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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatcctgagataatctactcctattccctaattgcttgattaatccagttttctgtgtcatacaacgtcttggctaaactgtgtccattgcttcatgcagTATCCAGTGTACTTTGCTTTGGATGACGACAATTTTGGTAACCTGCTGGCAGATATCCATAAAATTGCCTCTTCAGGCCAACCAGCCTCTGCAACAACAG

Basic information

species Zea mays
transcript GRMZM2G451366_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G451366_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os08g01180.1 (Oryza sativa), 3'ss of exon 2
gatcctgagataatctactc-ctattccctaattgcttgattaatccagttttctgtgtcatacaacgtcttggctaaactgtgtccattgcttcatgcagTATCCAGTGTACTTTGCTTTGGATGACGACAATTTTGGTAACCTGCTGGCAGATATCCATAAAATTGCCTCTTCAGGCCAACCAGCCTCTGCAACAACAG
  || ||  ||    || |  ||| |||  |  ||  |  |     |  | ||   |  | ||     |  | |||||  | | |||||| || | |||||||||| || ||||| |||||  | || ||| | |||| |||||||||||| ||||| | |||||||||||||||||| || |||||||| ||||||||||
cttcatgctatccattattttctactccacatatgtcttgtcccctctttgtttaataac-tattctatagtagctaacttatttccattactccgtgcagTATCCGGTCTACTTCGCTTTCCAGGATGACCACTTTGATAACCTGCTGGCGGATATACGTAAAATTGCCTCTTCAGGTCAGCCAGCCTCAGCAACAACAG
















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|211228900|gb|FK998494.1|FK998494
EST:     AAGGTGTACTGACTGAGCTGGAGAAGTTGCTTGTGCACGAACAAGTTCCA                         TATCCAGTGTACTTTGCTTTGCATGGCGACAATTTTGGTAACCTGCTGGCA
genomic: AAGGTGTACTGACTGAGCTGGAGAAGTTGCTTGTGCACGAACAAGTTCCAgtaagccata ... cttcatgcagTATCCAGTGTACTTTGCTTTGGATGACGACAATTTTGGTAACCTGCTGGCA
EST: gi|91869089|gb|EB400264.1|EB400264
EST:     AAGGTGTACTGACTGAGCTGGAGAAGTTGCTTGTGCACGAACAAGTTCCA                         TATCCAGTGTACTTTGCTTTGGATGACGACAATTTTGGTAACCTGCTGGCA
genomic: AAGGTGTACTGACTGAGCTGGAGAAGTTGCTTGTGCACGAACAAGTTCCAgtaagccata ... cttcatgcagTATCCAGTGTACTTTGCTTTGGATGACGACAATTTTGGTAACCTGCTGGCA
EST: gi|211228910|gb|FK998504.1|FK998504
EST:     AAGGTGTACTGACTGAGCTGGAGAAGTTGCTTGTGCACGAACAAGTTCCA                         TATCCAGTGTACTTTGCTTTGGATGACGACAATTTTGGTAACCTGCTGGCA
genomic: AAGGTGTACTGACTGAGCTGGAGAAGTTGCTTGTGCACGAACAAGTTCCAgtaagccata ... cttcatgcagTATCCAGTGTACTTTGCTTTGGATGACGACAATTTTGGTAACCTGCTGGCA
EST: gi|211228908|gb|FK998502.1|FK998502
EST:     AAGGTGTACTGACTGAGCTGGAGAAGTTGCTTGTGCACGAACAAGTTCCA                         TATCCAGTGTACTTTGCTTTGCATGGCGACAATTTTGGTAACCTGCTGGCA
genomic: AAGGTGTACTGACTGAGCTGGAGAAGTTGCTTGTGCACGAACAAGTTCCAgtaagccata ... cttcatgcagTATCCAGTGTACTTTGCTTTGGATGACGACAATTTTGGTAACCTGCTGGCA
EST: gi|91052384|gb|EB162802.1|EB162802
EST:     AAGGTGTACTGACTGAGCTGGAGAAGTTGCTTGTGCACGAACAAGTTCCA                         TATCCAGTGTACTTTGCTTTGGATGACGACAATTTTGGTAACCTGCTGGCA
genomic: AAGGTGTACTGACTGAGCTGGAGAAGTTGCTTGTGCACGAACAAGTTCCAgtaagccata ... cttcatgcagTATCCAGTGTACTTTGCTTTGGATGACGACAATTTTGGTAACCTGCTGGCA
EST: gi|211226848|gb|FK998488.1|FK998488
EST:     AAGGTGTACTGACTGAGCTGGAGAAGTTGCTTGTGCACGAACAAGTTCCA                         TATCCAGTGTACTTTGCTTTGCATGGCGACAATTTTGGTAACCTGCTGGCA
genomic: AAGGTGTACTGACTGAGCTGGAGAAGTTGCTTGTGCACGAACAAGTTCCAgtaagccata ... cttcatgcagTATCCAGTGTACTTTGCTTTGGATGACGACAATTTTGGTAACCTGCTGGCA
EST: gi|211226850|gb|FK998490.1|FK998490
EST:     AAGGTGTACTCACTGAGCTGGAGAAGTTGCTTGTGCACGAACAAGTTCCA                         TATCCAGTGTACTTTGCTTTGGATGACGACNATTTTGGTAACCTGCTGGCA
genomic: AAGGTGTACTGACTGAGCTGGAGAAGTTGCTTGTGCACGAACAAGTTCCAgtaagccata ... cttcatgcagTATCCAGTGTACTTTGCTTTGGATGACGACAATTTTGGTAACCTGCTGGCA
EST: gi|148957547|gb|EC903641.2|EC903641
EST:     AATGTGTACTGACTGAGCTGGAGAAGTTGCTTGTGCACGAACAAGTTCCA                         TATCCAGTGTACTTTGCTTTGGATGACGACAATTTTGGTAACCTGCTGGCA
genomic: AAGGTGTACTGACTGAGCTGGAGAAGTTGCTTGTGCACGAACAAGTTCCAgtaagccata ... cttcatgcagTATCCAGTGTACTTTGCTTTGGATGACGACAATTTTGGTAACCTGCTGGCA
EST: gi|101402114|gb|EB822664.1|EB822664
EST:     AAGGTGTACTGACTGAGCTGGAGAAGTTGCTTGTGCACGAACAAGTTCCA                         TATCCAGTGTACTTTGCTTTGGATGACGACAATTTTGGTAACCTGCTGGCA
genomic: AAGGTGTACTGACTGAGCTGGAGAAGTTGCTTGTGCACGAACAAGTTCCAgtaagccata ... cttcatgcagTATCCAGTGTACTTTGCTTTGGATGACGACAATTTTGGTAACCTGCTGGCA
EST: gi|211228907|gb|FK998501.1|FK998501
EST:     AAGGTGTACTGACTGAGCTGGAGAAGTTGCTTGTGCACGAACAAGTTCCA                         TATCCAGTGTACTTTGCTTTGCATGGCGACAATTTTGGTAACCTGCTGGCA
genomic: AAGGTGTACTGACTGAGCTGGAGAAGTTGCTTGTGCACGAACAAGTTCCAgtaagccata ... cttcatgcagTATCCAGTGTACTTTGCTTTGGATGACGACAATTTTGGTAACCTGCTGGCA
EST: gi|149084005|gb|EE173399.2|EE173399
EST:     AAGGTGTACTGACTGAGCTGGAGAAGTTGCTTGTGCACGAACAAGTTCCA                         TATCCAGTGTACTTTGCTTTGGATGACGACAATTTTGGTAACCTGCTGGCA
genomic: AAGGTGTACTGACTGAGCTGGAGAAGTTGCTTGTGCACGAACAAGTTCCAgtaagccata ... cttcatgcagTATCCAGTGTACTTTGCTTTGGATGACGACAATTTTGGTAACCTGCTGGCA
EST: gi|149109140|gb|EE190033.2|EE190033
EST:     AAGGTGTACTGACTGAGCTGGAGAAGTTGCTTGTGCACGAACAAGTTCCA                         TATCCAGTGTACTTTGCTTTGGATGA
genomic: AAGGTGTACTGACTGAGCTGGAGAAGTTGCTTGTGCACGAACAAGTTCCAgtaagccata ... cttcatgcagTATCCAGTGTACTTTGCTTTGGATGA
EST: gi|71326877|gb|DR800096.1|DR800096
EST:     AAGGTGTACTGACTGAGCTGGAGAAGTTGCTTGTGCACGAACAAGTTCCA                         TATCCAGTGTACTTTGCTTTGGATGACGACAATTTTGGTAACCTGCTGGCA
genomic: AAGGTGTACTGACTGAGCTGGAGAAGTTGCTTGTGCACGAACAAGTTCCAgtaagccata ... cttcatgcagTATCCAGTGTACTTTGCTTTGGATGACGACAATTTTGGTAACCTGCTGGCA
EST: gi|211228909|gb|FK998503.1|FK998503
EST:     AGGTGTACTGACTGAGCTGGAGAAAGT-GCTTGTGCACGACCAAGTTCCA                         TATCCAGTGTACTTTGCTTTGGATGACGAACA-TTTTGGTAAC
genomic: AGGTGTACTGACTGAGCTGGAGAA-GTTGCTTGTGCACGAACAAGTTCCAgtaagccata ... cttcatgcagTATCCAGTGTACTTTGCTTTGGATGACGA-CAATTTTGGTAAC
EST: gi|211228901|gb|FK998495.1|FK998495
EST:     AAGGTGTACTGACTGAGCTGGAGAAGTTGCTTGTGCACGAACAAGTTCCA                         TATCCAGTGTACTTTGCTTTGGATGACGACAATTTTGGTAACCTGCTGGCA
genomic: AAGGTGTACTGACTGAGCTGGAGAAGTTGCTTGTGCACGAACAAGTTCCAgtaagccata ... cttcatgcagTATCCAGTGTACTTTGCTTTGGATGACGACAATTTTGGTAACCTGCTGGCA
EST: gi|211226849|gb|FK998489.1|FK998489
EST:     AAGGTGTACTGACTGAGCTGGAGAAGTTGCTTGTGCACGAACAAGTTCCA                         TATCCAGTGTACTTTGC
genomic: AAGGTGTACTGACTGAGCTGGAGAAGTTGCTTGTGCACGAACAAGTTCCAgtaagccata ... cttcatgcagTATCCAGTGTACTTTGC
EST: gi|148933788|gb|EC877732.2|EC877732
EST:     AAGGTGTACTGACTGAGCTGGAGAAGTTGCTTGTGCACGAACAAGTTCCA                         TATCCAGTGTACTTTGCTTTGGATGACGACAATTTTGGTAACCTGCTGGCA
genomic: AAGGTGTACTGACTGAGCTGGAGAAGTTGCTTGTGCACGAACAAGTTCCAgtaagccata ... cttcatgcagTATCCAGTGTACTTTGCTTTGGATGACGACAATTTTGGTAACCTGCTGGCA
EST: gi|50335646|gb|CO530772.1|CO530772
EST:     AAGGTGTACTGACTGAGCTGGAGAAGTTGCTTGTGCACGAACAAGTTCCA                         TATCCAGTGTACTTTGCTTTGGATGACGACAATTTTGGTAACCTGCTGGCA
genomic: AAGGTGTACTGACTGAGCTGGAGAAGTTGCTTGTGCACGAACAAGTTCCAgtaagccata ... cttcatgcagTATCCAGTGTACTTTGCTTTGGATGACGACAATTTTGGTAACCTGCTGGCA
EST: gi|71440389|gb|DR821439.1|DR821439
EST:     AAGGTGTACTGACTGAGCTGGAGAAGTTGCTTGTGCACGAACAAGTTCCA                         TATCCAGTGTACTTTGCTTTGGATGACGACAATTTTGGTAACCTGCTGGCA
genomic: AAGGTGTACTGACTGAGCTGGAGAAGTTGCTTGTGCACGAACAAGTTCCAgtaagccata ... cttcatgcagTATCCAGTGTACTTTGCTTTGGATGACGACAATTTTGGTAACCTGCTGGCA

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), 48 (downstream exon)
Score: 101

CCCGACAAACCAGGGTGATAAGGATAGTGCGGATGACAAGGGTCAAGTCAAAGGTGTACTGACTGAGCTGGAGAAGTTGCTTGTGCACGAACAAGTTCCAgtaagccata ... cttcatgcagTATCCAGTGTACTTTGCTTTGGATGACGACAATTTTGGTAACCTGCTGGCAGATATCCATAAAATTGCCTCTTCAGGCCAACCAGCCTCTGCAACAACAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 98

CCCGACAAACCAGGGTGATAAGGATAGTGCGGATGACAAGGGTCAAGTCAAAGGTGTACTGACTGAGCTGGAGAAGTTGCTTGTGCACGAACAAGTTCCAgtaagccata ... cttcatgcagTATCCAGTGTACTTTGCTTTGGATGACGACAATTTTGGTAACCTGCTGGCAGATATCCATAAAATTGCCTCTTCAGGCCAACCAGCCTCTGCAACAACAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 81

CCCGACAAACCAGGGTGATAAGGATAGTGCGGATGACAAGGGTCAAGTCAAAGGTGTACTGACTGAGCTGGAGAAGTTGCTTGTGCACGAACAAGTTCCAgtaagccata ... cttcatgcagTATCCAGTGTACTTTGCTTTGGATGACGACAATTTTGGTAACCTGCTGGCAGATATCCATAAAATTGCCTCTTCAGGCCAACCAGCCTCTGCAACAACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 98

CCCGACAAACCAGGGTGATAAGGATAGTGCGGATGACAAGGGTCAAGTCAAAGGTGTACTGACTGAGCTGGAGAAGTTGCTTGTGCACGAACAAGTTCCAgtaagccata ... cttcatgcagTATCCAGTGTACTTTGCTTTGGATGACGACAATTTTGGTAACCTGCTGGCAGATATCCATAAAATTGCCTCTTCAGGCCAACCAGCCTCTGCAACAACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagttttctgtgtcatacaacgtcttggctaaactgtgtccattgcttcatgcagTATCCAGTGTACTTTGCTTTGGATGACGACAATTTTGGTAACCTGCTGGCAGATATCCATAAAATTGCCTCTTCAGGCCAACCAGCCTCTGCAACAACAG
                          ggctaaa  putative branch site (score: 98)
                                          ttgcttc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatcctgagataatctactcctattccctaattgcttgattaatccagttttctgtgtcatacaacgtcttggctaaactgtgtccattgcttcatgcagTATCCAGTGTACTTTGCTTTGGATGACGACAATTTTGGTAACCTGCTGGCAGATATCCATAAAATTGCCTCTTCAGGCCAACCAGCCTCTGCAACAACAG

gatcctg
- - - - - - - ctactcc
- - - - - - - - - - - - - - - - tgcttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - catacaa