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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgaatttctagtcgaactttttatatggcatccataactagctctgcatgtagaaatattgtacatttgtaactaaaaagtcttgctgaatcccaatagGACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTGGTCGTGGTGGCCATTGCTCTCCTGGGAATGCTACTGGGATATATCATGA

Basic information

species Zea mays
transcript GRMZM2G155543_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155543_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os04g45190.1 (Oryza sativa), 3'ss of exon 8
--atgaatttctagt-cgaactttttatatggcatccataactagctctgcatgtagaaatattgtacatttgtaactaaaaagtcttgctgaatcccaatagGACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTGGTCGTGGTGGCCATTGCTCTCCTGGGAATGCTACTGGGATATATCATGA
  ||| | |  |  |   |      ||  ||   |   | | | |   ||||  || ||  ||   |   ||||||  ||  | |  |  ||||||  || ||||||||  ||||||||||   | ||||||||||||||| ||| | |||||| ||||||||| | ||||||| |||||||| |||||||| ||||||||||
ttatgcagtgttgctataagggaaatacttgttgtattttatttg---tgcacataaaaccatgaaattgttgtaatcaagcatttcttttgaatcttaacagGACCTTGTGAGGAGGGAAATTAGCAAGCAGAATGGTGGTTTCCCTTTTGTGTTCGTGGTGGTCGTTGCTCTTCTGGGAATTCTACTGGGGTATATCATGA
















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|18166590|gb|BM336429.1|BM336429
EST:     AGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTTCGAGAGGAACTG                         GACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTG
genomic: AGAGAGAAACTCTGCCATTCAGCAGAACAATAAGC-TTCGAGAGGAACTGgttagtgcat ... atcccaatagGACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTG
EST: gi|71772475|gb|DR970407.1|DR970407
EST:     AAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTG                         GACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTG
genomic: AAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTGgttagtgcat ... atcccaatagGACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTG
EST: gi|7227720|gb|AW566361.1|AW566361
EST:     AAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTG                         GACCTTACGAGGAGGGAAGCCAGCAAGCAGAATGGTGGATTCTCCTTTGTG
genomic: AAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTGgttagtgcat ... atcccaatagGACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTG
EST: gi|29946302|gb|CB816081.1|CB816081
EST:     AAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTG                         GACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTG
genomic: AAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTGgttagtgcat ... atcccaatagGACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTG
EST: gi|76935911|gb|DV174526.1|DV174526
EST:     AAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTG                         GACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTG
genomic: AAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTGgttagtgcat ... atcccaatagGACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTG
EST: gi|93281411|gb|EB673675.1|EB673675
EST:     AAGAGAGAAAATCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTG                         GACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTG
genomic: AAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTGgttagtgcat ... atcccaatagGACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTG
EST: gi|76929778|gb|DV172159.1|DV172159
EST:     AAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTG                         GACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTG
genomic: AAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTGgttagtgcat ... atcccaatagGACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTG
EST: gi|91049216|gb|EB159634.1|EB159634
EST:     AAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTG                         GACCTTTCGAGGAGGGAAGCCAACAAGCCGAATGGTGGATTTTCCTTTGTG
genomic: AAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTGgttagtgcat ... atcccaatagGACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTG
EST: gi|211349055|gb|FL306904.1|FL306904
EST:     AAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTG                         GACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTG
genomic: AAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTGgttagtgcat ... atcccaatagGACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTG
EST: gi|7216902|gb|AW563024.1|AW563024
EST:     AAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTG                         GACCTTACGAGGAGGGAAGCCAGCAAGCAGAATGGTGGATTCTCCTTTGTG
genomic: AAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTGgttagtgcat ... atcccaatagGACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTG
EST: gi|60347102|gb|DN214075.1|DN214075
EST:     AAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTG                         GACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTG
genomic: AAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTGgttagtgcat ... atcccaatagGACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTG
EST: gi|71303117|gb|DR787664.1|DR787664
EST:     AAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTG                         GACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTG
genomic: AAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTGgttagtgcat ... atcccaatagGACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTG
EST: gi|71432736|gb|DR813786.1|DR813786
EST:     AAGAGAGAAATTTTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTG                         GCCCTTACGAGGAGGGAAGCCAACAAGCAGAATGGGGGATTTTCCTTTGTG
genomic: AAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTGgttagtgcat ... atcccaatagGACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTG
EST: gi|83278536|gb|DV942544.1|DV942544
EST:     AAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTG                         GACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTG
genomic: AAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTGgttagtgcat ... atcccaatagGACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTG
EST: gi|74242014|gb|DT649928.1|DT649928
EST:     AAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTG                         GACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTG
genomic: AAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTGgttagtgcat ... atcccaatagGACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTG
EST: gi|149109098|gb|EE293135.2|EE293135
EST:     AAGAGAGAAACTTTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTG                         GACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTTTCCTTTGTG
genomic: AAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTGgttagtgcat ... atcccaatagGACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTG
EST: gi|211179444|gb|FL364372.1|FL364372
EST:     AAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTG                         GACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTG
genomic: AAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTGgttagtgcat ... atcccaatagGACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTG
EST: gi|101381660|gb|EB812887.1|EB812887
EST:     AAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTG                         GACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTTTCCTTTGTG
genomic: AAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTGgttagtgcat ... atcccaatagGACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTG
EST: gi|211127671|gb|FL432566.1|FL432566
EST:     AAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTG                         GACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTG
genomic: AAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTGgttagtgcat ... atcccaatagGACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTG
EST: gi|60396382|gb|DN229251.1|DN229251
EST:     AAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTG                         GACCTTACGAGGAGGGAAGCCAGCAAGCAGAATGGTGGATTCTCCTTTGTG
genomic: AAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTGgttagtgcat ... atcccaatagGACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTG
EST: gi|78073696|gb|DV502130.1|DV502130
EST:     AAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTG                         GACCTTGCGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTTTCCTTTGTG
genomic: AAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTGgttagtgcat ... atcccaatagGACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTG
EST: gi|4647574|gb|AI622649.1|AI622649
EST:     AAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTG                         GCCCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTG
genomic: AAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTGgttagtgcat ... atcccaatagGACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTG
EST: gi|76011373|gb|DT938543.1|DT938543
EST:     AAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTG                         GACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTG
genomic: AAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTGgttagtgcat ... atcccaatagGACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTG
EST: gi|74240612|gb|DT648526.1|DT648526
EST:     AAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTG                         GACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTG
genomic: AAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTGgttagtgcat ... atcccaatagGACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTG
EST: gi|71431011|gb|DR812061.1|DR812061
EST:     AAGAGAGAAATTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTG                         GCCCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTG
genomic: AAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTGgttagtgcat ... atcccaatagGACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTG
EST: gi|78545068|gb|DV622566.1|DV622566
EST:     AAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTG                         GACCTTACGAGGAGGGAAGCCAGCAAGCAGAATGGTGGATTCTCCTTTGTG
genomic: AAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTGgttagtgcat ... atcccaatagGACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTG

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), 47 (downstream exon)
Score: 248

ACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTGgttagtgcat ... atcccaatagGACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTGGTCGTGGTGGCCATTGCTCTCCTGGGAATGCTACTGGGATATATCATGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 91

ACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTGgttagtgcat ... atcccaatagGACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTGGTCGTGGTGGCCATTGCTCTCCTGGGAATGCTACTGGGATATATCATGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 67

ACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTGgttagtgcat ... atcccaatagGACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTGGTCGTGGTGGCCATTGCTCTCCTGGGAATGCTACTGGGATATATCATGA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 198

ACATCTGCTTTGATTTCAAAGTTGACAGAAGAGAGAAACTCTGCCATTCAGCAGAACAATAAGCTTCGAGAGGAACTGgttagtgcat ... atcccaatagGACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTGGTCGTGGTGGCCATTGCTCTCCTGGGAATGCTACTGGGATATATCATGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcatgtagaaatattgtacatttgtaactaaaaagtcttgctgaatcccaatagGACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTGGTCGTGGTGGCCATTGCTCTCCTGGGAATGCTACTGGGATATATCATGA
                          aactaaa  putative branch site (score: 198)
         aaatattgtacattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgaatttctagtcgaactttttatatggcatccataactagctctgcatgtagaaatattgtacatttgtaactaaaaagtcttgctgaatcccaatagGACCTTACGAGGAGGGAAGCCAACAAGCAGAATGGTGGATTCTCCTTTGTGGTCGTGGTGGCCATTGCTCTCCTGGGAATGCTACTGGGATATATCATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG