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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggttcctgtcacattcgaaatgtttgctgttgaattattgtatactgacatctgtttttgtttactctatgttgaatgattgcagATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATG

Basic information

species Zea mays
transcript GRMZM2G149576_T02
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|211463999|gb|FL174252.1|FL174252
EST:     ATCCTTCTACAAGGGAATTCTGATGTGGGAGGGAGGAGACCAGGATTCTG                         ACGGAGACACGCGGGCGAGAAGAGCAATCCA-GTCTACCTGCG
genomic: ATCCTTCTACAAGGGCATTCTGATGTGG-AGGGAGGAGTCCAGGATTCTGgttggttcct ... atgattgcagATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCG
EST: gi|211071814|gb|FL187256.1|FL187256
EST:     TCCTTCTACAAGGGCATTCTGATGTGGGAGGGAGGAGTCCCAGGAT-CTG                         ATGGAGA-ACGCCGGGCGAGAAGAGCAATCCA-GTCTACCTGCGCTGCAG
genomic: TCCTTCTACAAGGGCATTCTGATGTGG-AGGGAGGAGTCC-AGGATTCTGgttggttcct ... atgattgcagATGGAGACACGC-GGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAA
EST: gi|211077290|gb|FL187281.1|FL187281
EST:     ATCCTTCTACA-GGGCATTCTGATGTGGAGGGAGGGAGTCCAG-ATTCTG                         ATGGAGACACG
genomic: ATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGG-AGTCCAGGATTCTGgttggttcct ... atgattgcagATGGAGACACG
EST: gi|93282425|gb|EB674689.1|EB674689
EST:     GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTG                         ATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGT
genomic: GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTGgttggttcct ... atgattgcagATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGT
EST: gi|211077292|gb|FL187283.1|FL187283
EST:     CCTTCTACAAGGGCATTCTGATGTGGAAGGGGAGGAGTCCCAG-ATTCTG                         ATGGAGACACG
genomic: CCTTCTACAAGGGCATTCTGATGTGGA-GGG-AGGAGTCC-AGGATTCTGgttggttcct ... atgattgcagATGGAGACACG
EST: gi|89762580|gb|DY690104.1|DY690104
EST:     GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTG                         ATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGT
genomic: GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTGgttggttcct ... atgattgcagATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGT
EST: gi|149106424|gb|EE188313.2|EE188313
EST:     GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTG                         ATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGNCA-G
genomic: GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTGgttggttcct ... atgattgcagATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTG-CAAG
EST: gi|149081528|gb|EE170664.2|EE170664
EST:     GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTG                         ATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGT
genomic: GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTGgttggttcct ... atgattgcagATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGT
EST: gi|32841700|gb|CD981381.1|CD981381
EST:     GATCCTTCTACAAGGGCAATCTGATGTGGAGGGAGGAGTCCAGGATTCTG                         ATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGT
genomic: GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTGgttggttcct ... atgattgcagATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGT
EST: gi|76917339|gb|DV166774.1|DV166774
EST:     GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTG                         ATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAA
genomic: GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTGgttggttcct ... atgattgcagATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAA
EST: gi|211469055|gb|FL174275.1|FL174275
EST:     GATCCTTCTACAAGGGAATTCTGATGTGGAGGGAGGAGAC-AGGATTCTG                         ACGGAGACACGCGGGCGAAGA-GAGCAATCCA-GTCTACCTGCGCTGCAGG
genomic: GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTGgttggttcct ... atgattgcagATGGAGACACGCGGGCGA-GAAGAGCAATCCAAGTCTACCTGCGCTGCAAG
EST: gi|71429319|gb|DR810369.1|DR810369
EST:     GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCTAGGATTCTG                         ATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGGCA-G
genomic: GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTGgttggttcct ... atgattgcagATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTG-CAAG
EST: gi|149081592|gb|EE170734.2|EE170734
EST:     GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTG                         ATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGT
genomic: GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTGgttggttcct ... atgattgcagATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGT
EST: gi|211074544|gb|FL187264.1|FL187264
EST:     GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTG                         ATGGAGACACGCGGGCGAGAAGAGCA-TCCAAGTCTACCTGCGCTGCAAGT
genomic: GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTGgttggttcct ... atgattgcagATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGT
EST: gi|71769068|gb|DR967005.1|DR967005
EST:     GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTG                         ATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGT
genomic: GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTGgttggttcct ... atgattgcagATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGT
EST: gi|32840339|gb|CD980020.1|CD980020
EST:     GATCCTTCTACAAGGGCAATCTGATGTGGAGGGAGGAGTCCAGGATTCTG                         ATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGT
genomic: GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTGgttggttcct ... atgattgcagATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGT
EST: gi|71763997|gb|DR961934.1|DR961934
EST:     GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTG                         ATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCTAGT
genomic: GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTGgttggttcct ... atgattgcagATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGT
EST: gi|78088725|gb|DV517118.1|DV517118
EST:     GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTG                         ATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGT
genomic: GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTGgttggttcct ... atgattgcagATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGT
EST: gi|148945267|gb|EC890477.2|EC890477
EST:     GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTG                         ATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGT
genomic: GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTGgttggttcct ... atgattgcagATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGT
EST: gi|148945370|gb|EC890591.2|EC890591
EST:     GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTG                         ATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGT
genomic: GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTGgttggttcct ... atgattgcagATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGT
EST: gi|211082768|gb|FL187309.1|FL187309
EST:     TCCTTCTACAAGGGCATTCTGATGTGGGAGGGAGGAGTCCNAGGATTCTG                         ATGGAGACACGCGGGCGAAGA-GAGCAATCCA-GTCTACCTGCGCTGCAA
genomic: TCCTTCTACAAGGGCATTCTGATGTGG-AGGGAGGAGTCC-AGGATTCTGgttggttcct ... atgattgcagATGGAGACACGCGGGCGA-GAAGAGCAATCCAAGTCTACCTGCGCTGCAA
EST: gi|76013549|gb|DT940719.1|DT940719
EST:     GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTG                         ATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGT
genomic: GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTGgttggttcct ... atgattgcagATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGT
EST: gi|13237072|gb|BG355086.1|BG355086
EST:     GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTG                         ATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGT
genomic: GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTGgttggttcct ... atgattgcagATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGT
EST: gi|149106747|gb|EE188643.2|EE188643
EST:     GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTG                         ATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGT
genomic: GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTGgttggttcct ... atgattgcagATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGT
EST: gi|50323960|gb|CO519086.1|CO519086
EST:     GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTG                         ATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCA
genomic: GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTGgttggttcct ... atgattgcagATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCA
EST: gi|71772906|gb|DR970829.1|DR970829
EST:     GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTG                         ATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGT
genomic: GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTGgttggttcct ... atgattgcagATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGT
EST: gi|149081259|gb|EE170373.2|EE170373
EST:     GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTG                         ATGGAGACACGCGGGCGAAGA-GAGCAATCCAAGTCTACCT
genomic: GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTGgttggttcct ... atgattgcagATGGAGACACGCGGGCGA-GAAGAGCAATCCAAGTCTACCT
EST: gi|93283801|gb|EB676065.1|EB676065
EST:     GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTG                         ATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGT
genomic: GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTGgttggttcct ... atgattgcagATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGT
EST: gi|149001890|gb|EE038842.2|EE038842
EST:     GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTG                         ATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGT
genomic: GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTGgttggttcct ... atgattgcagATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGT
EST: gi|78104608|gb|DV523026.1|DV523026
EST:     GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTG                         ATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGT
genomic: GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTGgttggttcct ... atgattgcagATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGT
EST: gi|71769874|gb|DR967811.1|DR967811
EST:     GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTG                         ATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGT
genomic: GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTGgttggttcct ... atgattgcagATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGT
EST: gi|13237258|gb|BG355272.1|BG355272
EST:     GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTG                         ATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGT
genomic: GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTGgttggttcct ... atgattgcagATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGT
EST: gi|93284314|gb|EB676578.1|EB676578
EST:     GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTG                         ATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGT
genomic: GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTGgttggttcct ... atgattgcagATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGT
EST: gi|211074549|gb|FL187269.1|FL187269
EST:     GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGNATTCTG                         ATGGAGA-ACGCGGGCGAGAAGAG-AATCCCAGTCTACCTGCGCTGCAAGT
genomic: GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTGgttggttcct ... atgattgcagATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGT
EST: gi|78082192|gb|DV510604.1|DV510604
EST:     GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTG                         ATGGAGACACGCGGGCGAGAAGAGCAATCAAAGTCTAACTGCGCTGCAAGT
genomic: GATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTGgttggttcct ... atgattgcagATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGT

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: 103

GCACCTCGTCGAGATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTGgttggttcct ... atgattgcagATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 267

GCACCTCGTCGAGATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTGgttggttcct ... atgattgcagATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 161

GCACCTCGTCGAGATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTGgttggttcct ... atgattgcagATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 136

GCACCTCGTCGAGATCCTTCTACAAGGGCATTCTGATGTGGAGGGAGGAGTCCAGGATTCTGgttggttcct ... atgattgcagATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaattattgtatactgacatctgtttttgtttactctatgttgaatgattgcagATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATG
            tactgac  putative branch site (score: 136)
                        tttttgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggttcctgtcacattcgaaatgtttgctgttgaattattgtatactgacatctgtttttgtttactctatgttgaatgattgcagATGGAGACACGCGGGCGAGAAGAGCAATCCAAGTCTACCTGCGCTGCAAGTGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA