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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaactattacagcactcactgcatgatactttggcatgctttgttcatagcgactagcattagttgcttgtactttgagctgatattcatattatggactaacatgttgtgatcaaatatgaacttgttgcagTGGTCATTGATCCCAGTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCAAGAAGTCTGCATGG

Basic information

species Zea mays
transcript GRMZM2G149576_T02
intron # 5
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|211071814|gb|FL187256.1|FL187256
EST:     A-ACGCCGGGCGAGAAGAGCAATCCA-GTCTACCTGCGCTGCAGGTGATG                         TGGTCATTGATCCCAGGTATGGGGA
genomic: ACACGC-GGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATGgtgagaacta ... cttgttgcagTGGTCATTGATCCCAGTTATGGGGA
EST: gi|93282425|gb|EB674689.1|EB674689
EST:     GACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATG                         TGGTCATTGATCCCAGTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCA
genomic: GACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATGgtgagaacta ... cttgttgcagTGGTCATTGATCCCAGTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCA
EST: gi|89762580|gb|DY690104.1|DY690104
EST:     GACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATG                         TGGTCATTGAT
genomic: GACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATGgtgagaacta ... cttgttgcagTGGTCATTGAT
EST: gi|149106424|gb|EE188313.2|EE188313
EST:     ACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGNCA-GTGATG                         TGGTCATTGATCCCAGTTATGGGGAGCCCCTCCTGACTCCACCTCAGCCC
genomic: ACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTG-CAAGTGATGgtgagaacta ... cttgttgcagTGGTCATTGATCCCAGTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCC
EST: gi|149081528|gb|EE170664.2|EE170664
EST:     GACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATG                         TGGTCATTGATCCCAGTTATGGGGAGCCCCTCCTGA
genomic: GACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATGgtgagaacta ... cttgttgcagTGGTCATTGATCCCAGTTATGGGGAGCCCCTCCTGA
EST: gi|32841700|gb|CD981381.1|CD981381
EST:     GACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATG                         TGGTCATTGATCCCAGTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCA
genomic: GACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATGgtgagaacta ... cttgttgcagTGGTCATTGATCCCAGTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCA
EST: gi|211469055|gb|FL174275.1|FL174275
EST:     ACACGCGGGCGAAGA-GAGCAATCCA-GTCTACCTGCGCTGCAGGTGATG                         TGGTCATTGATCCCAGTTATGGGG
genomic: ACACGCGGGCGA-GAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATGgtgagaacta ... cttgttgcagTGGTCATTGATCCCAGTTATGGGG
EST: gi|71429319|gb|DR810369.1|DR810369
EST:     ACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGGCA-GTGATG                         TGGTCATTGATCCCTAGT-ATGGGGGAGCCC
genomic: ACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTG-CAAGTGATGgtgagaacta ... cttgttgcagTGGTCATTGATCCC-AGTTATGGGG-AGCCC
EST: gi|211074544|gb|FL187264.1|FL187264
EST:     GACACGCGGGCGAGAAGAGCA-TCCAAGTCTACCTGCGCTGCAAGTGATG                         TGGTCATTGATCCCAGTTATGGGGTACCCCCTCCTGACTCAACCTCAGCCC
genomic: GACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATGgtgagaacta ... cttgttgcagTGGTCATTGATCCCAGTTATGGGG-AGCCCCTCCTGACTCAACCTCAGCCC
EST: gi|71769068|gb|DR967005.1|DR967005
EST:     GACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATG                         TGGTCATTGATCCCAGTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCC
genomic: GACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATGgtgagaacta ... cttgttgcagTGGTCATTGATCCCAGTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCA
EST: gi|32840339|gb|CD980020.1|CD980020
EST:     GACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATG                         TGGTCATTGATCCCAGTTATGGGGAGCCCCTCCTG
genomic: GACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATGgtgagaacta ... cttgttgcagTGGTCATTGATCCCAGTTATGGGGAGCCCCTCCTG
EST: gi|71763997|gb|DR961934.1|DR961934
EST:     GACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCTAGTGATG                         TGGTCATTGATCCCAGTTATGGGGAGCCCCTCCTGACTCTACCTCAGCCCA
genomic: GACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATGgtgagaacta ... cttgttgcagTGGTCATTGATCCCAGTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCA
EST: gi|78088725|gb|DV517118.1|DV517118
EST:     GACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATG                         TGGTCATTGATCCCAGTTATGGGGAGCCCC
genomic: GACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATGgtgagaacta ... cttgttgcagTGGTCATTGATCCCAGTTATGGGGAGCCCC
EST: gi|148945267|gb|EC890477.2|EC890477
EST:     GACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATG                         TGGTCATTGATCCCAGTTATGGGGAGCCCCTCCTGACTTCA-CCTCAGCCC
genomic: GACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATGgtgagaacta ... cttgttgcagTGGTCATTGATCCCAGTTATGGGGAGCCCCTCCTGACT-CAACCTCAGCCC
EST: gi|148945370|gb|EC890591.2|EC890591
EST:     GACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATG                         TGGTCATTGATCCCAGTTATGGGGAGCCCCTCCTGACTCAACCT
genomic: GACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATGgtgagaacta ... cttgttgcagTGGTCATTGATCCCAGTTATGGGGAGCCCCTCCTGACTCAACCT
EST: gi|76013549|gb|DT940719.1|DT940719
EST:     GACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATG                         TGGTCATTGATCCCAGTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCA
genomic: GACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATGgtgagaacta ... cttgttgcagTGGTCATTGATCCCAGTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCA
EST: gi|13237072|gb|BG355086.1|BG355086
EST:     GACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATG                         TGGTCATTGATCCCAGTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCA
genomic: GACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATGgtgagaacta ... cttgttgcagTGGTCATTGATCCCAGTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCA
EST: gi|71772906|gb|DR970829.1|DR970829
EST:     GACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATG                         TGGTCATTGATCCCAGTTATGGGGAGCCCCTCCTGACTCACCCTCAGCCCA
genomic: GACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATGgtgagaacta ... cttgttgcagTGGTCATTGATCCCAGTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCA
EST: gi|93283801|gb|EB676065.1|EB676065
EST:     GACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATG                         TGGTCATTGATCCCAGTTATGGGGAGCC
genomic: GACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATGgtgagaacta ... cttgttgcagTGGTCATTGATCCCAGTTATGGGGAGCC
EST: gi|149001890|gb|EE038842.2|EE038842
EST:     GACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATG                         TGGTCATTGATCCCAGTTATGGGGAGCCCCTCCTGA
genomic: GACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATGgtgagaacta ... cttgttgcagTGGTCATTGATCCCAGTTATGGGGAGCCCCTCCTGA
EST: gi|78104608|gb|DV523026.1|DV523026
EST:     GACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATG                         TGGTCATTGATCCCAGTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCA
genomic: GACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATGgtgagaacta ... cttgttgcagTGGTCATTGATCCCAGTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCA
EST: gi|71769874|gb|DR967811.1|DR967811
EST:     GACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATG                         TGGTCATTGATCCCAGTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCA
genomic: GACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATGgtgagaacta ... cttgttgcagTGGTCATTGATCCCAGTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCA
EST: gi|13237258|gb|BG355272.1|BG355272
EST:     GACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATG                         TGGTCATTGATCCCAGTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCA
genomic: GACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATGgtgagaacta ... cttgttgcagTGGTCATTGATCCCAGTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCA
EST: gi|93284314|gb|EB676578.1|EB676578
EST:     GACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATG                         TGGTCATTGATCCCAGTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCA
genomic: GACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATGgtgagaacta ... cttgttgcagTGGTCATTGATCCCAGTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCA
EST: gi|211074549|gb|FL187269.1|FL187269
EST:     GA-ACGCGGGCGAGAAGAG-AATCCCAGTCTACCTGCGCTGCAAGTGATG                         TGGTCATTGATCCCAGTTATGGGGAGCCCCTCCTGACTCAAC-TCAGCC-A
genomic: GACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATGgtgagaacta ... cttgttgcagTGGTCATTGATCCCAGTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCA
EST: gi|78082192|gb|DV510604.1|DV510604
EST:     GACACGCGGGCGAGAAGAGCAATCAAAGTCTAACTGCGCTGCAAGTGATG                         TGGTCATTGATCCCAG
genomic: GACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATGgtgagaacta ... cttgttgcagTGGTCATTGATCCCAG

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: 127

ATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATGgtgagaacta ... cttgttgcagTGGTCATTGATCCCAGTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCAAGAAGTCTGCATGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 441

ATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATGgtgagaacta ... cttgttgcagTGGTCATTGATCCCAGTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCAAGAAGTCTGCATGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 241

ATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATGgtgagaacta ... cttgttgcagTGGTCATTGATCCCAGTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCAAGAAGTCTGCATGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 185

ATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATGgtgagaacta ... cttgttgcagTGGTCATTGATCCCAGTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCAAGAAGTCTGCATGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctgatattcatattatggactaacatgttgtgatcaaatatgaacttgttgcagTGGTCATTGATCCCAGTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCAAGAAGTCTGCATGG
                  gactaac  putative branch site (score: 185)
     tattcatattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagaactattacagcactcactgcatgatactttggcatgctttgttcatagcgactagcattagttgcttgtactttgagctgatattcatattatggactaacatgttgtgatcaaatatgaacttgttgcagTGGTCATTGATCCCAGTTATGGGGAGCCCCTCCTGACTCAACCTCAGCCCAAGAAGTCTGCATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT