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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTCTCAAGTCCTGAAGATTCAACAACAGTTTTGGCCAGTTTTAGGTCCAACATACGCATCACTACAGGCGCAGCAGGGGTCGGTTTCTTCCAATCATAgtgagtaacatcactagttattgaattgcataaccattatgaaacctcatagcgagaacaacttgcctggctacctttgggtttgatattagagatttgc...

Basic information

species Zea mays
transcript GRMZM2G107309_T05
intron # 16
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|37384487|gb|CF629320.1|CF629320
EST:     AACATATGCATCACTACAGGCGCAGCAGGGGTCGGTTTCTTCCAATCATA                         GTAATGAGCTGAAGAAAAGGAAGCGTCCAGGAGGAGGACCAGGGCCCTTCT
genomic: AACATACGCATCACTACAGGCGCAGCAGGGGTCGGTTTCTTCCAATCATAgtgagtaaca ... atcaccaaagGTAATGAGCTGAAGAAAAGGAAGCGTCCAGGAGGAGGACCAGGGCCCTTCT
EST: gi|71449896|gb|DR830946.1|DR830946
EST:     AACATACGCATCACTACAGGCGCAGCAGGGGTCGGTTTCTTCCAATCATA                         GTAATGAGCTGAAGAAAAGGAAGCGTCCAGGAGGAGGACCAGGGCCCTTCT
genomic: AACATACGCATCACTACAGGCGCAGCAGGGGTCGGTTTCTTCCAATCATAgtgagtaaca ... atcaccaaagGTAATGAGCTGAAGAAAAGGAAGCGTCCAGGAGGAGGACCAGGGCCCTTCT
EST: gi|211440335|gb|FL443588.1|FL443588
EST:     AACATACGCATCACTACAGGCGCAGCAGGGGTCGGTTTCTTCCAATCATA                         GCAATGAGCTGAAGAAAAGGAAGCGTTCAGGAGGAGGACCAGGGCCCTTCT
genomic: AACATACGCATCACTACAGGCGCAGCAGGGGTCGGTTTCTTCCAATCATAgtgagtaaca ... atcaccaaagGTAATGAGCTGAAGAAAAGGAAGCGTCCAGGAGGAGGACCAGGGCCCTTCT
EST: gi|211416083|gb|FK952661.1|FK952661
EST:     AACATACGCATCACTACAGGCGCAGCAGGGGTCGGTTTCTTCCAATCATA                         GTAATGAGCTGAAGAAAAGGAAGCGTCCAGGAGGAGGACCAGGGCCCTTCT
genomic: AACATACGCATCACTACAGGCGCAGCAGGGGTCGGTTTCTTCCAATCATAgtgagtaaca ... atcaccaaagGTAATGAGCTGAAGAAAAGGAAGCGTCCAGGAGGAGGACCAGGGCCCTTCT
EST: gi|71763326|gb|DR961263.1|DR961263
EST:     AACATACGCATCACTACAGGCGCAGCAGGGGTCGGTTTCTTCCAATCATA                         GTAATGAGCTGAAGAAAAGGAAGCGTCCAGGAGGAGGACCAGGGCCCTTCT
genomic: AACATACGCATCACTACAGGCGCAGCAGGGGTCGGTTTCTTCCAATCATAgtgagtaaca ... atcaccaaagGTAATGAGCTGAAGAAAAGGAAGCGTCCAGGAGGAGGACCAGGGCCCTTCT
EST: gi|211183239|gb|FL432688.1|FL432688
EST:     AACATACGCATCACTACAGGCGCAGCAGGGGTCGGTTTCTTCCAATCATA                         GCAATGAGCTGAAGAAAAGGAAGCGTTCAGGAGGAGGACCAGGGCCCTTYT
genomic: AACATACGCATCACTACAGGCGCAGCAGGGGTCGGTTTCTTCCAATCATAgtgagtaaca ... atcaccaaagGTAATGAGCTGAAGAAAAGGAAGCGTCCAGGAGGAGGACCAGGGCCCTTCT
EST: gi|148946012|gb|EC891307.2|EC891307
EST:     AACATACGCATCACTACAGGCGCAGCAGGGGTCGGTTTTTTCCATTCATA                         GTAATGAGCTGAAGAAAAGGAAGCGTCCAGGAGGAGGACCAGGGCCCTTCT
genomic: AACATACGCATCACTACAGGCGCAGCAGGGGTCGGTTTCTTCCAATCATAgtgagtaaca ... atcaccaaagGTAATGAGCTGAAGAAAAGGAAGCGTCCAGGAGGAGGACCAGGGCCCTTCT
EST: gi|5688538|gb|AI941553.1|AI941553
EST:     AACATATGCATCACTACAGGCGCAGCAGGGGTCGGTTTCTTCCAATCATA                         GTAATGAGCTGAAGAAAAGGAAGCGTCCAGGAGGAGGACCAGGGCCCTTCT
genomic: AACATACGCATCACTACAGGCGCAGCAGGGGTCGGTTTCTTCCAATCATAgtgagtaaca ... atcaccaaagGTAATGAGCTGAAGAAAAGGAAGCGTCCAGGAGGAGGACCAGGGCCCTTCT
EST: gi|71445686|gb|DR826736.1|DR826736
EST:     AACATACGCATCACTACAGGCGCAGCAGGGGTCGGTTTCTTCCAATCATA                         GTAATGAGCTGAAGAAAAGGAAGCGTCCAGGAGGAGGACCAGGGCCCTTCT
genomic: AACATACGCATCACTACAGGCGCAGCAGGGGTCGGTTTCTTCCAATCATAgtgagtaaca ... atcaccaaagGTAATGAGCTGAAGAAAAGGAAGCGTCCAGGAGGAGGACCAGGGCCCTTCT
EST: gi|149082860|gb|EE172086.2|EE172086
EST:     AACATACGCATCCCTACAGGCGCAGCAGGGGTCGGTTTCTTCCAATCATA                         GTAATGAGCTGAAGAAAAGGAAGCGTCCAGGAGGAGGACCAGGGCCCTTCT
genomic: AACATACGCATCACTACAGGCGCAGCAGGGGTCGGTTTCTTCCAATCATAgtgagtaaca ... atcaccaaagGTAATGAGCTGAAGAAAAGGAAGCGTCCAGGAGGAGGACCAGGGCCCTTCT
EST: gi|91050278|gb|EB160696.1|EB160696
EST:     AACATACGCATCACTACAGGCGCAGCAGGGGTCGGTTTCTTCCAATCATA                         GTAATGAGCTGAAGAAAAGGAAGCGTCCAGGAGGAGGACCAGGGCCCTTCT
genomic: AACATACGCATCACTACAGGCGCAGCAGGGGTCGGTTTCTTCCAATCATAgtgagtaaca ... atcaccaaagGTAATGAGCTGAAGAAAAGGAAGCGTCCAGGAGGAGGACCAGGGCCCTTCT

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 3 RNA-Seq libraries.


Block sizes: 39 (upstream exon), 49 (downstream exon)
Score: 6

GTTTCTCAAGTCCTGAAGATTCAACAACAGTTTTGGCCAGTTTTAGGTCCAACATACGCATCACTACAGGCGCAGCAGGGGTCGGTTTCTTCCAATCATAgtgagtaaca ... atcaccaaagGTAATGAGCTGAAGAAAAGGAAGCGTCCAGGAGGAGGACCAGGGCCCTTCTGGTGGAAGATGGGAAGCAAAAGGCTTCTATACGAAGCGCTTATTGAGCC


Block sizes: 9 (upstream exon), 47 (downstream exon)
Score: 2

GTTTCTCAAGTCCTGAAGATTCAACAACAGTTTTGGCCAGTTTTAGGTCCAACATACGCATCACTACAGGCGCAGCAGGGGTCGGTTTCTTCCAATCATAgtgagtaaca ... atcaccaaagGTAATGAGCTGAAGAAAAGGAAGCGTCCAGGAGGAGGACCAGGGCCCTTCTGGTGGAAGATGGGAAGCAAAAGGCTTCTATACGAAGCGCTTATTGAGCC


Block sizes: 27 (upstream exon), 49 (downstream exon)
Score: 5

GTTTCTCAAGTCCTGAAGATTCAACAACAGTTTTGGCCAGTTTTAGGTCCAACATACGCATCACTACAGGCGCAGCAGGGGTCGGTTTCTTCCAATCATAgtgagtaaca ... atcaccaaagGTAATGAGCTGAAGAAAAGGAAGCGTCCAGGAGGAGGACCAGGGCCCTTCTGGTGGAAGATGGGAAGCAAAAGGCTTCTATACGAAGCGCTTATTGAGCC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTCTCAAGTCCTGAAGATTCAACAACAGTTTTGGCCAGTTTTAGGTCCAACATACGCATCACTACAGGCGCAGCAGGGGTCGGTTTCTTCCAATCATAgtgagtaacatcactagttattgaattgcataaccattatgaaacctcatagcgagaacaacttgcctggctacctttgggtttgatattagagatttgc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gagaacaa