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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcagtatttcacttgtttcatgccatgatatcattatcctactattccacaatatgctaatactggtggtgttgggtttgtcgcgtagACGGATGACGAGAAGGAAATGGTCATGCGAACTGTCTATTGTACAAACATAGATAAGATG

Basic information

species Zea mays
transcript GRMZM2G051043_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G051043_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g11120.1 (Oryza sativa), 3'ss of exon 5
gtgagc---agtatttcac---ttgtttcatgccatgatatc---attatcctactattccacaatatgctaatactggtg--gtgttgggtttgtcgcgtagACGGATGACGAGAAGGAAATGGTCATGCGAACTGTCTATTGTACAAACATAGATAAGATG
|| ||     |||||  |    ||||||||     ||||  |   ||||| |  ||  ||||||  |   || ||||  |   |||||| || || | | |||||||| || |||||||||||||||||  ||||||| |||||||||||||||||||||| |
gtaagttcttgtattgtatgcgttgtttcaccttttgatgccagaattattcctcttctccacataaccttagtactcatactgtgttgtgtctggcccatagACGGAGGATGAGAAGGAAATGGTCATAAGAACTGTTTATTGTACAAACATAGATAAGAAG
















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|78180075|gb|DV550448.1|DV550448
EST:     TGCCGTCAAAGACAGCTATCTTACCTGTTAATCCAAAGTTTCTTCCCAGG                         ACGGATGACGAGAAGGAAATGGTCATGCGAACTGTCTATTGTACAAACATA
genomic: TGCCGTCAAAGACAGCTATCTTACCTGTTAATCCAAAGTTTCTTCCCAGGgtgagcagta ... tgtcgcgtagACGGATGACGAGAAGGAAATGGTCATGCGAACTGTCTATTGTACAAACATA
EST: gi|108823990|gb|EC277998.1|EC277998
EST:     TGCCGTCAAAGACAGCTATCTTACCTGTTAATCCAAAGTTTCTTCCCAGG                         ACGGATGACGAGAAGGAAATGGTCATGCGAACTGTCTATTGTACAAACATA
genomic: TGCCGTCAAAGACAGCTATCTTACCTGTTAATCCAAAGTTTCTTCCCAGGgtgagcagta ... tgtcgcgtagACGGATGACGAGAAGGAAATGGTCATGCGAACTGTCTATTGTACAAACATA
EST: gi|108953255|gb|EC364659.1|EC364659
EST:     TGCCGTCAAAGACAGCTATCTTACCTGTTAATCCAAAGTTTCTTCCCAGG                         ACGGATGACGAGAAGGAAATGGTCATGCGAACTGTCTATTGTACAAACATA
genomic: TGCCGTCAAAGACAGCTATCTTACCTGTTAATCCAAAGTTTCTTCCCAGGgtgagcagta ... tgtcgcgtagACGGATGACGAGAAGGAAATGGTCATGCGAACTGTCTATTGTACAAACATA
EST: gi|4730461|gb|AI649627.1|AI649627
EST:     TGCCGTCAAAGACAGCTATCTTACCTGTTAATCCAAAGTTTCTTCCCAGG                         ACGGATGACGAGAAGGAAATGGTCATGCGAACTGTCTATTG
genomic: TGCCGTCAAAGACAGCTATCTTACCTGTTAATCCAAAGTTTCTTCCCAGGgtgagcagta ... tgtcgcgtagACGGATGACGAGAAGGAAATGGTCATGCGAACTGTCTATTG
EST: gi|61236519|gb|DN586269.1|DN586269
EST:     TGCCGTCAAAGACAGCTATCTTACCTGTTAATCCAAAGTTTCTTCCCAGG                         ACGGATGACGAGAAGGAAATGGTCATGCGAACTGTCTATTGTACAAACATA
genomic: TGCCGTCAAAGACAGCTATCTTACCTGTTAATCCAAAGTTTCTTCCCAGGgtgagcagta ... tgtcgcgtagACGGATGACGAGAAGGAAATGGTCATGCGAACTGTCTATTGTACAAACATA
EST: gi|12046008|gb|BF728043.1|BF728043
EST:     TGCCGTCAAAGACAGCTATCTTACCTGTTAATCCAAAGTTTCTTCCCAGG                         ACGGATGACGAGAAGGAAATGGTCATGCGAACTGTCTATTGTACAAACATA
genomic: TGCCGTCAAAGACAGCTATCTTACCTGTTAATCCAAAGTTTCTTCCCAGGgtgagcagta ... tgtcgcgtagACGGATGACGAGAAGGAAATGGTCATGCGAACTGTCTATTGTACAAACATA
EST: gi|38502629|gb|CF972489.1|CF972489
EST:     TGCCGTCAAAGACAGCTATCTTACCTGTTAATCCAAAGTTTCTTCCCAGG                         ACGGATGACGAGAAGGAAATGGTCATGCGAACTGTCTATTGTACAAACATA
genomic: TGCCGTCAAAGACAGCTATCTTACCTGTTAATCCAAAGTTTCTTCCCAGGgtgagcagta ... tgtcgcgtagACGGATGACGAGAAGGAAATGGTCATGCGAACTGTCTATTGTACAAACATA
EST: gi|4730460|gb|AI649626.1|AI649626
EST:     TGCCGTCAAAGACAGCTATCTTACCTGTTAATCCAAAGTTTCTTCCCAGG                         ACGGATGACGAGAAGGAAATGGTCATGCGAACTGTCTATTGTACAAACATA
genomic: TGCCGTCAAAGACAGCTATCTTACCTGTTAATCCAAAGTTTCTTCCCAGGgtgagcagta ... tgtcgcgtagACGGATGACGAGAAGGAAATGGTCATGCGAACTGTCTATTGTACAAACATA
EST: gi|33771172|gb|CF272833.1|CF272833
EST:     TGCCGTCAAAGACAGCTATCTTACCTGTTAATCCAAAGTTTCTTCCCAGG                         ACGGATGACGAGAAGGAAATGGTCATGCGAACTGTCTATTGTACAAACATA
genomic: TGCCGTCAAAGACAGCTATCTTACCTGTTAATCCAAAGTTTCTTCCCAGGgtgagcagta ... tgtcgcgtagACGGATGACGAGAAGGAAATGGTCATGCGAACTGTCTATTGTACAAACATA
EST: gi|6827432|gb|AW331075.1|AW331075
EST:     TGCCGTCAAAGACAGCTATCTTACCTGTTAATCCAAAGTTTCTTCCCAGG                         ACGGATGACGAGAAGGAAATGGTCATGCGAACTGTCTATTGTACAAACATA
genomic: TGCCGTCAAAGACAGCTATCTTACCTGTTAATCCAAAGTTTCTTCCCAGGgtgagcagta ... tgtcgcgtagACGGATGACGAGAAGGAAATGGTCATGCGAACTGTCTATTGTACAAACATA

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: 85

TGCGCTTAACCTGGGAGGCACAATTTTTGGTTTCTACCCTGTTAGAGTTTTGCCGTCAAAGACAGCTATCTTACCTGTTAATCCAAAGTTTCTTCCCAGGgtgagcagta ... tgtcgcgtagACGGATGACGAGAAGGAAATGGTCATGCGAACTGTCTATTGTACAAACATAGATAAGATG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 113

TGCGCTTAACCTGGGAGGCACAATTTTTGGTTTCTACCCTGTTAGAGTTTTGCCGTCAAAGACAGCTATCTTACCTGTTAATCCAAAGTTTCTTCCCAGGgtgagcagta ... tgtcgcgtagACGGATGACGAGAAGGAAATGGTCATGCGAACTGTCTATTGTACAAACATAGATAAGATG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 190

TGCGCTTAACCTGGGAGGCACAATTTTTGGTTTCTACCCTGTTAGAGTTTTGCCGTCAAAGACAGCTATCTTACCTGTTAATCCAAAGTTTCTTCCCAGGgtgagcagta ... tgtcgcgtagACGGATGACGAGAAGGAAATGGTCATGCGAACTGTCTATTGTACAAACATAGATAAGATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 141

TGCGCTTAACCTGGGAGGCACAATTTTTGGTTTCTACCCTGTTAGAGTTTTGCCGTCAAAGACAGCTATCTTACCTGTTAATCCAAAGTTTCTTCCCAGGgtgagcagta ... tgtcgcgtagACGGATGACGAGAAGGAAATGGTCATGCGAACTGTCTATTGTACAAACATAGATAAGATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatcctactattccacaatatgctaatactggtggtgttgggtttgtcgcgtagACGGATGACGAGAAGGAAATGGTCATGCGAACTGTCTATTGTACAAACATAGATAAGATG
                     tgctaat  putative branch site (score: 141)
      tactatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcagtatttcacttgtttcatgccatgatatcattatcctactattccacaatatgctaatactggtggtgttgggtttgtcgcgtagACGGATGACGAGAAGGAAATGGTCATGCGAACTGTCTATTGTACAAACATAGATAAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG