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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGTAAATACATGGGTTAGTGCTAATGGTAAAAATGGAATGCGTAGGGATTGGCATATACGTGATTCTATGACAGGCCACACAATACTGAAGGCGACAAGgttcgaatctctgccacactcattatatcattaatcaattttattagccatttatttctaccaactgccatgttacgattgaccctgcatttatagtttatctgctcaaagtccgtgtaacttaccctgttgcattttattttctaatttgtgtctttgtgcag

Basic information

species Zea mays
transcript GRMZM2G079308_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G079308_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os06g39520.2 (Oryza sativa), 5'ss of exon 4
AAGTAAATACATGGGTTAGTGCTAATGGTAAAAATGGAATGCGTAGGGATTGGCATATACGTGATTCTATGACAGGCCACACAATACTGAAGGCGACAAGgttcgaatctctgccacactcatta-tatcattaatca-----attttattagc--catttattt---ctaccaactgccatgttacgattgaccctgcatttatagtttatctgctcaaagtccgtgtaacttaccct--gttgcattttatt--ttctaatttgtgtctttgtgcag--------------------
||||| ||||||||||| ||||| ||||||||||||||||||| || || |||||||||||||||||| | |||||||| |||||| ||||||| |||||||| ||||   || ||| ||||| | ||    | ||||     | | |||||||  |   ||||     | | | |   | | |||| | ||    ||||| |  ||| ||   | ||    ||     ||| ||   |  | ||| ||  |        ||  |   | ||||| |                      
AAGTAGATACATGGGTTGGTGCTCATGGTAAAAATGGAATGCGCAGAGACTGGCATATACGTGATTCTGTAACAGGCCATACAATATTGAAGGCTACAAGgtttgaattattgtcactctcataaatactgatgatcatgaaaactgtattagcatctgctattcaacttcctacccatcttattaccactg--tttgcatatgaagtctagaagttctgtttcttctgaacatattataagctgccttacagcaacatgaagctacctatttgtcctaattgtttgctcaatgtgcag
















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|211198985|gb|FL379479.1|FL379479
EST:     TGGCATATACGTGATTCTATGACAGGCCACACAATACTGAAGGCGACAAG                         TAAATGGGTTATGATGAACAAACTCACTAGGAAGCTTGCAAGAATTCCAGA
genomic: TGGCATATACGTGATTCTATGACAGGCCACACAATACTGAAGGCGACAAGgttcgaatct ... ctttgtgcagTAAATGGGTTATGATGAACAAACTCACTAGGAAGCTTGCAAGAATTCCAGA
EST: gi|211076640|gb|FL394059.1|FL394059
EST:     TGGCATATACGTGATTCTATGACAGGCCACACAATACTGAAGGCGACAAG                         TAAATGGGTTATGATGAACAAACTCACTAGGAAGCTTGCAAGAATTCCAGA
genomic: TGGCATATACGTGATTCTATGACAGGCCACACAATACTGAAGGCGACAAGgttcgaatct ... ctttgtgcagTAAATGGGTTATGATGAACAAACTCACTAGGAAGCTTGCAAGAATTCCAGA
EST: gi|32867853|gb|CF007535.1|CF007535
EST:     TGGCATATACGTGATTCTATGACAGGCCACACAATACTGAAGGCGACAAG                         TAAATGGGTTATGATGAACAAACTCACTAGGAAGCTTGCAAGAATTCCAGA
genomic: TGGCATATACGTGATTCTATGACAGGCCACACAATACTGAAGGCGACAAGgttcgaatct ... ctttgtgcagTAAATGGGTTATGATGAACAAACTCACTAGGAAGCTTGCAAGAATTCCAGA
EST: gi|32870399|gb|CF010081.1|CF010081
EST:     TGGCATATACGTGATTCTATGACAGGCCACACAATACTGAAGGCGACAAG                         TAAATGGGTTATGATGAACAAACTCACTAGGAAGCTTGCAAGAATTCCAGA
genomic: TGGCATATACGTGATTCTATGACAGGCCACACAATACTGAAGGCGACAAGgttcgaatct ... ctttgtgcagTAAATGGGTTATGATGAACAAACTCACTAGGAAGCTTGCAAGAATTCCAGA
EST: gi|7227656|gb|AW566297.1|AW566297
EST:     TGGCATATACGTGATTCTATGACAGGCCACACAATACTGAAGGCGACAAG                         TAAATGGGTTATGATGAACAAACTCACTAGGAAGCTTGCAAGAATTCCAGA
genomic: TGGCATATACGTGATTCTATGACAGGCCACACAATACTGAAGGCGACAAGgttcgaatct ... ctttgtgcagTAAATGGGTTATGATGAACAAACTCACTAGGAAGCTTGCAAGAATTCCAGA
EST: gi|6012678|gb|AW062115.1|AW062115
EST:     TGGCATATACGTGATTCTATGACAGGCCACACAATACTGAAGGCGACAAG                         TAAATGGGTTATGATGAACAAACTCACTAGGAAGCTTGCAAGAATTCCAGA
genomic: TGGCATATACGTGATTCTATGACAGGCCACACAATACTGAAGGCGACAAGgttcgaatct ... ctttgtgcagTAAATGGGTTATGATGAACAAACTCACTAGGAAGCTTGCAAGAATTCCAGA

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: 401

AAGTAAATACATGGGTTAGTGCTAATGGTAAAAATGGAATGCGTAGGGATTGGCATATACGTGATTCTATGACAGGCCACACAATACTGAAGGCGACAAGgttcgaatct ... ctttgtgcagTAAATGGGTTATGATGAACAAACTCACTAGGAAGCTTGCAAGAATTCCAGATGAAGTGCGGACTGAAATAGAGCCATACTTTGTTGGGCGTTCTGCTATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 323

AAGTAAATACATGGGTTAGTGCTAATGGTAAAAATGGAATGCGTAGGGATTGGCATATACGTGATTCTATGACAGGCCACACAATACTGAAGGCGACAAGgttcgaatct ... ctttgtgcagTAAATGGGTTATGATGAACAAACTCACTAGGAAGCTTGCAAGAATTCCAGATGAAGTGCGGACTGAAATAGAGCCATACTTTGTTGGGCGTTCTGCTATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 314

AAGTAAATACATGGGTTAGTGCTAATGGTAAAAATGGAATGCGTAGGGATTGGCATATACGTGATTCTATGACAGGCCACACAATACTGAAGGCGACAAGgttcgaatct ... ctttgtgcagTAAATGGGTTATGATGAACAAACTCACTAGGAAGCTTGCAAGAATTCCAGATGAAGTGCGGACTGAAATAGAGCCATACTTTGTTGGGCGTTCTGCTATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 368

AAGTAAATACATGGGTTAGTGCTAATGGTAAAAATGGAATGCGTAGGGATTGGCATATACGTGATTCTATGACAGGCCACACAATACTGAAGGCGACAAGgttcgaatct ... ctttgtgcagTAAATGGGTTATGATGAACAAACTCACTAGGAAGCTTGCAAGAATTCCAGATGAAGTGCGGACTGAAATAGAGCCATACTTTGTTGGGCGTTCTGCTATT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGTAAATACATGGGTTAGTGCTAATGGTAAAAATGGAATGCGTAGGGATTGGCATATACGTGATTCTATGACAGGCCACACAATACTGAAGGCGACAAGgttcgaatctctgccacactcattatatcattaatcaattttattagccatttatttctaccaactgccatgttacgattgaccctgcatttatagtttatctgctcaaagtccgtgtaacttaccctgttgcattttattttctaatttgtgtctttgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG