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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gactgcagtttttacaagattttatggtcttgccgcttcatttttctgactgtttgcattggaccgataccttctgatggccttgtccgcctattttcagGTTCGCTACCAAAGCAGGAAGAGGCTTGCTGAGCAGCGGCCACGGGTCCGAGGACAGTTTGTGCGACAATCTGAGCAAGAAGATCAAACAGCGCAAGGTT

Basic information

species Zea mays
transcript GRMZM2G095727_T04
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G095727_T04 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os03g17570.5 (Oryza sativa), 3'ss of exon 11
gactgcagtttt----tacaagattttatggtcttgccgcttcatttttctgactgtttgcattggaccgatacctt-ctgatggccttgtccgcctattttcagGTTCGCTACCAAAGCAGGAAGAGGCTTGCTGAGCAGCGGCCACGGGTCCGAGGACAGTTTGTGCGACAATCTGAGCAAGAAGATCAAACAGCGCAAGGTT
     || ||||     | ||||   | |  |||||| | |     |  || |  ||| |||||| |||| || ||| |||||||| |||||||||||||||||||| ||||| || ||||| |||||| | ||||||||||| || ||| |||| || || || |||||||||||||  || ||||||||  |||  ||||   
----tcacttttgaggaaaaagacacttttttcttgctgttgtgcctgactaag-gttagcattgaaccggtatctttctgatggctttgtccgcctattttcagGTGCGCTATCAGAGCAGAAAGAGGTTGGCTGAGCAGCGCCCTCGGATCCGCGGGCAATTCGTGCGACAATCTGGACAGGAAGATCAGGCAGGCCAAGACG
















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|211517684|gb|FL470599.1|FL470599
EST:     AGAAGCTGCATTGAACAAATTCAGACTGAAGCGGAAAGATCGGAACTTTGGTAAAAAG                  
genomic: AGAAGCTGCATTGAACAAATTCAGACTGAAGCGGAAAGATCGGAAC-TT--T-----Ggtaaaaaggt ... cta
EST: gi|32849437|gb|CD989118.1|CD989118
EST:     AGAAGCTGCATTGAACAAATTCAGACTGAAGCGGAAAGATCGGAACTTTGGTAAAAAG                  
genomic: AGAAGCTGCATTGAACAAATTCAGACTGAAGCGGAAAGATCGGAAC-TT--T-----Ggtaaaaaggt ... cta
EST: gi|211517683|gb|FL470598.1|FL470598
EST:     AGAAGCTGCATTGAACAAATTCAGACTGAAGCGGAAAGATCGGAACTTTGGTAAAAAG                  
genomic: AGAAGCTGCATTGAACAAATTCAGACTGAAGCGGAAAGATCGGAAC-TT--T-----Ggtaaaaaggt ... cta
EST: gi|28983754|gb|BQ538748.2|BQ538748
EST:     AGAAGCTGCATTGAACAAATTCAGACTGAAGCGGAAAGATCGGAACTTTGGTAAAAAG                  
genomic: AGAAGCTGCATTGAACAAATTCAGACTGAAGCGGAAAGATCGGAAC-TT--T-----Ggtaaaaaggt ... cta
EST: gi|71429496|gb|DR810546.1|DR810546
EST:     AGAAGCTGCATTGAACAAATTCAGACTGAAGCGGAAAGATCGGAACTTTGGTAAAAAG                  
genomic: AGAAGCTGCATTGAACAAATTCAGACTGAAGCGGAAAGATCGGAAC-TT--T-----Ggtaaaaaggt ... cta
EST: gi|78086697|gb|DV515090.1|DV515090
EST:     AGAAGCTGCATTGAACAAATTCAGACTGAAGCGGAAAGATCGGAACTTTGGTAAAAAG                  
genomic: AGAAGCTGCATTGAACAAATTCAGACTGAAGCGGAAAGATCGGAAC-TT--T-----Ggtaaaaaggt ... cta
EST: gi|24934395|gb|CA452613.1|CA452613
EST:     AGAAGCTGCATTGAACAAATTCAGACTGAAGCGGAAAGATCGGAACTTTGGTAAAAAG                  
genomic: AGAAGCTGCATTGAACAAATTCAGACTGAAGCGGAAAGATCGGAAC-TT--T-----Ggtaaaaaggt ... cta
EST: gi|67041687|gb|CO467942.1|CO467942
EST:     AGAAGCTGCATTGAACAAATTCAGACTGAAGCGGAAAGATCGGAACTTTG                         GTAAAAAGGTTCGCTACCAAAGCAGGAAGAGGCTTGCTGAGCAGCGGCCAC
genomic: AGAAGCTGCATTGAACAAATTCAGACTGAAGCGGAAAGATCGGAACTTTGgtaaaaaggt ... ctattttcagGT-------T-CGCTACCAAAGCAGGAAGAGGCTTGCTGAGCAGCGGCCAC
EST: gi|37396419|gb|CF635500.1|CF635500
EST:     AGAAGCTGCATTGAACAAATTCAGACTGAAGCGGAAAGATCGGAACTTTGGTAAAAAG                  
genomic: AGAAGCTGCATTGAACAAATTCAGACTGAAGCGGAAAGATCGGAAC-TT--T-----Ggtaaaaaggt ... cta
EST: gi|9953402|gb|BE639985.1|BE639985
EST:     AGAAGCTGCATTGAACAAATTCAGACTGAAGCGGAAAGATCGGAACTTTG                         GTTCGCTACCAAAGCAGGAAGAGGCTTGCTGAGCAGCGGCCACGGGTCCGA
genomic: AGAAGCTGCATTGAACAAATTCAGACTGAAGCGGAAAGATCGGAACTTTGgtaaaaaggt ... ctattttcagGTTCGCTACCAAAGCAGGAAGAGGCTTGCTGAGCAGCGGCCACGGGTCCGA
EST: gi|5555423|gb|AI881374.1|AI881374
EST:     AGAAGCTGCATTGAACAAATTCAGACTGAAGCGGAAAGATCGGAACTTTGGTAAAAAG                  
genomic: AGAAGCTGCATTGAACAAATTCAGACTGAAGCGGAAAGATCGGAAC-TT--T-----Ggtaaaaaggt ... cta
EST: gi|5607707|gb|AI901374.1|AI901374
EST:     AGAAGCTGCATTGAACAAATTCAGACTGAAGCGGAAAGATCGGAACTTTGGTAAAAAG                  
genomic: AGAAGCTGCATTGAACAAATTCAGACTGAAGCGGAAAGATCGGAAC-TT--T-----Ggtaaaaaggt ... cta
EST: gi|60397823|gb|DN230639.1|DN230639
EST:     AGAAGCTGCATTGAACAAATTCAGACTGAAGCGGAAAGATCGGAACTTTGGTAAAAAG                  
genomic: AGAAGCTGCATTGAACAAATTCAGACTGAAGCGGAAAGATCGGAAC-TT--T-----Ggtaaaaaggt ... cta
EST: gi|32848172|gb|CD987853.1|CD987853
EST:     AGAAGCTGCATTGAACAAATTCAGACTGAAGCGGAAAGATCGGAACTTTGGTAAAAAG                  
genomic: AGAAGCTGCATTGAACAAATTCAGACTGAAGCGGAAAGATCGGAAC-TT--T-----Ggtaaaaaggt ... cta
EST: gi|45568110|gb|CK985907.1|CK985907
EST:     AGAAGCTGCATTGAACAAATTCAGACTGAAGCGGAAAGATCGGAACTTTGGTAAAAAG                  
genomic: AGAAGCTGCATTGAACAAATTCAGACTGAAGCGGAAAGATCGGAAC-TT--T-----Ggtaaaaaggt ... cta

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: 7

AGTGGGAGTGGGAGTGGCAATGACATGTATCAGAATCGGTTCCTGCAACGAGAAGCTGCATTGAACAAATTCAGACTGAAGCGGAAAGATCGGAACTTTGgtaaaaaggt ... ctattttcagGTTCGCTACCAAAGCAGGAAGAGGCTTGCTGAGCAGCGGCCACGGGTCCGAGGACAGTTTGTGCGACAATCTGAGCAAGAAGATCAAACAGCGCAAGGTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 9

AGTGGGAGTGGGAGTGGCAATGACATGTATCAGAATCGGTTCCTGCAACGAGAAGCTGCATTGAACAAATTCAGACTGAAGCGGAAAGATCGGAACTTTGgtaaaaaggt ... ctattttcagGTTCGCTACCAAAGCAGGAAGAGGCTTGCTGAGCAGCGGCCACGGGTCCGAGGACAGTTTGTGCGACAATCTGAGCAAGAAGATCAAACAGCGCAAGGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 6

AGTGGGAGTGGGAGTGGCAATGACATGTATCAGAATCGGTTCCTGCAACGAGAAGCTGCATTGAACAAATTCAGACTGAAGCGGAAAGATCGGAACTTTGgtaaaaaggt ... ctattttcagGTTCGCTACCAAAGCAGGAAGAGGCTTGCTGAGCAGCGGCCACGGGTCCGAGGACAGTTTGTGCGACAATCTGAGCAAGAAGATCAAACAGCGCAAGGTT


Block sizes: 36 (upstream exon), 49 (downstream exon)
Score: 10

AGTGGGAGTGGGAGTGGCAATGACATGTATCAGAATCGGTTCCTGCAACGAGAAGCTGCATTGAACAAATTCAGACTGAAGCGGAAAGATCGGAACTTTGgtaaaaaggt ... ctattttcagGTTCGCTACCAAAGCAGGAAGAGGCTTGCTGAGCAGCGGCCACGGGTCCGAGGACAGTTTGTGCGACAATCTGAGCAAGAAGATCAAACAGCGCAAGGTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgactgtttgcattggaccgataccttctgatggccttgtccgcctattttcagGTTCGCTACCAAAGCAGGAAGAGGCTTGCTGAGCAGCGGCCACGGGTCCGAGGACAGTTTGTGCGACAATCTGAGCAAGAAGATCAAACAGCGCAAGGTT
                                            cctattttc  CT-rich tract
                                              tattttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gactgcagtttttacaagattttatggtcttgccgcttcatttttctgactgtttgcattggaccgataccttctgatggccttgtccgcctattttcagGTTCGCTACCAAAGCAGGAAGAGGCTTGCTGAGCAGCGGCCACGGGTCCGAGGACAGTTTGTGCGACAATCTGAGCAAGAAGATCAAACAGCGCAAGGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA