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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaattccattggctattctggacatgatcgaagaaagggagaaatggatgctccttacagcatacaaatatcttagtatgattgtcctgatttgtacagGTAAGTTTGAGAGAACCCATCCGTACTGGTGTTGATGACGCTGGACTGAAGGAGATAATTGGTGCCGCG

Basic information

species Zea mays
transcript GRMZM2G135816_T01
intron # 4
splice site 3'
intron type U2

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|5058882|gb|AI737358.1|AI737358
EST:     TCAAGGTGTGCTTATTTGGCCCCTCAGAG                         GTAAGTTTGAGAGACCCCATCCGTTCTGGTGTTGATGACGCTGGACTGAAG
genomic: TCAAGGTGTGCTTATTTGGCCCCTCAGAGgtatgccgta ... atttgtacagGTAAGTTTGAGAGAACCCATCCGTACTGGTGTTGATGACGCTGGACTGAAG
EST: gi|6020607|gb|AW065640.1|AW065640
EST:     GGTTATTGGCTGATGGAAACCTCAAGGTGTGCTTATTTGGCCCCTCAGAG                         GTAAGTTTGAGAGAACCCATCCGTACTGGTGTTGATGACGCTGGACTGAAG
genomic: GGTTATTGGCTGATGGAAACCTCAAGGTGTGCTTATTTGGCCCCTCAGAGgtatgccgta ... atttgtacagGTAAGTTTGAGAGAACCCATCCGTACTGGTGTTGATGACGCTGGACTGAAG
EST: gi|6194756|gb|AW146860.1|AW146860
EST:     GGTTATTGGCTGATGGAAACCTCAAGGTGTGCTTATTTGGCCCCTCAGAG                         GTAAGTTTGAGAGAACCCATCCGTACTGGTGTTGATGACGCTGGACTGAAG
genomic: GGTTATTGGCTGATGGAAACCTCAAGGTGTGCTTATTTGGCCCCTCAGAGgtatgccgta ... atttgtacagGTAAGTTTGAGAGAACCCATCCGTACTGGTGTTGATGACGCTGGACTGAAG
EST: gi|78090417|gb|DV518791.1|DV518791
EST:     GGTTATTGGCTGATGGAAACCTCAAGGTGTGCTTATTTGGCCCCTCAGAG                         GTAAGTTTGAGAGAACCCATCCGTACTGGTGTTGATGACGCTGGACTGAAG
genomic: GGTTATTGGCTGATGGAAACCTCAAGGTGTGCTTATTTGGCCCCTCAGAGgtatgccgta ... atttgtacagGTAAGTTTGAGAGAACCCATCCGTACTGGTGTTGATGACGCTGGACTGAAG
EST: gi|149048405|gb|EE048313.2|EE048313
EST:     GGTTATTGGCTGATGGAAACCTCAAGGTGTGCTTATTTGGCCCCTCAGAG                         GTAAGTTTGAGAGAACCCATCCGTACTGGTGTTGATGACGCTGGACTGAAG
genomic: GGTTATTGGCTGATGGAAACCTCAAGGTGTGCTTATTTGGCCCCTCAGAGgtatgccgta ... atttgtacagGTAAGTTTGAGAGAACCCATCCGTACTGGTGTTGATGACGCTGGACTGAAG
EST: gi|91054281|gb|EB164699.1|EB164699
EST:     GGTTATTGGCTGATGGAAACCTCAAGGTGTGCTTATTTGGCCCCTCAGAG                         GTAAGTTTGAGAGAACCCATCCGTACTGGTGTTGATGACGCTGGACTGAAG
genomic: GGTTATTGGCTGATGGAAACCTCAAGGTGTGCTTATTTGGCCCCTCAGAGgtatgccgta ... atttgtacagGTAAGTTTGAGAGAACCCATCCGTACTGGTGTTGATGACGCTGGACTGAAG
EST: gi|16378519|gb|BI992468.1|BI992468
EST:     GGTTATTGGCTGATGGAANCCTCAAGGTGTGCTTATTTGGCCCCTCAGAG                         GTAAGTTTGAGAGAACCCATCCGTACTGGTGTTGATGACGCTGGACTGAAG
genomic: GGTTATTGGCTGATGGAAACCTCAAGGTGTGCTTATTTGGCCCCTCAGAGgtatgccgta ... atttgtacagGTAAGTTTGAGAGAACCCATCCGTACTGGTGTTGATGACGCTGGACTGAAG
EST: gi|13249841|gb|BG360746.1|BG360746
EST:     TGGCTGATGGAAACCTCAAGGTGTGCTTATTTGGCCCCTCAGAG                         GTAAGTTTGAGAGAACCCATCCGTACTGGTGTTGATGACGCTGGACTGAAG
genomic: TGGCTGATGGAAACCTCAAGGTGTGCTTATTTGGCCCCTCAGAGgtatgccgta ... atttgtacagGTAAGTTTGAGAGAACCCATCCGTACTGGTGTTGATGACGCTGGACTGAAG
EST: gi|91874219|gb|EB404176.1|EB404176
EST:     GGTTATTGGCTGATGGAAACCTCAAGGTGTGGTTATTTGGCCCCTCAGAG                         GTAAGTTTGAGAGAACCCATCCGTACTGGTGTTGATGACGCTGGACTGAAG
genomic: GGTTATTGGCTGATGGAAACCTCAAGGTGTGCTTATTTGGCCCCTCAGAGgtatgccgta ... atttgtacagGTAAGTTTGAGAGAACCCATCCGTACTGGTGTTGATGACGCTGGACTGAAG
EST: gi|32859387|gb|CD999068.1|CD999068
EST:     GGTTATTGGCTGATGGAAACCTCAAGGTGTGCTTATTTGGCCCCTCAGAG                         GTAAGTTTGAGAGAACCCATCCGTACTGGTGTTGATGACGCTGGACTGAAG
genomic: GGTTATTGGCTGATGGAAACCTCAAGGTGTGCTTATTTGGCCCCTCAGAGgtatgccgta ... atttgtacagGTAAGTTTGAGAGAACCCATCCGTACTGGTGTTGATGACGCTGGACTGAAG
EST: gi|148946521|gb|EC891833.2|EC891833
EST:     GGTTATTGGCTGATGGAAACCTCAAGGTGTGCTTATTTGGCCCCTCAGAG                         GTAAGTTTGAGAGAACCCATCCGTACTGGTGTTGATGACGCTGGACTGAAG
genomic: GGTTATTGGCTGATGGAAACCTCAAGGTGTGCTTATTTGGCCCCTCAGAGgtatgccgta ... atttgtacagGTAAGTTTGAGAGAACCCATCCGTACTGGTGTTGATGACGCTGGACTGAAG
EST: gi|148928476|gb|EE285290.2|EE285290
EST:     GGTTATTGGCTGATGGAAACCTCAAGGTGTGCTTATTTGGCCCCTCAGAG                         GTAAGTTTGAGAGAACCCATCCGTACTGGTGTTGATGACGCTGGACTGAAG
genomic: GGTTATTGGCTGATGGAAACCTCAAGGTGTGCTTATTTGGCCCCTCAGAGgtatgccgta ... atttgtacagGTAAGTTTGAGAGAACCCATCCGTACTGGTGTTGATGACGCTGGACTGAAG

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: 46 (upstream exon), 46 (downstream exon)
Score: 19

ATTTATTACATCAATGACAGAGCATTTTTGTGCTGGCTGCAATAGATTACGGTTATTGGCTGATGGAAACCTCAAGGTGTGCTTATTTGGCCCCTCAGAGgtatgccgta ... atttgtacagGTAAGTTTGAGAGAACCCATCCGTACTGGTGTTGATGACGCTGGACTGAAGGAGATAATTGGTGCCGCG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 142

ATTTATTACATCAATGACAGAGCATTTTTGTGCTGGCTGCAATAGATTACGGTTATTGGCTGATGGAAACCTCAAGGTGTGCTTATTTGGCCCCTCAGAGgtatgccgta ... atttgtacagGTAAGTTTGAGAGAACCCATCCGTACTGGTGTTGATGACGCTGGACTGAAGGAGATAATTGGTGCCGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 165

ATTTATTACATCAATGACAGAGCATTTTTGTGCTGGCTGCAATAGATTACGGTTATTGGCTGATGGAAACCTCAAGGTGTGCTTATTTGGCCCCTCAGAGgtatgccgta ... atttgtacagGTAAGTTTGAGAGAACCCATCCGTACTGGTGTTGATGACGCTGGACTGAAGGAGATAATTGGTGCCGCG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 89

ATTTATTACATCAATGACAGAGCATTTTTGTGCTGGCTGCAATAGATTACGGTTATTGGCTGATGGAAACCTCAAGGTGTGCTTATTTGGCCCCTCAGAGgtatgccgta ... atttgtacagGTAAGTTTGAGAGAACCCATCCGTACTGGTGTTGATGACGCTGGACTGAAGGAGATAATTGGTGCCGCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggatgctccttacagcatacaaatatcttagtatgattgtcctgatttgtacagGTAAGTTTGAGAGAACCCATCCGTACTGGTGTTGATGACGCTGGACTGAAGGAGATAATTGGTGCCGCG
                 atacaaatatctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaattccattggctattctggacatgatcgaagaaagggagaaatggatgctccttacagcatacaaatatcttagtatgattgtcctgatttgtacagGTAAGTTTGAGAGAACCCATCCGTACTGGTGTTGATGACGCTGGACTGAAGGAGATAATTGGTGCCGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - -catgatc
- - - - - - - - - - - - - - - gaagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcataca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtcctg