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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTTGATGTTGTGCGTGATCAACTTGGACTCGTCCGTTCAGAGTTCCCTCATACATTCTATGGTGTTGCTGGAACGCAGgtcgtgttaatctttatgccttgaaaacctaagcattgacaaaagtagccattgttactatcaaatcttgaaatgcttttgatgtctatcacatagtgct...

Basic information

species Zea mays
transcript AC208327.4_FGT003
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC208327.4_FGT003 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os12g03822.1 (Oryza sativa), 5'ss of exon 4
TTTTGATGTTGTGCGTGATCAACTTGGACTCGTCCGTTCAGAGTTCCCTCATACATTCTATGGTGTTGCTGGAACGCAGgtcgtgttaatctttatgccttgaaaacctaagcattgacaaaagtagccattgttactatcaaatcttgaaatgcttttgatgtctatcacatagtgct-
||| ||||||||||| ||||||||||||||||| || || || ||||| |||||||| ||||| ||||||||||| ||||| |  ||  ||| |||             ||   ||     | | |   |    || | ||  || ||||        |  |||| |  ||| | |    
TTTCGATGTTGTGCGGGATCAACTTGGACTCGTGCGATCGGAATTCCCACATACATTATATGGCGTTGCTGGAACTCAGgttgcattc-tctctataatgctttccttcaaaatttacatgatgaatatacatatattttcctattttgattaatgaattctgtcaacaacaaaattagg

upper sequence: AC208327.4_FGT003 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os11g03990.1 (Oryza sativa), 5'ss of exon 4
TTTTGATGTTGTGCGTGATCAACTTGGACTCGTCCGTTCAGAGTTCCCTCATACATTCTATGGTGTTGCTGGAACGCAGgtcgtgttaa-tctttatgccttgaaaacctaagcattgacaaaagtagccattgttactatcaaatcttgaaatgcttttgatgtctatcacatagtgct
||||||||||||||| ||||||||||| || || || || || ||||| |||||||| ||||| ||||||||||| |||||||  ||   ||||||  ||||      | ||   |  |  |      |   | ||  | | |  |  | ||   ||| || |  | |  | ||   | |
TTTTGATGTTGTGCGGGATCAACTTGGCCTTGTGCGATCTGAATTCCCACATACATTATATGGCGTTGCTGGAACTCAGgtcgcattctctctttactccttttccttcaaaatttgcattacgactacgtatatttatgt-atttgattaataacttctgttaacaacaaaattaggat
















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|20811103|gb|BQ295581.1|BQ295581
EST:     TCGTCCGTTCAGAGTTCCCTCATACATTCTATGGTGTTGCTGGAACGCAG                         GCTGAGAAAGCTTCATGGAACTATATTGGCGTTTTCAAGCTTTCTAACATA
genomic: TCGTCCGTTCAGAGTTCCCTCATACATTCTATGGTGTTGCTGGAACGCAGgtcgtgttaa ... tgttgttcagGCTGAGAAAGCTTCATGGAACTATATTGGCGTTTTCAAGCTTTCTAACATA
EST: gi|9732023|gb|BE510775.1|BE510775
EST:     TCGTCCGTTCAGAGTTCCCTCATACATTCTATGGTGTTGCTGGAACGCAG                         GCTGAGAAAGCTTCATGGAACTATATTGGCGTTTTCAAGCTTTCTAACATA
genomic: TCGTCCGTTCAGAGTTCCCTCATACATTCTATGGTGTTGCTGGAACGCAGgtcgtgttaa ... tgttgttcagGCTGAGAAAGCTTCATGGAACTATATTGGCGTTTTCAAGCTTTCTAACATA
EST: gi|78089597|gb|DV517971.1|DV517971
EST:     TCGTCCGTTCAGAGTTCCCTCATACATTCTATGGTGTTGCTGGAACGCAG                         GCTGAGAAAGCTTCATGGAACTATATTGGCGTTTTCAAGCTTTCTAACATA
genomic: TCGTCCGTTCAGAGTTCCCTCATACATTCTATGGTGTTGCTGGAACGCAGgtcgtgttaa ... tgttgttcagGCTGAGAAAGCTTCATGGAACTATATTGGCGTTTTCAAGCTTTCTAACATA
EST: gi|211516191|gb|FL166755.1|FL166755
EST:     TCGTCCGTTCAGAGTTCCCTCATACATTCTATGGTGTTGCTGGAACGCAG                         GCTGAGAAAGCTTCATGGAACTATATTGGCGTTTTCAAGCTTTCTAACATA
genomic: TCGTCCGTTCAGAGTTCCCTCATACATTCTATGGTGTTGCTGGAACGCAGgtcgtgttaa ... tgttgttcagGCTGAGAAAGCTTCATGGAACTATATTGGCGTTTTCAAGCTTTCTAACATA
EST: gi|33467487|gb|CF244536.1|CF244536
EST:     TCGTCCGTTCAGAGTTCCCTCATACATTCTATGGTGTTGCTGGAACGCAG                         GCTGAGAAAGCTTCATGGAACTATATTGGCGTTTTCAAGCTTTCTAACATA
genomic: TCGTCCGTTCAGAGTTCCCTCATACATTCTATGGTGTTGCTGGAACGCAGgtcgtgttaa ... tgttgttcagGCTGAGAAAGCTTCATGGAACTATATTGGCGTTTTCAAGCTTTCTAACATA
EST: gi|148933097|gb|EC876730.2|EC876730
EST:     TCGTCCGTTCAGAGTTCCCTCATACATTCTATGGTGTTGCTGGAACGCAG                         GCTGAGAAAGCTTCATGGAACTATATTGGCGTTTTCAAGCTTTCTAACATA
genomic: TCGTCCGTTCAGAGTTCCCTCATACATTCTATGGTGTTGCTGGAACGCAGgtcgtgttaa ... tgttgttcagGCTGAGAAAGCTTCATGGAACTATATTGGCGTTTTCAAGCTTTCTAACATA
EST: gi|211466442|gb|FL172133.1|FL172133
EST:     TCGTCCGTTCAGAGTTCCCTCATACATTCTATGGTGTTGCTGGAACGCAG                         GCTGAGAAAGCTTCATGGAACTATATTGGCGTTTTCAAGCTTTCTAACATA
genomic: TCGTCCGTTCAGAGTTCCCTCATACATTCTATGGTGTTGCTGGAACGCAGgtcgtgttaa ... tgttgttcagGCTGAGAAAGCTTCATGGAACTATATTGGCGTTTTCAAGCTTTCTAACATA
EST: gi|19822069|gb|BQ048093.1|BQ048093
EST:     TCGTCCGTTCAGAGTTCCCTCATACATTCTATGGTGTTGCTGGAACGCAG                         GCTGAGAAAGCTTCATGGAACTATATTGGCGTTTTCAAGCTTTCTAACATA
genomic: TCGTCCGTTCAGAGTTCCCTCATACATTCTATGGTGTTGCTGGAACGCAGgtcgtgttaa ... tgttgttcagGCTGAGAAAGCTTCATGGAACTATATTGGCGTTTTCAAGCTTTCTAACATA
EST: gi|31349324|gb|CD433681.1|CD433681
EST:     ATTCTATGGTGTTGCTGGAACGCAG                         GCTGAGAAAGCTCCATGGAACTATATTGGCGTTTTCAAGCTTTCTAACATA
genomic: ATTCTATGGTGTTGCTGGAACGCAGgtcgtgttaa ... tgttgttcagGCTGAGAAAGCTTCATGGAACTATATTGGCGTTTTCAAGCTTTCTAACATA
EST: gi|31350283|gb|CD434640.1|CD434640
EST:     ATTCTATGGTGTTGCTGGAACGCAG                         GCTGAGAAACCTTCATGGAACTATATTGGCGTTTTCAAGCTTTCTAACATA
genomic: ATTCTATGGTGTTGCTGGAACGCAGgtcgtgttaa ... tgttgttcagGCTGAGAAAGCTTCATGGAACTATATTGGCGTTTTCAAGCTTTCTAACATA
EST: gi|211516190|gb|FL166754.1|FL166754
EST:     TCGTCCGTTCAGAGTTCCCTCATACATTCTATGGTGTTGCTGGAACGCAG                         GCTGAGAAAGCTTCATGGAACTATATTGGCGTTTTCAAGCTTTCTAACATA
genomic: TCGTCCGTTCAGAGTTCCCTCATACATTCTATGGTGTTGCTGGAACGCAGgtcgtgttaa ... tgttgttcagGCTGAGAAAGCTTCATGGAACTATATTGGCGTTTTCAAGCTTTCTAACATA
EST: gi|26457087|gb|CA828670.1|CA828670
EST:     TCGTCCGTTCAGAGTTCCCTCATACATTCTATGGCGTTGCTGGAACGCAG                         GCTGAGAAAGCTTCATGGAACTATATTGGCGTTTTCAAGCTTTCTAACATA
genomic: TCGTCCGTTCAGAGTTCCCTCATACATTCTATGGTGTTGCTGGAACGCAGgtcgtgttaa ... tgttgttcagGCTGAGAAAGCTTCATGGAACTATATTGGCGTTTTCAAGCTTTCTAACATA

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: 349

TTTTGATGTTGTGCGTGATCAACTTGGACTCGTCCGTTCAGAGTTCCCTCATACATTCTATGGTGTTGCTGGAACGCAGgtcgtgttaa ... tgttgttcagGCTGAGAAAGCTTCATGGAACTATATTGGCGTTTTCAAGCTTTCTAACATAAGTGGCAAGAAGCGGGAACCTATACCAGCTTCAGCAGTTGAAGCTGACA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 131

TTTTGATGTTGTGCGTGATCAACTTGGACTCGTCCGTTCAGAGTTCCCTCATACATTCTATGGTGTTGCTGGAACGCAGgtcgtgttaa ... tgttgttcagGCTGAGAAAGCTTCATGGAACTATATTGGCGTTTTCAAGCTTTCTAACATAAGTGGCAAGAAGCGGGAACCTATACCAGCTTCAGCAGTTGAAGCTGACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 96

TTTTGATGTTGTGCGTGATCAACTTGGACTCGTCCGTTCAGAGTTCCCTCATACATTCTATGGTGTTGCTGGAACGCAGgtcgtgttaa ... tgttgttcagGCTGAGAAAGCTTCATGGAACTATATTGGCGTTTTCAAGCTTTCTAACATAAGTGGCAAGAAGCGGGAACCTATACCAGCTTCAGCAGTTGAAGCTGACA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 144

TTTTGATGTTGTGCGTGATCAACTTGGACTCGTCCGTTCAGAGTTCCCTCATACATTCTATGGTGTTGCTGGAACGCAGgtcgtgttaa ... tgttgttcagGCTGAGAAAGCTTCATGGAACTATATTGGCGTTTTCAAGCTTTCTAACATAAGTGGCAAGAAGCGGGAACCTATACCAGCTTCAGCAGTTGAAGCTGACA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTTGATGTTGTGCGTGATCAACTTGGACTCGTCCGTTCAGAGTTCCCTCATACATTCTATGGTGTTGCTGGAACGCAGgtcgtgttaatctttatgccttgaaaacctaagcattgacaaaagtagccattgttactatcaaatcttgaaatgcttttgatgtctatcacatagtgct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gacaaaag