTCTTTTATGTATGATGGTGTACCTCTTCTAGCTATGTTGGATGAGTATGTTATGCTCAGGCAGGAAAGGGAAGAAGAGAAGAAAAGAACGCGGgtaagtgtgatatgctctttaaatctagaatccattatcacctggatgccaattcatttattgtccattgagttctgtttggacctatgctggagtctgg
||||||||| ||||||||||||||||||||||||||||||||||||||||| ||||| ||||| |||||||||||||||||||| |||||||||| | |||| ||||  |  | |||||||||| | ||||||||| ||      | |      | || |  ||  || || |||| ||    |   || ||     || 
TGGTCTGTCCTTTATGTATGATGGTGTACCTCTTCTAGCTATGTTGGATGAATATGTCATGCTAAGGCAGGAAAGGGAAGAAGATAAGAAAAGAATGAGGgtgagtgccacttcctctttaaatgttgaatccattttcttgaacacgtatcacccttgagcgttgatcgaattcttttaaatctcgtgttgagtcatgt

upper sequence: GRMZM2G465169_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA02G46450.3 (Glycine max), 5'ss of exon 9
TGGTCTGTCTTTTATGTATGATGGTGTACCTCTTCTAGCTATGTTGGATGAGTATGTTATGCTCAGGCAGGAAAGGGAAGAAGAGAAGAAAAGAACGCGGgtaagtg----tgatatgctctttaa-atctagaatccattatcacctggatgccaattcattta-ttgtccattgagttctgtttggacctatgctggagtctgg
|||  |||| ||||  ||||||||||| |||||||| || ||||| ||||| ||||  |||||||| || ||| ||||||| || ||    || | | ||||||||     | ||| | |  |||  || ||| ||  |   |||  |  |     |||     | |||   ||     |  |       || |||  |       
TGGCATGTCATTTACATATGATGGTGTTCCTCTTCTTGCCATGTTAGATGAATATGCCATGCTCAGACATGAACGGGAAGAGGAAAAACGGAGGATGAGGgtaagtaacactaataagatgattaggatttaggattgac--tcattttcagcttgatttgagcacttgctgataataataagaccaccactctgcgaggaa----

upper sequence: GRMZM2G465169_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA08G43450.1 (Glycine max), 5'ss of exon 16
------------------------------TGGTCTGTCTTTTATGTATGATGGTGTACCTCTTCTAGCTATGTTGGATGAGTATGTTATGCTCAGGCAGGAAAGGGAAGAAGAGAAGAAAAGAACGCGGgtaagtgtgatatgctctttaaatctag-aatccattatcacctggatgccaattcatttattgtccattgagtt--ctgtttggacctatgctggagtctgg--------------
                              ||   |||| || |  ||||||||||| |||||||| |||||||||||||| ||||  ||||||||||| | | ||||||| ||  |   ||| | || ||||||| | ||        | | |  |  |||  |||||||     ||   |   || ||  |    |   |||   |    || ||        ||||                  
TGCTAAAACTCGTGTTTGGGAAGAAGCACCTGACATGTCATTCACATATGATGGTGTTCCTCTTCTTGCTATGTTGGATGAATATGCCATGCTCAGGCATgtatgggaagaggaagaatgaaggatgcaggtaagtttcattgatgggatgattagaataattgattatcaaaataattttag--cacttgctaataaaaaagtaagcaaagtgaactatcaaaagagttcatatcacattctttag

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|50338234|gb|CO533360.1|CO533360
EST:     GAAGAGAAGAAAAGAACGCGG                         GAACAAAAGCGCTACGTTGAGCAGCAATTGAACACTGATCATGAAGGGCCA
genomic: GAAGAGAAGAAAAGAACGCGGgtaagtgtga ... gacatctcagGAACAAAAGCGCTACGTTGAGCAGCAATTGAACACTGATCATGAAGGGCCA
EST: gi|32906926|gb|CF011739.1|CF011739
EST:     AGTATGTTATGCTCAGGCAGGAAAGGGAAGAAGAGAAGAAAAGAATGCGG                         GAACAAAAGCGCTACGTTGAGCAGCAATTGAACACTGATCATGAAGGGCCA
genomic: AGTATGTTATGCTCAGGCAGGAAAGGGAAGAAGAGAAGAAAAGAACGCGGgtaagtgtga ... gacatctcagGAACAAAAGCGCTACGTTGAGCAGCAATTGAACACTGATCATGAAGGGCCA
EST: gi|113693349|gb|DW845654.1|DW845654
EST:     AGTATGTTATGCTCAGGCAGGAAAGGGAAGAAGAGAAGAAAAGAACGCGG                         GAACAAAAGCGCTACGTTGAGCAGCAA
genomic: AGTATGTTATGCTCAGGCAGGAAAGGGAAGAAGAGAAGAAAAGAACGCGGgtaagtgtga ... gacatctcagGAACAAAAGCGCTACGTTGAGCAGCAA
EST: gi|37389353|gb|CF631896.1|CF631896
EST:     AGTATGTTATGCTCAGGCAGGAAAGGGAAGAAGAGAAGAAAAGAATGCGG                         GAACAAAAGCGCTACGTTGAGCAGCAA-TGNAACACTGATCATGAAGGGCC
genomic: AGTATGTTATGCTCAGGCAGGAAAGGGAAGAAGAGAAGAAAAGAACGCGGgtaagtgtga ... gacatctcagGAACAAAAGCGCTACGTTGAGCAGCAATTG-AACACTGATCATGAAGGGCC
EST: gi|211470732|gb|FL464833.1|FL464833
EST:     AAGAGAAGAAAAGAACGCGG                         GAACAAAAGCGCTACGTTGAGCAGCAATTGAACACTGATCATGAAGGGCCA
genomic: AAGAGAAGAAAAGAACGCGGgtaagtgtga ... gacatctcagGAACAAAAGCGCTACGTTGAGCAGCAATTGAACACTGATCATGAAGGGCCA
EST: gi|33097054|gb|CF057014.1|CF057014
EST:     AGTATGTTATGCTCAGGCAGGAAAGGGAAGAAGAGAAGAAAAGAATGCGG                         GAACCAAAAGCGCTACGTTGAGCAGCAATTGAACACTGATCATGAAGGGCC
genomic: AGTATGTTATGCTCAGGCAGGAAAGGGAAGAAGAGAAGAAAAGAACGCGGgtaagtgtga ... gacatctcagGAA-CAAAAGCGCTACGTTGAGCAGCAATTGAACACTGATCATGAAGGGCC
EST: gi|9731735|gb|BE510487.1|BE510487
EST:     AGAAGAAAAGAACGCGG                         GAACAAAAGCGCTACGTTGAGCAGCAATTGAACACTGATCATGAAGGGCCA
genomic: AGAAGAAAAGAACGCGGgtaagtgtga ... gacatctcagGAACAAAAGCGCTACGTTGAGCAGCAATTGAACACTGATCATGAAGGGCCA
EST: gi|16927317|gb|BM080386.1|BM080386
EST:     AGTATGTTATGCTCAGGCAGGAAAGGGAAGAAGAGAAGAAAAGAACGCGG                         GAACAAAAGCGCTACGTTGAGCAGCAATTGAACACTGATCATGAAGGGCCA
genomic: AGTATGTTATGCTCAGGCAGGAAAGGGAAGAAGAGAAGAAAAGAACGCGGgtaagtgtga ... gacatctcagGAACAAAAGCGCTACGTTGAGCAGCAATTGAACACTGATCATGAAGGGCCA

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 2 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 4

TGGTCTGTCTTTTATGTATGATGGTGTACCTCTTCTAGCTATGTTGGATGAGTATGTTATGCTCAGGCAGGAAAGGGAAGAAGAGAAGAAAAGAACGCGGgtaagtgtga ... gacatctcagGAACAAAAGCGCTACGTTGAGCAGCAATTGAACACTGATCATGAAGGGCCATTCGGATCGCGAGTGAGTCCAAACCGGCCTGCCAGTTCGAAGAAGGCCA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 4

TGGTCTGTCTTTTATGTATGATGGTGTACCTCTTCTAGCTATGTTGGATGAGTATGTTATGCTCAGGCAGGAAAGGGAAGAAGAGAAGAAAAGAACGCGGgtaagtgtga ... gacatctcagGAACAAAAGCGCTACGTTGAGCAGCAATTGAACACTGATCATGAAGGGCCATTCGGATCGCGAGTGAGTCCAAACCGGCCTGCCAGTTCGAAGAAGGCCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTCTGTCTTTTATGTATGATGGTGTACCTCTTCTAGCTATGTTGGATGAGTATGTTATGCTCAGGCAGGAAAGGGAAGAAGAGAAGAAAAGAACGCGGgtaagtgtgatatgctctttaaatctagaatccattatcacctggatgccaattcatttattgtccattgagttctgtttggacctatgctggagtctgg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC