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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCCGTGTTAGTGACAGCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAGgtctaagattaatctttctttttattaatactgaatcatactatctgttgcccatatgaaatatgcgctcattttgttgagcgaaaggatcaaatgaata...

Basic information

species Zea mays
transcript GRMZM2G166345_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G166345_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g60660.1 (Oryza sativa), 5'ss of exon 4
ATCCGTGTTAGTGACAGCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAGgtctaagattaatctttctttttattaatactgaatcatactat-ctgttgcccatatgaaatatgcgctcattttgttgagcgaaaggatcaaatgaata--
|  | | || |||| | ||||||||||||||||||||||||| |||||||||||||||| || |||||   | || || |||| ||| | ||  ||||  |||||||| |  |  |  |  | |  |   | |   | |    |      |    ||| |     |   
AGTCATCTTGGTGAAAACGAGTTGCAGAAATATCCACATGTATTGCGGTGGATGGACTATATCCAGgttcgaaataaaactttatttattttg-tact--atcatactttgttagtatcttttttcatactacctccgtgccataatataagcacatctagcatttgaa
















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|22935750|gb|BU572025.1|BU572025
EST:     GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAG                         AACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGACCAAGTCT
genomic: GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAGgtctaagatt ... tctgatgcagAACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGACCAAGTCT
EST: gi|211305838|gb|FL207346.1|FL207346
EST:     GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAG                         AACACTGTTGGTGCTGGTACAACTTTGCAAAAGAT
genomic: GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAGgtctaagatt ... tctgatgcagAACACTGTTGGTGCTGGTACAACTTTGCAAAAGAT
EST: gi|9953234|gb|BE639817.1|BE639817
EST:     GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAG                         AACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGACCAAGTCT
genomic: GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAGgtctaagatt ... tctgatgcagAACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGACCAAGTCT
EST: gi|211165089|gb|FL207337.1|FL207337
EST:     GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAG                         AACACTGTTGGTG
genomic: GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAGgtctaagatt ... tctgatgcagAACACTGTTGGTG
EST: gi|71436812|gb|DR817862.1|DR817862
EST:     GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAG                         AACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGACCAAGTCT
genomic: GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAGgtctaagatt ... tctgatgcagAACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGACCAAGTCT
EST: gi|93012239|gb|EB637759.1|EB637759
EST:     GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAG                         AACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGACCAAGTCT
genomic: GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAGgtctaagatt ... tctgatgcagAACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGACCAAGTCT
EST: gi|211165084|gb|FL207332.1|FL207332
EST:     GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAG                         AACACTGTTGGTGCTGGTACAACTTTGCAAAAGAT
genomic: GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAGgtctaagatt ... tctgatgcagAACACTGTTGGTGCTGGTACAACTTTGCAAAAGAT
EST: gi|91874367|gb|EB404324.1|EB404324
EST:     GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAG                         AACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGACCAAGTCT
genomic: GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAGgtctaagatt ... tctgatgcagAACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGACCAAGTCT
EST: gi|71320983|gb|DR797210.1|DR797210
EST:     GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAG                         AACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGACCAAGTCT
genomic: GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAGgtctaagatt ... tctgatgcagAACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGACCAAGTCT
EST: gi|211165094|gb|FL207342.1|FL207342
EST:     GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAG                         AACACTGTTGGTGCTGGTACAACTTTGC
genomic: GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAGgtctaagatt ... tctgatgcagAACACTGTTGGTGCTGGTACAACTTTGC
EST: gi|211307866|gb|FL207361.1|FL207361
EST:     GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAG                         AACACTGTTGG
genomic: GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAGgtctaagatt ... tctgatgcagAACACTGTTGG
EST: gi|211307864|gb|FL207359.1|FL207359
EST:     GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAG                         AACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAA
genomic: GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAGgtctaagatt ... tctgatgcagAACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAA
EST: gi|93280899|gb|EB673163.1|EB673163
EST:     GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAG                         AACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGACCAAGTCT
genomic: GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAGgtctaagatt ... tctgatgcagAACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGACCAAGTCT
EST: gi|211165091|gb|FL207339.1|FL207339
EST:     GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAG                         AACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGGTCAAGTCT
genomic: GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAGgtctaagatt ... tctgatgcagAACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGACCAAGTCT
EST: gi|4753387|gb|AI657292.1|AI657292
EST:     GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAG                         AACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGACCAAGTCT
genomic: GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAGgtctaagatt ... tctgatgcagAACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGACCAAGTCT
EST: gi|88756567|gb|DY540708.1|DY540708
EST:     GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAG                         AACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGACCAAGTCT
genomic: GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAGgtctaagatt ... tctgatgcagAACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGACCAAGTCT
EST: gi|89248432|gb|DY620218.1|DY620218
EST:     GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAG                         AACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGACCAAGTCT
genomic: GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAGgtctaagatt ... tctgatgcagAACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGACCAAGTCT
EST: gi|87155285|gb|DY400074.1|DY400074
EST:     GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAG                         AACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGACCAAGTCT
genomic: GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAGgtctaagatt ... tctgatgcagAACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGACCAAGTCT
EST: gi|32913166|gb|CF017978.1|CF017978
EST:     GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAG                         AACACNTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGGCCAAGTC
genomic: GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAGgtctaagatt ... tctgatgcagAACAC-TGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGACCAAGTC
EST: gi|91873663|gb|EB403620.1|EB403620
EST:     GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAG                         AACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGACCAAGTCT
genomic: GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAGgtctaagatt ... tctgatgcagAACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGACCAAGTCT
EST: gi|94477637|gb|EB706595.1|EB706595
EST:     GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAG                         AACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGACCAAGTCT
genomic: GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAGgtctaagatt ... tctgatgcagAACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGACCAAGTCT
EST: gi|211165095|gb|FL207343.1|FL207343
EST:     GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAG                         AACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGGCCAAGTCT
genomic: GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAGgtctaagatt ... tctgatgcagAACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGACCAAGTCT
EST: gi|149110255|gb|EE190312.2|EE190312
EST:     GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAG                         AACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGACCAAGTCT
genomic: GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAGgtctaagatt ... tctgatgcagAACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGACCAAGTCT
EST: gi|86469720|gb|DY236090.1|DY236090
EST:     GCGAGTTGCAAAAATATCCACATGTACTGCGGTGGATGGACTACATTCAG                         AACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGAGACCAAGTCT
genomic: GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAGgtctaagatt ... tctgatgcagAACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGACCAAGTCT
EST: gi|76286901|gb|DV026469.1|DV026469
EST:     GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAG                         AACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGACCAAGTCT
genomic: GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAGgtctaagatt ... tctgatgcagAACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGACCAAGTCT
EST: gi|61118563|gb|DN559524.1|DN559524
EST:     GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAG                         AACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGACCAAGTCT
genomic: GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAGgtctaagatt ... tctgatgcagAACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGACCAAGTCT
EST: gi|211533214|gb|FL395813.1|FL395813
EST:     GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGRTGGACTACATTCAG                         AACACTGTTGGTGCTGG
genomic: GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAGgtctaagatt ... tctgatgcagAACACTGTTGGTGCTGG
EST: gi|211305849|gb|FL207357.1|FL207357
EST:     GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAG                         AACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGGTCAAGTCT
genomic: GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAGgtctaagatt ... tctgatgcagAACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGACCAAGTCT
EST: gi|211305843|gb|FL207351.1|FL207351
EST:     GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAG                         AACACTGTTGGTGCTGGTA
genomic: GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAGgtctaagatt ... tctgatgcagAACACTGTTGGTGCTGGTA
EST: gi|211305844|gb|FL207352.1|FL207352
EST:     GCGAGTTGCAGAAATATCCACATGTTCTGCGGTGGATGGACTACATTCAG                         AACACTGTTGGTG
genomic: GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAGgtctaagatt ... tctgatgcagAACACTGTTGGTG
EST: gi|211165087|gb|FL207335.1|FL207335
EST:     GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAG                         AACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGGCCAAGTCT
genomic: GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAGgtctaagatt ... tctgatgcagAACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGACCAAGTCT
EST: gi|211098810|gb|FL225932.1|FL225932
EST:     GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAG                         AACACTGTTGGTGCTGGTACAACTTTGC
genomic: GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAGgtctaagatt ... tctgatgcagAACACTGTTGGTGCTGGTACAACTTTGC
EST: gi|78112560|gb|DV530954.1|DV530954
EST:     GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAG                         AACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGACCAAGTCT
genomic: GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAGgtctaagatt ... tctgatgcagAACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGACCAAGTCT
EST: gi|26559559|gb|CA831794.1|CA831794
EST:     GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAG                         AACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGACCAAGTCT
genomic: GCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAGgtctaagatt ... tctgatgcagAACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGACCAAGTCT

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: 227

ATCCGTGTTAGTGACAGCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAGgtctaagatt ... tctgatgcagAACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGACCAAGTCTGACTTTGATCCACCTTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 193

ATCCGTGTTAGTGACAGCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAGgtctaagatt ... tctgatgcagAACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGACCAAGTCTGACTTTGATCCACCTTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 213

ATCCGTGTTAGTGACAGCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAGgtctaagatt ... tctgatgcagAACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGACCAAGTCTGACTTTGATCCACCTTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 162

ATCCGTGTTAGTGACAGCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAGgtctaagatt ... tctgatgcagAACACTGTTGGTGCTGGTACAACTTTGCAAAAGATAAATGTGACCAAGTCTGACTTTGATCCACCTTCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCCGTGTTAGTGACAGCGAGTTGCAGAAATATCCACATGTACTGCGGTGGATGGACTACATTCAGgtctaagattaatctttctttttattaatactgaatcatactatctgttgcccatatgaaatatgcgctcattttgttgagcgaaaggatcaaatgaata

- - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaatgaa