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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtacatcgatctgtacaagctaggaggtcagtacatcgatctctacaaggtgctcttgtgcattattcagGAGTTCGGGAAGATGAAGGAGAGAGCGCCGGAGAACTTCCGGGTCGACTACGCCGTCAGCCGGGAGCAGACGAACGCGGCGGGGGAGAGGATGTACATCC

Basic information

species Zea mays
transcript GRMZM2G168143_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G168143_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os06g01850.1 (Oryza sativa), 3'ss of exon 6
----gtcagtacatcgatctgtacaag-----ctaggaggtcagtac---atcgatctctacaaggtgctct-tgtgcatt-------attcagGAGTTCGGGAAGATGAAGGAGAGAGCGCCGGAGAACTTCCGGGTCGACTACGCCGTCAGCCGGGAGCAGACGAACGCGGCGGGGGAGAGGATGTACATCC
    |    |||||  |||| | ||||     ||   |  |  ||     |  ||  |     |  ||| || | || |||       ||||||||||| |  || ||||||| || |||||| ||||||||||||||||| || || || ||| |||||||||| || ||    || |||| ||||||||| |
gtcagcttatacatacatctctgcaagtgctactgctacttttgtgtgctactgaaattcctcacttgcactgtatgtatttgttaaaattcagGAGTTTGACAAAATGAAGGCGAAAGCGCCAGAGAACTTCCGGGTCGATTATGCTGTGAGCAGGGAGCAGACCAATGCTCAAGGAGAGAAGATGTACATTC
















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|6696066|gb|AW289174.1|AW289174
EST:     GCTGGCTCTTCCTGGGTGTTCCAACGAGCAGCTCGTTGCTCTACAAGGAG                         GAGTTCGGGAAGATGAAGGAGAGAGCGCCGGAGAACTTCCGGGTCGACTAC
genomic: GCTGGCTCTTCCTGGGTGTTCCAACGAGCAGCTCGTTGCTCTACAAGGAGgtcagtacat ... cattattcagGAGTTCGGGAAGATGAAGGAGAGAGCGCCGGAGAACTTCCGGGTCGACTAC
EST: gi|8929977|gb|BE224741.1|BE224741
EST:     GCTGGCTCTTCCTGGGTGTTCCAACGAGCAGCTCGTTGCTCTACAAGGAG                         GAGTTCGGGAAGATGAAGGAGAGAGCGCCGGAGAACTTCCGGGTCGACTAC
genomic: GCTGGCTCTTCCTGGGTGTTCCAACGAGCAGCTCGTTGCTCTACAAGGAGgtcagtacat ... cattattcagGAGTTCGGGAAGATGAAGGAGAGAGCGCCGGAGAACTTCCGGGTCGACTAC
EST: gi|32844649|gb|CD984330.1|CD984330
EST:     GCTGGCTCTTCCTGGGTGTTCCAACGAGCAGCTCGTTGCTCTCCAAGGAG                         GAGTTCGGGAAGATGAAGGAGAGAGCGCCGGAGAACTTCCGGGTCGACTAC
genomic: GCTGGCTCTTCCTGGGTGTTCCAACGAGCAGCTCGTTGCTCTACAAGGAGgtcagtacat ... cattattcagGAGTTCGGGAAGATGAAGGAGAGAGCGCCGGAGAACTTCCGGGTCGACTAC
EST: gi|32843935|gb|CD983616.1|CD983616
EST:     GCTGGCTCTTCCTGGGTGTTCCAACGAGCAGCTCGTTGCTCTACAAGGAG                         GAGTTCGGGAAGATGAAGGAGAGAGCGCCGGAGAACTTCCGGGTCGACTAC
genomic: GCTGGCTCTTCCTGGGTGTTCCAACGAGCAGCTCGTTGCTCTACAAGGAGgtcagtacat ... cattattcagGAGTTCGGGAAGATGAAGGAGAGAGCGCCGGAGAACTTCCGGGTCGACTAC
EST: gi|71441571|gb|DR822621.1|DR822621
EST:     GCTGGCTCTTCCTGGGTGTTCCAACGAGCAGCTCGTTGCTCTACAAGGAG                         GAGTTCGGGAAGATGAAGGAGAGAGCGCCGGAGAACTTCCGGGTCGATTAC
genomic: GCTGGCTCTTCCTGGGTGTTCCAACGAGCAGCTCGTTGCTCTACAAGGAGgtcagtacat ... cattattcagGAGTTCGGGAAGATGAAGGAGAGAGCGCCGGAGAACTTCCGGGTCGACTAC
EST: gi|32844588|gb|CD984269.1|CD984269
EST:     GCTGGCTCTTCCTGGGTGTTCCAACGAGCAGCTCGTTGCTCTACAAGGAG                         GAGTTCGGGAAGATGAAGGAGAGAGCGCCGGAGAACTTCCGGGTCGACTAC
genomic: GCTGGCTCTTCCTGGGTGTTCCAACGAGCAGCTCGTTGCTCTACAAGGAGgtcagtacat ... cattattcagGAGTTCGGGAAGATGAAGGAGAGAGCGCCGGAGAACTTCCGGGTCGACTAC
EST: gi|32923856|gb|CF028668.1|CF028668
EST:     GCTGGCTCTTCCTGGGTGTTCCAACGAGCAGCTCGTTGCTCTACAAGGAG                         GAGTTCGGGAAGATGAAGGAGAGAGCGCCGGAGAACTTCCGGGTCGACTAC
genomic: GCTGGCTCTTCCTGGGTGTTCCAACGAGCAGCTCGTTGCTCTACAAGGAGgtcagtacat ... cattattcagGAGTTCGGGAAGATGAAGGAGAGAGCGCCGGAGAACTTCCGGGTCGACTAC
EST: gi|89246872|gb|DY618658.1|DY618658
EST:     GCTGGCTCTTCCTGGGTGTTCCAACGAGCAGCTCGTTGCTCTACAAGGAG                         GAGTTCGGGAAGATGAAGGAGAGAGCGCCGGAGAACTTCCGGGTCGATTAC
genomic: GCTGGCTCTTCCTGGGTGTTCCAACGAGCAGCTCGTTGCTCTACAAGGAGgtcagtacat ... cattattcagGAGTTCGGGAAGATGAAGGAGAGAGCGCCGGAGAACTTCCGGGTCGACTAC
EST: gi|32848617|gb|CD988298.1|CD988298
EST:     GCTGGCTCTTCCTGGGTGTTCCAACGAGCAGCTCGTTGCTCTACAAGGAG                         GAGTTCGGGAAGATGAAGGAGAGAGCGCCGGAGAACTTCCGGGTCGACTAC
genomic: GCTGGCTCTTCCTGGGTGTTCCAACGAGCAGCTCGTTGCTCTACAAGGAGgtcagtacat ... cattattcagGAGTTCGGGAAGATGAAGGAGAGAGCGCCGGAGAACTTCCGGGTCGACTAC
EST: gi|8665549|gb|BE186365.1|BE186365
EST:     GCTGGCTCTTCCTGGGTGTTCCAACGAGCAGCTCGTTGCTCTACAAGGAG                         GAGTTCGGGAAGATGAAGGAGAGAGCGCCGGAGAACTTCCGGGTCGACTAC
genomic: GCTGGCTCTTCCTGGGTGTTCCAACGAGCAGCTCGTTGCTCTACAAGGAGgtcagtacat ... cattattcagGAGTTCGGGAAGATGAAGGAGAGAGCGCCGGAGAACTTCCGGGTCGACTAC
EST: gi|76923045|gb|DV169307.1|DV169307
EST:     GCTGGCTCTTCCTGGGTGTTCCAACGAGCAGCTCGTTGCTCTACAAGGAG                         GAGTTCGGGAAGATGAAGGAGAGAGCGCCGGAGAACTTCCGGGTCGACTAC
genomic: GCTGGCTCTTCCTGGGTGTTCCAACGAGCAGCTCGTTGCTCTACAAGGAGgtcagtacat ... cattattcagGAGTTCGGGAAGATGAAGGAGAGAGCGCCGGAGAACTTCCGGGTCGACTAC
EST: gi|78122840|gb|DV541224.1|DV541224
EST:     GCTGGCTCTTCCTGGGTGTTCCAACGAGCAGCTCGTTGCTCTACAAGGAG                         GAGTTCGGGAAGATGAAGGAGAGAGCGCCGGAGAACTTCCGGGTCGACTAC
genomic: GCTGGCTCTTCCTGGGTGTTCCAACGAGCAGCTCGTTGCTCTACAAGGAGgtcagtacat ... cattattcagGAGTTCGGGAAGATGAAGGAGAGAGCGCCGGAGAACTTCCGGGTCGACTAC

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: 39

TTCAACGGTCTGGGCTGGCTCTTCCTGGGTGTTCCAACGAGCAGCTCGTTGCTCTACAAGGAGgtcagtacat ... cattattcagGAGTTCGGGAAGATGAAGGAGAGAGCGCCGGAGAACTTCCGGGTCGACTACGCCGTCAGCCGGGAGCAGACGAACGCGGCGGGGGAGAGGATGTACATCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 121

TTCAACGGTCTGGGCTGGCTCTTCCTGGGTGTTCCAACGAGCAGCTCGTTGCTCTACAAGGAGgtcagtacat ... cattattcagGAGTTCGGGAAGATGAAGGAGAGAGCGCCGGAGAACTTCCGGGTCGACTACGCCGTCAGCCGGGAGCAGACGAACGCGGCGGGGGAGAGGATGTACATCC


Block sizes: 45 (upstream exon), 33 (downstream exon)
Score: 10

TTCAACGGTCTGGGCTGGCTCTTCCTGGGTGTTCCAACGAGCAGCTCGTTGCTCTACAAGGAGgtcagtacat ... cattattcagGAGTTCGGGAAGATGAAGGAGAGAGCGCCGGAGAACTTCCGGGTCGACTACGCCGTCAGCCGGGAGCAGACGAACGCGGCGGGGGAGAGGATGTACATCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 115

TTCAACGGTCTGGGCTGGCTCTTCCTGGGTGTTCCAACGAGCAGCTCGTTGCTCTACAAGGAGgtcagtacat ... cattattcagGAGTTCGGGAAGATGAAGGAGAGAGCGCCGGAGAACTTCCGGGTCGACTACGCCGTCAGCCGGGAGCAGACGAACGCGGCGGGGGAGAGGATGTACATCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagctaggaggtcagtacatcgatctctacaaggtgctcttgtgcattattcagGAGTTCGGGAAGATGAAGGAGAGAGCGCCGGAGAACTTCCGGGTCGACTACGCCGTCAGCCGGGAGCAGACGAACGCGGCGGGGGAGAGGATGTACATCC
                                              attattca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtacatcgatctgtacaagctaggaggtcagtacatcgatctctacaaggtgctcttgtgcattattcagGAGTTCGGGAAGATGAAGGAGAGAGCGCCGGAGAACTTCCGGGTCGACTACGCCGTCAGCCGGGAGCAGACGAACGCGGCGGGGGAGAGGATGTACATCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG