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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcctctgtccatgcctgcaccatgttggttagttcataacatttttttctttacactttttactactagggcaatgcaatctagttgaataccaataatcatgtgctgtagtgggaatagagttatgttctttattttgtaccacatatttacgggggaatacatcttatgcagCCATGAGCAGATTGTTGAGAGCTTGAAGGGCCTTAATATGAGGACCTACATGCTCGCAAAGAACATCGTTGAGCCAGCTCAGCAGGCAACTCGGTGAGGA

Basic information

species Zea mays
transcript GRMZM2G151549_T01
intron # 6
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|5871211|gb|AW017682.1|AW017682
EST:     ATCGATTCAGTATCAGGAACTCTCATCATGACAACCAATCACGTCAATGT                         CCATGAGCAGATTGTTGAGAGCTTGAAGGGCCTTAATATGAGGACCTACAT
genomic: ATCGATTCAGTATCAGGAACTCTCATCATGACAACCAATCACGTCAATGTgtaagttcct ... tcttatgcagCCATGAGCAGATTGTTGAGAGCTTGAAGGGCCTTAATATGAGGACCTACAT
EST: gi|60354741|gb|DN221714.1|DN221714
EST:     ATCGATTCAGTATCAGGAACTCTCATCATGACAACCAATCACGTCAATGT                         CCATGAGCAGATTGTTGAGAGCTTGAAGGGCCTTAATATGAGGACCTACAT
genomic: ATCGATTCAGTATCAGGAACTCTCATCATGACAACCAATCACGTCAATGTgtaagttcct ... tcttatgcagCCATGAGCAGATTGTTGAGAGCTTGAAGGGCCTTAATATGAGGACCTACAT
EST: gi|211496877|gb|FL295235.1|FL295235
EST:     ATCGATTCAGTATCAGGAACTCTCATCATGACAACCAATCACGTCAATGT                         CCATGAGCAGATTGTTGAGAGCTTGAAGGGCCTTAATATGAGGACCTACAT
genomic: ATCGATTCAGTATCAGGAACTCTCATCATGACAACCAATCACGTCAATGTgtaagttcct ... tcttatgcagCCATGAGCAGATTGTTGAGAGCTTGAAGGGCCTTAATATGAGGACCTACAT
EST: gi|67023707|gb|CO452456.1|CO452456
EST:     ATCGATTCAGTATCAGGAACTCTCATCATGACAACCAATCACGTCAATGT                         CCATGAGCAGATTGTTGAGAGCTTGAAGGGCCTTAATATGAGGACCTACAT
genomic: ATCGATTCAGTATCAGGAACTCTCATCATGACAACCAATCACGTCAATGTgtaagttcct ... tcttatgcagCCATGAGCAGATTGTTGAGAGCTTGAAGGGCCTTAATATGAGGACCTACAT
EST: gi|60354489|gb|DN221462.1|DN221462
EST:     ATCGATTCAGTATCAGGAACTCTCATCATGACAACCAATCACGTCAATGT                         CCATGAGCAGATTGTTGAGAGCTTGAAGGGCCTTAATATGAGGACCTACAT
genomic: ATCGATTCAGTATCAGGAACTCTCATCATGACAACCAATCACGTCAATGTgtaagttcct ... tcttatgcagCCATGAGCAGATTGTTGAGAGCTTGAAGGGCCTTAATATGAGGACCTACAT
EST: gi|71772603|gb|DR970531.1|DR970531
EST:     ATCGATTCAGTATCAGGAACTCTCATCATGACAACCAATCACGTCAATGT                         CCATGAGCAGATTGTTGAGAGCTTGAAGGGCCTTAATATGAGGACCTACAT
genomic: ATCGATTCAGTATCAGGAACTCTCATCATGACAACCAATCACGTCAATGTgtaagttcct ... tcttatgcagCCATGAGCAGATTGTTGAGAGCTTGAAGGGCCTTAATATGAGGACCTACAT
EST: gi|148929371|gb|EC875323.2|EC875323
EST:     ATCGATTCAGTATCAGGAACTCTCATCATGACAACCAATCACGTCAATGT                         CCATGAGCAGATTGTTGAGAGCTTGAAGGGCCTTAATATGAGGACCTACAT
genomic: ATCGATTCAGTATCAGGAACTCTCATCATGACAACCAATCACGTCAATGTgtaagttcct ... tcttatgcagCCATGAGCAGATTGTTGAGAGCTTGAAGGGCCTTAATATGAGGACCTACAT
EST: gi|5915274|gb|AW052915.1|AW052915
EST:     ATCGATTCAGTATCAGGAACTCTCATCATGACAACCAATCACGTCAATGT                         CCATGAGCAGATTGTTGAGAGCTTGAAGGGCCTTAATATGAGGACCTACAT
genomic: ATCGATTCAGTATCAGGAACTCTCATCATGACAACCAATCACGTCAATGTgtaagttcct ... tcttatgcagCCATGAGCAGATTGTTGAGAGCTTGAAGGGCCTTAATATGAGGACCTACAT
EST: gi|211221048|gb|FL468686.1|FL468686
EST:     ATCGATTCAGTATCAGGAACTCTCATCATGACAACCAATCACGTCAATGT                         CCATGAGCAGATTGTTGAGAGCTTGAAGGGCCTTAATATGAGGACCTACAT
genomic: ATCGATTCAGTATCAGGAACTCTCATCATGACAACCAATCACGTCAATGTgtaagttcct ... tcttatgcagCCATGAGCAGATTGTTGAGAGCTTGAAGGGCCTTAATATGAGGACCTACAT
EST: gi|78113788|gb|DV532177.1|DV532177
EST:     ATCGATTCAGTATCAGGAACTCTCATCATGACAACCAATCACGTCAATGT                         CCATGAGCAGATTGTTGAGAGCTTGAAGGGCCTTAATATGAGAACCTACAT
genomic: ATCGATTCAGTATCAGGAACTCTCATCATGACAACCAATCACGTCAATGTgtaagttcct ... tcttatgcagCCATGAGCAGATTGTTGAGAGCTTGAAGGGCCTTAATATGAGGACCTACAT
EST: gi|31406350|gb|CD485082.1|CD485082
EST:     ATCGATTCAGTATCAGGAACTCTCATCATGACAACCAATCACGTCAATGT                         CCATGAGCAGATTGTTGAGAGCTTGAAGGGCCTTAATATGAGGACCTACAT
genomic: ATCGATTCAGTATCAGGAACTCTCATCATGACAACCAATCACGTCAATGTgtaagttcct ... tcttatgcagCCATGAGCAGATTGTTGAGAGCTTGAAGGGCCTTAATATGAGGACCTACAT
EST: gi|61119784|gb|DN560745.1|DN560745
EST:     ATCGATTCAGTATCAGGAACTCTCATCATGACAACCAATCACGTCAATGT                         CCATGAGCAGATTGTTGAGAGCTTGAAGGGCCTTAATATGAGGACCTACAT
genomic: ATCGATTCAGTATCAGGAACTCTCATCATGACAACCAATCACGTCAATGTgtaagttcct ... tcttatgcagCCATGAGCAGATTGTTGAGAGCTTGAAGGGCCTTAATATGAGGACCTACAT
EST: gi|6020868|gb|AW065796.1|AW065796
EST:     ATCGATTCAGTATCAGGAACTCTCATCATGACAACCAATCACGTCAATGT                         CCATGAGCAGATTGNTGAGAGCTTGAAGGGCCTTAATATGAGGACCTACAT
genomic: ATCGATTCAGTATCAGGAACTCTCATCATGACAACCAATCACGTCAATGTgtaagttcct ... tcttatgcagCCATGAGCAGATTGTTGAGAGCTTGAAGGGCCTTAATATGAGGACCTACAT
EST: gi|148988253|gb|EE031627.2|EE031627
EST:     ATCGATTCAGTATCAGGAACTCTCATCATGACAACCAATCACGTCAATGT                         CCATGAGCAGATTGTTGAGAGCTTGAAGGGCCTTAATATGAGGACCTACAT
genomic: ATCGATTCAGTATCAGGAACTCTCATCATGACAACCAATCACGTCAATGTgtaagttcct ... tcttatgcagCCATGAGCAGATTGTTGAGAGCTTGAAGGGCCTTAATATGAGGACCTACAT
EST: gi|148947188|gb|EC892526.2|EC892526
EST:     ATCGATTCAGTATCAGGAACTTTCATCATGACAACCAATCACGTCAATGT                         CCATGAGCAGATTGTTGAGAGCTTGAAGGGCCTTAATATGAGGACCTCCAT
genomic: ATCGATTCAGTATCAGGAACTCTCATCATGACAACCAATCACGTCAATGTgtaagttcct ... tcttatgcagCCATGAGCAGATTGTTGAGAGCTTGAAGGGCCTTAATATGAGGACCTACAT
EST: gi|33092079|gb|CF052073.1|CF052073
EST:     ATCGATTCAGTATCAGGAACTCTCATCATGACAACCAATCACGTCAATGT                         CCATGAGCAGATTGTTGAGAGCTTGAAGGGCCTTAATATGAGGACCTACAT
genomic: ATCGATTCAGTATCAGGAACTCTCATCATGACAACCAATCACGTCAATGTgtaagttcct ... tcttatgcagCCATGAGCAGATTGTTGAGAGCTTGAAGGGCCTTAATATGAGGACCTACAT
EST: gi|6194537|gb|AW146641.1|AW146641
EST:     ATCGATTCAGTATCAGGAACTCTCATCATGACAACCAATCACGTCAATGT                         CCATGAGCAGATTGTTGAGAGCTTGAAGGGCCTTAATA
genomic: ATCGATTCAGTATCAGGAACTCTCATCATGACAACCAATCACGTCAATGTgtaagttcct ... tcttatgcagCCATGAGCAGATTGTTGAGAGCTTGAAGGGCCTTAATA
EST: gi|29946191|gb|CB816025.1|CB816025
EST:     ATCGATTCAGTATCAGGAACTCTCATCATGACAACCAATCACGTCAATGT                         CCATGAGCAGATTGTTGAGAGCTTGAAGGGCCTTAATATGAGGACCTACAT
genomic: ATCGATTCAGTATCAGGAACTCTCATCATGACAACCAATCACGTCAATGTgtaagttcct ... tcttatgcagCCATGAGCAGATTGTTGAGAGCTTGAAGGGCCTTAATATGAGGACCTACAT

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: 48 (upstream exon), 48 (downstream exon)
Score: 307

CCGAGTTGTGGATCATGAATTTGGTTAGAAGCTCAAAACTGGATGCCAGGATCGATTCAGTATCAGGAACTCTCATCATGACAACCAATCACGTCAATGTgtaagttcct ... tcttatgcagCCATGAGCAGATTGTTGAGAGCTTGAAGGGCCTTAATATGAGGACCTACATGCTCGCAAAGAACATCGTTGAGCCAGCTCAGCAGGCAACTCGGTGAGGA


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 224

CCGAGTTGTGGATCATGAATTTGGTTAGAAGCTCAAAACTGGATGCCAGGATCGATTCAGTATCAGGAACTCTCATCATGACAACCAATCACGTCAATGTgtaagttcct ... tcttatgcagCCATGAGCAGATTGTTGAGAGCTTGAAGGGCCTTAATATGAGGACCTACATGCTCGCAAAGAACATCGTTGAGCCAGCTCAGCAGGCAACTCGGTGAGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 255

CCGAGTTGTGGATCATGAATTTGGTTAGAAGCTCAAAACTGGATGCCAGGATCGATTCAGTATCAGGAACTCTCATCATGACAACCAATCACGTCAATGTgtaagttcct ... tcttatgcagCCATGAGCAGATTGTTGAGAGCTTGAAGGGCCTTAATATGAGGACCTACATGCTCGCAAAGAACATCGTTGAGCCAGCTCAGCAGGCAACTCGGTGAGGA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 182

CCGAGTTGTGGATCATGAATTTGGTTAGAAGCTCAAAACTGGATGCCAGGATCGATTCAGTATCAGGAACTCTCATCATGACAACCAATCACGTCAATGTgtaagttcct ... tcttatgcagCCATGAGCAGATTGTTGAGAGCTTGAAGGGCCTTAATATGAGGACCTACATGCTCGCAAAGAACATCGTTGAGCCAGCTCAGCAGGCAACTCGGTGAGGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagttatgttctttattttgtaccacatatttacgggggaatacatcttatgcagCCATGAGCAGATTGTTGAGAGCTTGAAGGGCCTTAATATGAGGACCTACATGCTCGCAAAGAACATCGTTGAGCCAGCTCAGCAGGCAACTCGGTGAGGA
     atgttctttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttcctctgtccatgcctgcaccatgttggttagttcataacatttttttctttacactttttactactagggcaatgcaatctagttgaataccaataatcatgtgctgtagtgggaatagagttatgttctttattttgtaccacatatttacgggggaatacatcttatgcagCCATGAGCAGATTGTTGAGAGCTTGAAGGGCCTTAATATGAGGACCTACATGCTCGCAAAGAACATCGTTGAGCCAGCTCAGCAGGCAACTCGGTGAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA