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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCCGTACTCGAACCATCGAGCCGCCGCCGCCGCCGCCGCAGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAGgtccgtgtgctctctccttctcgggccatcgccgatctttgcctatgcttgttactcctgtacctcttcgtgcttgcgcgtatgcctgtgcatctcccct...

Basic information

species Zea mays
transcript GRMZM2G134109_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|211241797|gb|FL220663.1|FL220663
EST:     AGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAG                         TTGCTGCTGCGGTAGTCCCCAACCATCATCATGCAGAACGAGGAGGGTAAG
genomic: AGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAGgtccgtgtgc ... tgctgttcagTTGCTGCTGCGGTAGTCCCCAACCATCATCATGCAGAACGAGGAGGGTAAG
EST: gi|211239565|gb|FL220655.1|FL220655
EST:     AGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAG                         TTGCTGCTGCGGTAGTCCCCAACCATCATCATGCAGAACGAGGAGGGTAAG
genomic: AGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAGgtccgtgtgc ... tgctgttcagTTGCTGCTGCGGTAGTCCCCAACCATCATCATGCAGAACGAGGAGGGTAAG
EST: gi|211244033|gb|FL220677.1|FL220677
EST:     AGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAG                         TTGCTGCTGCGGTAGTCCCCAACCATCATCATGCAGAACGAGGAGGGTAAG
genomic: AGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAGgtccgtgtgc ... tgctgttcagTTGCTGCTGCGGTAGTCCCCAACCATCATCATGCAGAACGAGGAGGGTAAG
EST: gi|211241800|gb|FL220666.1|FL220666
EST:     AGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAG                         TTGCTGCTGCGGTAGTCCCCAACCATCATCATGCAGAACGAGGAGGGTAAG
genomic: AGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAGgtccgtgtgc ... tgctgttcagTTGCTGCTGCGGTAGTCCCCAACCATCATCATGCAGAACGAGGAGGGTAAG
EST: gi|84980738|gb|DW531087.1|DW531087
EST:     AGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAG                         TTGCTGCTGCGGTAGTCCCCAACCATCATCATGCAGAACGAGGAGGGTAAG
genomic: AGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAGgtccgtgtgc ... tgctgttcagTTGCTGCTGCGGTAGTCCCCAACCATCATCATGCAGAACGAGGAGGGTAAG
EST: gi|166615631|gb|EG195784.1|EG195784
EST:     CTCACCTTCGAGAGATCAAG                         TTGCTGCTGCGGTAGTCCCCAACCATCATCATGCAGAACGAGGAGGGTAAG
genomic: CTCACCTTCGAGAGATCAAGgtccgtgtgc ... tgctgttcagTTGCTGCTGCGGTAGTCCCCAACCATCATCATGCAGAACGAGGAGGGTAAG
EST: gi|211235091|gb|FL220624.1|FL220624
EST:     AGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAG                         TTGCTGCTGCGGTACTCCCCAACCATCATCATGCAGAACGAGGAGGGTAAG
genomic: AGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAGgtccgtgtgc ... tgctgttcagTTGCTGCTGCGGTAGTCCCCAACCATCATCATGCAGAACGAGGAGGGTAAG
EST: gi|9742525|gb|BE518637.1|BE518637
EST:     CGTGCTCACCTTCGAGAGATCAAG                         TTGCTGCTGCGGTAGTCCCCCAACCATCATCATGCAGAACGAGGAGGGCTA
genomic: CGTGCTCACCTTCGAGAGATCAAGgtccgtgtgc ... tgctgttcagTTGCTGCTGCGGTAGT-CCCCAACCATCATCATGCAGAACGAGGAGGG-TA
EST: gi|211241802|gb|FL220668.1|FL220668
EST:     AGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAG                         TTGCTGCTGCGGTAGTCCCCAACCATCATCATGCAGAACGAGGAGGGTAAG
genomic: AGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAGgtccgtgtgc ... tgctgttcagTTGCTGCTGCGGTAGTCCCCAACCATCATCATGCAGAACGAGGAGGGTAAG
EST: gi|211239555|gb|FL220645.1|FL220645
EST:     AGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAG                         TTGCTGCTGCGGTAGTCCCCAACCATCATCATGCAGAACGAGGAGGGTAAG
genomic: AGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAGgtccgtgtgc ... tgctgttcagTTGCTGCTGCGGTAGTCCCCAACCATCATCATGCAGAACGAGGAGGGTAAG
EST: gi|211244035|gb|FL220679.1|FL220679
EST:     AGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAG                         TTGCTGCTGCGGTAGTCCCCAACCATCATCATGCAGAACGAGGAGGGTAAG
genomic: AGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAGgtccgtgtgc ... tgctgttcagTTGCTGCTGCGGTAGTCCCCAACCATCATCATGCAGAACGAGGAGGGTAAG
EST: gi|211239552|gb|FL220642.1|FL220642
EST:     AGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAG                         TTGCTGCTGCGGTAGTCCCCAACCATCATCATGCAGAACGAGGAGGGTAAG
genomic: AGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAGgtccgtgtgc ... tgctgttcagTTGCTGCTGCGGTAGTCCCCAACCATCATCATGCAGAACGAGGAGGGTAAG
EST: gi|211244039|gb|FL220683.1|FL220683
EST:     AGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAG                         TTGCTGCTGCGGTAGTCCCCAACCATCATCATGCAGAACGAGGAGGGTAAG
genomic: AGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAGgtccgtgtgc ... tgctgttcagTTGCTGCTGCGGTAGTCCCCAACCATCATCATGCAGAACGAGGAGGGTAAG
EST: gi|211241790|gb|FL220656.1|FL220656
EST:     CG-CG-CGCAGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAG                         TTGCTGCTGCGGTAGTCCCCAACCATCATCATGCAGAACGAGGAGGGTAAG
genomic: CGCCGCCGCAGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAGgtccgtgtgc ... tgctgttcagTTGCTGCTGCGGTAGTCCCCAACCATCATCATGCAGAACGAGGAGGGTAAG
EST: gi|211237336|gb|FL220639.1|FL220639
EST:     CG-CG-CGCAGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAG                         TTGCTGCTGCGGTAGTCCCCAACCATCATCATGCAGAACGAGGAGGGTAAG
genomic: CGCCGCCGCAGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAGgtccgtgtgc ... tgctgttcagTTGCTGCTGCGGTAGTCCCCAACCATCATCATGCAGAACGAGGAGGGTAAG
EST: gi|32829876|gb|CD969554.1|CD969554
EST:     CGCCGCAGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAG                         TTGCTGCTGCGGTAGTCCCCCAACCATCATCATGCAGAACGAGGAGGGTAA
genomic: CGCCGCAGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAGgtccgtgtgc ... tgctgttcagTTGCTGCTGCGGTAGTCCCC-AACCATCATCATGCAGAACGAGGAGGGTAA
EST: gi|33098495|gb|CF058455.1|CF058455
EST:     CCGCCGCAGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAG                         TTGCTGCTGCGGTAGTCCCCCAACCATCATCATGCAGAACGAGGAGGGTAA
genomic: CCGCCGCAGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAGgtccgtgtgc ... tgctgttcagTTGCTGCTGCGGTAGTCCCC-AACCATCATCATGCAGAACGAGGAGGGTAA
EST: gi|32838780|gb|CD978461.1|CD978461
EST:     CCGCAGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAG                         TTGCTGCTGCGGTAGTCCCCCAACCATCATCATGCAGAACGAGGAGGGTAA
genomic: CCGCAGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAGgtccgtgtgc ... tgctgttcagTTGCTGCTGCGGTAGTCCCC-AACCATCATCATGCAGAACGAGGAGGGTAA
EST: gi|211237328|gb|FL220631.1|FL220631
EST:     AGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAG                         TTGCTGCTGCGGTAGTCCCCAACCATCATCATGCAGAACGAGGAGGGTAAG
genomic: AGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAGgtccgtgtgc ... tgctgttcagTTGCTGCTGCGGTAGTCCCCAACCATCATCATGCAGAACGAGGAGGGTAAG
EST: gi|211244040|gb|FL220684.1|FL220684
EST:     AGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAG                         TTGCTGCTGCGGTAGTCCCCAACCATCATCATGCAGAACGAGGAGGGTAAG
genomic: AGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAGgtccgtgtgc ... tgctgttcagTTGCTGCTGCGGTAGTCCCCAACCATCATCATGCAGAACGAGGAGGGTAAG
EST: gi|32829918|gb|CD969596.1|CD969596
EST:     CGCAGTTGTCTTCGGTCTTCCGTGCTCACCTTTGAGAGATCAAG                         TTGCTGCTGCGGTAGTCCCCCAACCATCATCATGCAGAACGAGGAGGGTAA
genomic: CGCAGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAGgtccgtgtgc ... tgctgttcagTTGCTGCTGCGGTAGT-CCCCAACCATCATCATGCAGAACGAGGAGGGTAA
EST: gi|211244030|gb|FL220674.1|FL220674
EST:     AGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAG                         TTGCTGCTGCGGTAGTCCCCAACCATCATCATGCAGAACGAGGAGGGTAAG
genomic: AGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAGgtccgtgtgc ... tgctgttcagTTGCTGCTGCGGTAGTCCCCAACCATCATCATGCAGAACGAGGAGGGTAAG
EST: gi|32828852|gb|CD968530.1|CD968530
EST:     CGAGAGATCAAG                         TTGCTGCTGCGGTAGTCCCCCAACCATCATCATGCAGAACGAGGAGGGTAA
genomic: CGAGAGATCAAGgtccgtgtgc ... tgctgttcagTTGCTGCTGCGGTAGT-CCCCAACCATCATCATGCAGAACGAGGAGGGTAA
EST: gi|211239560|gb|FL220650.1|FL220650
EST:     AGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAG                         TTGCTGCTGCGGTAGTCCCCAACCATCATCATGCAGAACGAGGAGGGTAAG
genomic: AGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAGgtccgtgtgc ... tgctgttcagTTGCTGCTGCGGTAGTCCCCAACCATCATCATGCAGAACGAGGAGGGTAAG
EST: gi|18649857|gb|BM498676.1|BM498676
EST:     GTGCTCACCTTCGAGAGATCAAG                         TTGCTGCTGCGGTAGTCCCCCAACCATCATCATGCAGAACGAGGAGGGTAA
genomic: GTGCTCACCTTCGAGAGATCAAGgtccgtgtgc ... tgctgttcagTTGCTGCTGCGGTAGT-CCCCAACCATCATCATGCAGAACGAGGAGGGTAA
EST: gi|33093009|gb|CF053003.1|CF053003
EST:     CGCCGCCGCAGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAG                         TTGCTGCTGCGGTAGTCCCCCAACCATCATCATGCAGAACGAGGAGGGTAA
genomic: CGCCGCCGCAGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAGgtccgtgtgc ... tgctgttcagTTGCTGCTGCGGTAGTCCCC-AACCATCATCATGCAGAACGAGGAGGGTAA

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: 1485

TCCCGTACTCGAACCATCGAGCCGCCGCCGCCGCCGCCGCAGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAGgtccgtgtgc ... tgctgttcagTTGCTGCTGCGGTAGTCCCCAACCATCATCATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 2160

TCCCGTACTCGAACCATCGAGCCGCCGCCGCCGCCGCCGCAGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAGgtccgtgtgc ... tgctgttcagTTGCTGCTGCGGTAGTCCCCAACCATCATCATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1646

TCCCGTACTCGAACCATCGAGCCGCCGCCGCCGCCGCCGCAGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAGgtccgtgtgc ... tgctgttcagTTGCTGCTGCGGTAGTCCCCAACCATCATCATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1092

TCCCGTACTCGAACCATCGAGCCGCCGCCGCCGCCGCCGCAGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAGgtccgtgtgc ... tgctgttcagTTGCTGCTGCGGTAGTCCCCAACCATCATCATGCAGAACGAGGAGGGTAAGACGGTGGACCTCTACGTCCCCAGGAAGTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCCGTACTCGAACCATCGAGCCGCCGCCGCCGCCGCCGCAGTTGTCTTCGGTCTTCCGTGCTCACCTTCGAGAGATCAAGgtccgtgtgctctctccttctcgggccatcgccgatctttgcctatgcttgttactcctgtacctcttcgtgcttgcgcgtatgcctgtgcatctcccct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctctctc