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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCGCCAGGTACCACGCCGCCGACAACGAGGACCTGCCGGAGTCCGTCGACTGGAGGGCCAAGGGCGCCGTCGCCGAGGTCAAGGACCAGGGCAGCTGCGgtaaaggagcttccataccaatctccgccctcttcctctctcttttttttattactatactcctgctgaaataaagctgacctgcttagtaactctagct...

Basic information

species Zea mays
transcript GRMZM2G166281_T01
intron # 1
splice site 5'
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|16920327|gb|BM074601.1|BM074601
EST:     CTGGAGGGCCAAGGGCGCCGTCGCCGAGGTCAAGGACCAGGGCAGCTGCG                         GGAGCTGTTGGGCTTTCTCAACAATAGCAGCTGTGGAAGGCATCAACCAGA
genomic: CTGGAGGGCCAAGGGCGCCGTCGCCGAGGTCAAGGACCAGGGCAGCTGCGgtaaaggagc ... tctctttcagGGAGCTGTTGGGCTTTCTCAACAATAGCAGCTGTGGAAGGCATCAACCAGA
EST: gi|26558146|gb|CA830381.1|CA830381
EST:     CTGGAGGGCCAAGGGCGCCGTCGCCGAGGTCAAGGACCAGGGCAGCTGCG                         GGAGCTGTTGGGCTTTCTCAACAATAGCAGCTGTGGAAGGCATCAACCAGA
genomic: CTGGAGGGCCAAGGGCGCCGTCGCCGAGGTCAAGGACCAGGGCAGCTGCGgtaaaggagc ... tctctttcagGGAGCTGTTGGGCTTTCTCAACAATAGCAGCTGTGGAAGGCATCAACCAGA
EST: gi|18170436|gb|BM340276.1|BM340276
EST:     GGGCCAAGGGCGCCGTCGCCGAGGTCAAGGACCAGGGCAGCTGCG                         GGAGCTGTTGGGCTTTCTCAACAATAGCAGCTGTGGAAGGCATCAACCAGA
genomic: GGGCCAAGGGCGCCGTCGCCGAGGTCAAGGACCAGGGCAGCTGCGgtaaaggagc ... tctctttcagGGAGCTGTTGGGCTTTCTCAACAATAGCAGCTGTGGAAGGCATCAACCAGA
EST: gi|18162525|gb|BM332364.1|BM332364
EST:     CTGGAGGGCCAAGGGCGCCGTCGCCGAGGTCAAGGACCAGGGCAGCTGCG                         GGAGCTGTTGGGCTTTCTCAACAATAGCAGCTGTGGAAGGCATCAACCAGA
genomic: CTGGAGGGCCAAGGGCGCCGTCGCCGAGGTCAAGGACCAGGGCAGCTGCGgtaaaggagc ... tctctttcagGGAGCTGTTGGGCTTTCTCAACAATAGCAGCTGTGGAAGGCATCAACCAGA
EST: gi|211362165|gb|FL445531.1|FL445531
EST:     CTGGAGGGCCAAGGGCGCCGTCGCCGAGGTCAAGGACCAGGGCAGCTGCG                         GGAGCTGTTGGGCTTTCTCAACAATAGCAGCTGTGGAAGGCATCAACCAGA
genomic: CTGGAGGGCCAAGGGCGCCGTCGCCGAGGTCAAGGACCAGGGCAGCTGCGgtaaaggagc ... tctctttcagGGAGCTGTTGGGCTTTCTCAACAATAGCAGCTGTGGAAGGCATCAACCAGA
EST: gi|86465870|gb|DY232243.1|DY232243
EST:     CTGGAGGGCCAAGGGCGCCGTCGCCGAGGTCAAGGACCAGGGCAGCTGCG                         GGAGCTGTTGGGCTTTCTCAACAATAGCAGCTGTGGAAGGCATCAACCATA
genomic: CTGGAGGGCCAAGGGCGCCGTCGCCGAGGTCAAGGACCAGGGCAGCTGCGgtaaaggagc ... tctctttcagGGAGCTGTTGGGCTTTCTCAACAATAGCAGCTGTGGAAGGCATCAACCAGA
EST: gi|18662256|gb|BM501826.1|BM501826
EST:     CTGGAGGGCCAAGGGCGCCGTCGCCGAGGTCAAGGACCAGGGCAGCTGCG                         GGAGCTGTTGGGCTTTCTCAACAATAGCAGCTGTG
genomic: CTGGAGGGCCAAGGGCGCCGTCGCCGAGGTCAAGGACCAGGGCAGCTGCGgtaaaggagc ... tctctttcagGGAGCTGTTGGGCTTTCTCAACAATAGCAGCTGTG
EST: gi|16922847|gb|BM075839.1|BM075839
EST:     CTGGAGGGCCAAGGGCGCCGTCGCCGAGGTCAAGGACCAGGGCAGCTGCG                         GGAGCTGTTGGGCTTTCTCAACAATAGCAGCTGTGGAAGGCATCAACCAGA
genomic: CTGGAGGGCCAAGGGCGCCGTCGCCGAGGTCAAGGACCAGGGCAGCTGCGgtaaaggagc ... tctctttcagGGAGCTGTTGGGCTTTCTCAACAATAGCAGCTGTGGAAGGCATCAACCAGA
EST: gi|86467301|gb|DY233671.1|DY233671
EST:     CTGGAGGGCCAAGGGCGCCGTCGCCGAGGTCAAGGACCAGGGCAGCTGCG                         GGAGCTGTTGGGCTTTCTCAACAAT
genomic: CTGGAGGGCCAAGGGCGCCGTCGCCGAGGTCAAGGACCAGGGCAGCTGCGgtaaaggagc ... tctctttcagGGAGCTGTTGGGCTTTCTCAACAAT
EST: gi|71444253|gb|DR825303.1|DR825303
EST:     CTGGAGGGCCAAGGGCGCCGTCGCCGAGGTCAAGGACCAGGGCAGCTGCG                         GGAGCTGTTGGGCTTTCTCAACAATAGCAGCTGTGGAAGGCATCAACCAGA
genomic: CTGGAGGGCCAAGGGCGCCGTCGCCGAGGTCAAGGACCAGGGCAGCTGCGgtaaaggagc ... tctctttcagGGAGCTGTTGGGCTTTCTCAACAATAGCAGCTGTGGAAGGCATCAACCAGA
EST: gi|18173836|gb|BM349224.1|BM349224
EST:     CTGGAGGGCCAAGGGCGCCGTCGCCGAGGTCAAGGACCAGGGCAGCTGCG                         GGAGCTGTTGGGCTTTCTCAACAATAGCAGCTGTGGAAGGCATCAACCAGA
genomic: CTGGAGGGCCAAGGGCGCCGTCGCCGAGGTCAAGGACCAGGGCAGCTGCGgtaaaggagc ... tctctttcagGGAGCTGTTGGGCTTTCTCAACAATAGCAGCTGTGGAAGGCATCAACCAGA
EST: gi|71444254|gb|DR825304.1|DR825304
EST:     CTGGAGGGCCAAGGGCGCCGTCGCCGAGGTCAAGGACCAGGGCAGCTGCG                         GGAGCTGTTGGGCTTTCTCAACAATAGCAGCTGTGGAAGGCATCAACCAGA
genomic: CTGGAGGGCCAAGGGCGCCGTCGCCGAGGTCAAGGACCAGGGCAGCTGCGgtaaaggagc ... tctctttcagGGAGCTGTTGGGCTTTCTCAACAATAGCAGCTGTGGAAGGCATCAACCAGA
EST: gi|18172588|gb|BM347976.1|BM347976
EST:     CTGGAGGGCCAAGGGCGCCGTCGCCGAGGTCAAGGACCAGGGCAGCTGCG                         GGAGCTGTTGGGCTTTCTCAACAATAGCAGCTGTGGAAGGCATCAACCAGA
genomic: CTGGAGGGCCAAGGGCGCCGTCGCCGAGGTCAAGGACCAGGGCAGCTGCGgtaaaggagc ... tctctttcagGGAGCTGTTGGGCTTTCTCAACAATAGCAGCTGTGGAAGGCATCAACCAGA
EST: gi|211384516|gb|FL378678.1|FL378678
EST:     CTGGAGGGCCAAGGGCGCCGTCGCCGAGGTCAAGGACCAGGGCAGCTGCG                         GGAGCTGTTGGGCTTTCTCAACAATAGCAGCTGTGGAAGGCATCAACCAGA
genomic: CTGGAGGGCCAAGGGCGCCGTCGCCGAGGTCAAGGACCAGGGCAGCTGCGgtaaaggagc ... tctctttcagGGAGCTGTTGGGCTTTCTCAACAATAGCAGCTGTGGAAGGCATCAACCAGA

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: 262

GGCGCCAGGTACCACGCCGCCGACAACGAGGACCTGCCGGAGTCCGTCGACTGGAGGGCCAAGGGCGCCGTCGCCGAGGTCAAGGACCAGGGCAGCTGCGgtaaaggagc ... tctctttcagGGAGCTGTTGGGCTTTCTCAACAATAGCAGCTGTGGAAGGCATCAACCAGATTGTTACAGGCGACTTGATCTCCTTGTCTGAACAAGAGCTTGTCGACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1606

GGCGCCAGGTACCACGCCGCCGACAACGAGGACCTGCCGGAGTCCGTCGACTGGAGGGCCAAGGGCGCCGTCGCCGAGGTCAAGGACCAGGGCAGCTGCGgtaaaggagc ... tctctttcagGGAGCTGTTGGGCTTTCTCAACAATAGCAGCTGTGGAAGGCATCAACCAGATTGTTACAGGCGACTTGATCTCCTTGTCTGAACAAGAGCTTGTCGACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1291

GGCGCCAGGTACCACGCCGCCGACAACGAGGACCTGCCGGAGTCCGTCGACTGGAGGGCCAAGGGCGCCGTCGCCGAGGTCAAGGACCAGGGCAGCTGCGgtaaaggagc ... tctctttcagGGAGCTGTTGGGCTTTCTCAACAATAGCAGCTGTGGAAGGCATCAACCAGATTGTTACAGGCGACTTGATCTCCTTGTCTGAACAAGAGCTTGTCGACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1124

GGCGCCAGGTACCACGCCGCCGACAACGAGGACCTGCCGGAGTCCGTCGACTGGAGGGCCAAGGGCGCCGTCGCCGAGGTCAAGGACCAGGGCAGCTGCGgtaaaggagc ... tctctttcagGGAGCTGTTGGGCTTTCTCAACAATAGCAGCTGTGGAAGGCATCAACCAGATTGTTACAGGCGACTTGATCTCCTTGTCTGAACAAGAGCTTGTCGACTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCGCCAGGTACCACGCCGCCGACAACGAGGACCTGCCGGAGTCCGTCGACTGGAGGGCCAAGGGCGCCGTCGCCGAGGTCAAGGACCAGGGCAGCTGCGgtaaaggagcttccataccaatctccgccctcttcctctctcttttttttattactatactcctgctgaaataaagctgacctgcttagtaactctagct

- - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctccgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaataaa