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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATCAAGTGAGAAGTTGGCAATGGGTGAATTTTTTGGGATAAAACCTCCTGTGAAGAAGgcaagtataatttcagatgctgtgctgcactgcgctatctgggtttaggaatcttttcaactgaaatctgtgaattacctctattttagggagatggaaa...

Basic information

species Zea mays
transcript GRMZM2G066496_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G066496_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os12g05650.1 (Oryza sativa), 5'ss of exon 6
GAATCAAGTGAGAAGTTGGCAATGGGTGAATTTTTTGGGATAAAACCTCCTGTGAAGAAGgcaagtataat-----ttcagatgctgtgc-tgcactg--cgctatctgggtttaggaatcttttcaactg-aaatctgtgaatta-cctctattttagggagatggaaa
|||||||||||||| || || ||||||||||||||||| |||||| |||||| ||||||||  |||  | |     |||  || |||    | |||    |    ||||   | | | ||||| |||| |  |||  ||||  ||  |||| ||||||            
GAATCAAGTGAGAATTTAGCCATGGGTGAATTTTTTGGAATAAAAGCTCCTGAGAAGAAGgtgagttcattggatgttctcattctgcttgttcaccacccatgctctgttatcaagcatcttctcaattttaaagttgtgtgttttcctcaattttaac----------
















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|67022635|gb|CO451384.1|CO451384
EST:     AGAAGTTGGCAATGGGTGAATTTTTTGGGATAAAACCTCCTGTGAAGAAG                         GTTGATATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAA
genomic: AGAAGTTGGCAATGGGTGAATTTTTTGGGATAAAACCTCCTGTGAAGAAGgcaagtataa ... gaactggcagGTTGATATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAA
EST: gi|32830465|gb|CD970143.1|CD970143
EST:     AGAAGTTGGCAATGGGTGAATTTTTTGGGATAAAACCTCCTGTGAAGAAG                         GTTGATATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAA
genomic: AGAAGTTGGCAATGGGTGAATTTTTTGGGATAAAACCTCCTGTGAAGAAGgcaagtataa ... gaactggcagGTTGATATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAA
EST: gi|32804124|gb|CD956360.1|CD956360
EST:     AGAAGTTGGCAATGGGTGAATTTTTTGGGATAAAACCTCCTGTGAAGAAG                         GTTGATATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAA
genomic: AGAAGTTGGCAATGGGTGAATTTTTTGGGATAAAACCTCCTGTGAAGAAGgcaagtataa ... gaactggcagGTTGATATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAA
EST: gi|32859901|gb|CD999582.1|CD999582
EST:     GGGTGAATTTTTTGGGATAAAACCTCCTGTGAAGAAG                         GTTGATATCGATATTGCAACACATATAGTT-TTTAAGACGACGGGCCAAAA
genomic: GGGTGAATTTTTTGGGATAAAACCTCCTGTGAAGAAGgcaagtataa ... gaactggcagGTTGATATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAA
EST: gi|148954707|gb|EC900159.2|EC900159
EST:     AGAAGTTGGCAAGGGGTGAATTTTTTGGGATAAAACCTCCTGTGAAGAAG                         GTTGATATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAA
genomic: AGAAGTTGGCAATGGGTGAATTTTTTGGGATAAAACCTCCTGTGAAGAAGgcaagtataa ... gaactggcagGTTGATATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAA
EST: gi|32801615|gb|CD953851.1|CD953851
EST:     AGAAGTTGGCAATGGGTGAATTTTTTGGGATAAAACCTCTTGTGAAGAAG                         GTTGATATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAA
genomic: AGAAGTTGGCAATGGGTGAATTTTTTGGGATAAAACCTCCTGTGAAGAAGgcaagtataa ... gaactggcagGTTGATATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAA
EST: gi|18164129|gb|BM333968.1|BM333968
EST:     GTTGGCAATGGGTGAATTTTTTGGGATAAAACCTCCTGTGAAGAAG                         GTTGATATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAA
genomic: GTTGGCAATGGGTGAATTTTTTGGGATAAAACCTCCTGTGAAGAAGgcaagtataa ... gaactggcagGTTGATATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAA
EST: gi|118406764|gb|EH038212.1|EH038212
EST:     AGAAGTTGGCAATGGGTGAATTTTTTGGGATAAAACCTCCTGTGAAGAAG                         GTTGATATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAA
genomic: AGAAGTTGGCAATGGGTGAATTTTTTGGGATAAAACCTCCTGTGAAGAAGgcaagtataa ... gaactggcagGTTGATATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAA
EST: gi|89759755|gb|DY688471.1|DY688471
EST:     CTCCTGTGAAGAAG                         GTTGATATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAA
genomic: CTCCTGTGAAGAAGgcaagtataa ... gaactggcagGTTGATATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAA
EST: gi|60359682|gb|DN226655.1|DN226655
EST:     TTGGGATAAAACCTCCTGTGAAGAAG                         GTTGATATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAA
genomic: TTGGGATAAAACCTCCTGTGAAGAAGgcaagtataa ... gaactggcagGTTGATATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAA

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: 253

GAATCAAGTGAGAAGTTGGCAATGGGTGAATTTTTTGGGATAAAACCTCCTGTGAAGAAGgcaagtataa ... gaactggcagGTTGATATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAAAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 546

GAATCAAGTGAGAAGTTGGCAATGGGTGAATTTTTTGGGATAAAACCTCCTGTGAAGAAGgcaagtataa ... gaactggcagGTTGATATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAAAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 595

GAATCAAGTGAGAAGTTGGCAATGGGTGAATTTTTTGGGATAAAACCTCCTGTGAAGAAGgcaagtataa ... gaactggcagGTTGATATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAAAGAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 238

GAATCAAGTGAGAAGTTGGCAATGGGTGAATTTTTTGGGATAAAACCTCCTGTGAAGAAGgcaagtataa ... gaactggcagGTTGATATCGATATTGCAACACATATAGTTGTTGAAGACGACGGGCCAAAAAGAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAATCAAGTGAGAAGTTGGCAATGGGTGAATTTTTTGGGATAAAACCTCCTGTGAAGAAGgcaagtataatttcagatgctgtgctgcactgcgctatctgggtttaggaatcttttcaactgaaatctgtgaattacctctattttagggagatggaaa

- - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG