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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGAGAATTGTATGACATGAACCTGAAGGGTCGCCCGCTTGCATATACTCCATTCTGTGATAACAACAAGGATATGGATGGTTTTCGATTTTGGAAGCAAgttagtcactgatttataataaatcatgttactacgcaaacaattgttcatgataataatataaaagtggatttgttttctcaagtttttcgttgacactttcttttatcctctgaag

Basic information

species Zea mays
transcript GRMZM5G846198_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G846198_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os02g44510.1 (Oryza sativa), 5'ss of exon 13
GGGAGAATTGTATGACATGAACCTGAAGGGTCGCCCGCTTGCATATACTCCATTCTGTGATAACAACAAGGATATGGATGGTTTTCGATTTTGGAAGCAAgttagtcactgatttataataaatcatgttactacgcaaacaattgttcatgataataatataaaagtggatttgttttctcaagtttttcgttgacactttcttttatcctctgaag
||||||| ||||||||||||| ||||||||||| || ||||| |||||||||||||| |||||||||||||| |||||||| | |||||||||||||||||| ||| ||  | || |  |   |        |||  ||  |||  ||  || | |   | |    |   | |   |||  |      |  ||  |                      
GGGAGAACTGTATGACATGAATCTGAAGGGTCGTCCCCTTGCGTATACTCCATTCTGCGATAACAACAAGGAGATGGATGGCTATCGATTTTGGAAGCAAgtaagttaccaaattgttgttggt--------tacataataaatgttttttggtcaagttgttt--gctaactcccttttgctttccctctgtgaaag--------------------

upper sequence: GRMZM5G846198_T02 (Zea mays), 5'ss of exon 6
lower sequence: Vv12s0034g02230.t01 (Vitis vinifera), 5'ss of exon 34
GGGAGAATTGTATGACATGAACCTGAAGGGTCGCCCGCTTGCATATACTCCATTCTGTGATAACAACAAGGATATGGATGGTTTTCGATTTTGGAAGCAAgt---tagtcactgat-ttataataaatcatgttactacgcaaa---caattgttcatgataataatataaaagtggatttgttttctcaagttt-ttcgttgacactttcttttatcctctgaag-----
||||||| | ||||||||| |  | || ||  | || ||||||||||| || |||||||| |||||||| ||||||||||| | |||||||||||  |||||   ||  |    || | ||  |   | |||||      ||     | |||   ||||  | | | ||     | ||| |  ||   | | | | || | | | | | ||  ||||  | ||  |     
GGGAGAACTCTATGACATGGATATAAAAGGAAGACCACTTGCATATACACCTTTCTGTGACAACAACAAAGATATGGATGGATATCGATTTTGGAGACAAgtagatacccttcaatatcatcctcttttatgtttgggttcatggttctattaagcatgccattgaaatgctgattgatctaattgtcctactctattggcttatattatcccttattttttgttgaacag

upper sequence: GRMZM5G846198_T02 (Zea mays), 5'ss of exon 6
lower sequence: EFJ07070 (Selaginella moellendorffii), 5'ss of exon 30
GGGAGAATTGTATGACATGAACCTGAAGGGTCGCCCGCTTGCATATACTCCATTCTGTGATAACAACAAGGATATGGATGGTTTTCGATTTTGGAAGCAAgttagtcactgatttataataaatcatgttactacgcaaacaattgttcatgataataatataaaagtggatttgttttctcaagtttttcgttgacactttcttttatcctctgaag
||| ||| | ||||||||| |  | |||||  | || || || || || || ||||| ||||||||||| ||||||||||||| ||| |||||||  || ||   |  ||  ||  |   |   | ||||  |  | || | ||| |   | |                                                                 
GGGGGAACTATATGACATGGATATAAAGGGCAGACCCCTCGCTTACACGCCTTTCTGCGATAACAACAAAGATATGGATGGTTATCGCTTTTGGAGTCAGgt--attcctttttactgccattgcttgtt-ttgtgtaa-ctattatatgtcag----------------------------------------------------------------

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|32930138|gb|CF034950.1|CF034950
EST:     CATTCTGTGATAACAACAAGGATATGGATGGTTTTCGATTTTGGAAGCAA                         GGTTTTTGGAAAGATCATCTGCGAGGAAGACCGT
genomic: CATTCTGTGATAACAACAAGGATATGGATGGTTTTCGATTTTGGAAGCAAgttagtcact ... tcctctgaagGGTTTTTGGAAAGATCATCTGCGAGGAAGACCGT
EST: gi|32850563|gb|CD990244.1|CD990244
EST:     CATTCTGTGATAACAACAAGGATATGGATGGTTTTCGATTTTGGAAGCAA                         GGTTTTTGGAAAGATCATCTGCGAGGAAGACCGTA
genomic: CATTCTGTGATAACAACAAGGATATGGATGGTTTTCGATTTTGGAAGCAAgttagtcact ... tcctctgaagGGTTTTTGGAAAGATCATCTGCGAGGAAGACCGTA
EST: gi|32834967|gb|CD974645.1|CD974645
EST:     CATTCTGTGATAACAACAAGGATATGGATGGTTTTCGATTTTGGAAGCAA                         GGTTTTTGGAAAGATCATCTGCGAGGAAGACCGTACC
genomic: CATTCTGTGATAACAACAAGGATATGGATGGTTTTCGATTTTGGAAGCAAgttagtcact ... tcctctgaagGGTTTTTGGAAAGATCATCTGCGAGGAAGACCGTACC
EST: gi|32835266|gb|CD974944.1|CD974944
EST:     CATTCTGTGATAACAACAAGGATATGGATGGTTTTCGATTTTGGAAGCAA                         GGTTTTTGGAAAGATCATCTGCGAGGAAGACCGT
genomic: CATTCTGTGATAACAACAAGGATATGGATGGTTTTCGATTTTGGAAGCAAgttagtcact ... tcctctgaagGGTTTTTGGAAAGATCATCTGCGAGGAAGACCGT
EST: gi|116823777|gb|EC867342.1|EC867342
EST:     CATTCTGTGATAACAACAAGGATATGGATGGTTTTCGATTTTGGAAGCAA                         GGTTTTTGGAAAGATCATCTGCGAGGAAGACCGTACCATATCAG
genomic: CATTCTGTGATAACAACAAGGATATGGATGGTTTTCGATTTTGGAAGCAAgttagtcact ... tcctctgaagGGTTTTTGGAAAGATCATCTGCGAGGAAGACCGTACCATATCAG
EST: gi|32850558|gb|CD990239.1|CD990239
EST:     CATTCTGTGATAACAACAAGGATATGGATGGTTTTCGATTTTGGAAGCAA                         GGTTTTTGGAAAGATCATCTGCGAGGAAGACCGTA
genomic: CATTCTGTGATAACAACAAGGATATGGATGGTTTTCGATTTTGGAAGCAAgttagtcact ... tcctctgaagGGTTTTTGGAAAGATCATCTGCGAGGAAGACCGTA
EST: gi|32850631|gb|CD990312.1|CD990312
EST:     CATTCTGTGATAACAACAAGGATATGGATGGTTTTCGATTTTGGAAGCAA                         GGTTTTTGGAAAGATCATCTGCGAGGAAGACCGTA
genomic: CATTCTGTGATAACAACAAGGATATGGATGGTTTTCGATTTTGGAAGCAAgttagtcact ... tcctctgaagGGTTTTTGGAAAGATCATCTGCGAGGAAGACCGTA

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: 156

GGGAGAATTGTATGACATGAACCTGAAGGGTCGCCCGCTTGCATATACTCCATTCTGTGATAACAACAAGGATATGGATGGTTTTCGATTTTGGAAGCAAgttagtcact ... tcctctgaagGGTTTTTGGAAAGATCATCTGCGAGGAAGACCGTACCATATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 99

GGGAGAATTGTATGACATGAACCTGAAGGGTCGCCCGCTTGCATATACTCCATTCTGTGATAACAACAAGGATATGGATGGTTTTCGATTTTGGAAGCAAgttagtcact ... tcctctgaagGGTTTTTGGAAAGATCATCTGCGAGGAAGACCGTACCATATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 121

GGGAGAATTGTATGACATGAACCTGAAGGGTCGCCCGCTTGCATATACTCCATTCTGTGATAACAACAAGGATATGGATGGTTTTCGATTTTGGAAGCAAgttagtcact ... tcctctgaagGGTTTTTGGAAAGATCATCTGCGAGGAAGACCGTACCATATCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 113

GGGAGAATTGTATGACATGAACCTGAAGGGTCGCCCGCTTGCATATACTCCATTCTGTGATAACAACAAGGATATGGATGGTTTTCGATTTTGGAAGCAAgttagtcact ... tcctctgaagGGTTTTTGGAAAGATCATCTGCGAGGAAGACCGTACCATATCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGAGAATTGTATGACATGAACCTGAAGGGTCGCCCGCTTGCATATACTCCATTCTGTGATAACAACAAGGATATGGATGGTTTTCGATTTTGGAAGCAAgttagtcactgatttataataaatcatgttactacgcaaacaattgttcatgataataatataaaagtggatttgttttctcaagtttttcgttgacactttcttttatcctctgaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA