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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatgttttgagttgtcatatagtggatggatagctttctaacttgtgtaacagcttttgttaatgggagccactgagaggcacaaccttttatgtgcagGTGCTGTTTGCAACTGCATTCTACCAGAGTCCCTCAAGATCAACGCGGCCGGTCATGACCCAGCTTCTCGAGCTGAAGATAGCGAGAGAAAAATGCTGAC

Basic information

species Zea mays
transcript GRMZM2G049382_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|76286587|gb|DV026155.1|DV026155
EST:     GTTGACAGGAAATTTTATTCCAAAATGGGTGAATCGACTTGCT-GAATGG                         GTGCTGTTTGCAACTGCATTCTACCAGAGTCCCTCAAGATCAACGCGGCCG
genomic: GTTGACAGGAAATTTTATTCCAAAATGGGTGAATCGACTTGCTAGAATGGgtaggagttc ... ttatgtgcagGTGCTGTTTGCAACTGCATTCTACCAGAGTCCCTCAAGATCAACGCGGCCG
EST: gi|93016747|gb|EB642267.1|EB642267
EST:     GTTGACAGGAAATTTTATTCCAAAATGGGTGAATCGACTTGCTAGAATGG                         GTGCTGNTTTGCA-CTGCATTCTA
genomic: GTTGACAGGAAATTTTATTCCAAAATGGGTGAATCGACTTGCTAGAATGGgtaggagttc ... ttatgtgcagGTGCTG-TTTGCAACTGCATTCTA
EST: gi|71775361|gb|DR973239.1|DR973239
EST:     GTTGACAGGAAATTTTATTCCAAAATGGGTGAATCGACTTGCTAGAATGG                         GTGCTGTTTGCAACTGCATTCTACCAGAGTCCCTCAAGATCAACGCGGCCG
genomic: GTTGACAGGAAATTTTATTCCAAAATGGGTGAATCGACTTGCTAGAATGGgtaggagttc ... ttatgtgcagGTGCTGTTTGCAACTGCATTCTACCAGAGTCCCTCAAGATCAACGCGGCCG
EST: gi|101389927|gb|EB816894.1|EB816894
EST:     GTTGACAGGAAATTTTATTCCAAAATGGGTGAATCGACTTGCT-GAATGG                         GTGCTGTTTGCAACTGCATTCTACCAGAGTCCCTCAAGATCAACGCGGCCG
genomic: GTTGACAGGAAATTTTATTCCAAAATGGGTGAATCGACTTGCTAGAATGGgtaggagttc ... ttatgtgcagGTGCTGTTTGCAACTGCATTCTACCAGAGTCCCTCAAGATCAACGCGGCCG
EST: gi|71444264|gb|DR825314.1|DR825314
EST:     GTTGACAGGAAATTTTATTCCAAAATGGGTGAATCGACTTGCTAGAATGG                         GTGCTGTTTGCAACTGCATTCTACCAGAGTCCCTTCA-GATCAACGCGGC
genomic: GTTGACAGGAAATTTTATTCCAAAATGGGTGAATCGACTTGCTAGAATGGgtaggagttc ... ttatgtgcagGTGCTGTTTGCAACTGCATTCTACCAGAGTCCCT-CAAGATCAACGCGGC
EST: gi|76015122|gb|DT942292.1|DT942292
EST:     GTTGACAGGAAATTTTATTCCAAAATGGGTGAATCGACTTGCTAGAATGG                         GTGCTGTTTGCAACTGCATTCTACCAGAGTCCCTCAAGATCAACGCGGCCG
genomic: GTTGACAGGAAATTTTATTCCAAAATGGGTGAATCGACTTGCTAGAATGGgtaggagttc ... ttatgtgcagGTGCTGTTTGCAACTGCATTCTACCAGAGTCCCTCAAGATCAACGCGGCCG
EST: gi|71437491|gb|DR818541.1|DR818541
EST:     GTTGACAGGAAATTTTATTCCAAAATGGGTGAATCGACTTGCTAGAATGG                         GTGCTGTTTGCAACTGCATTCTACCAGAGTCCCTCAAGATCAACGCGGCCG
genomic: GTTGACAGGAAATTTTATTCCAAAATGGGTGAATCGACTTGCTAGAATGGgtaggagttc ... ttatgtgcagGTGCTGTTTGCAACTGCATTCTACCAGAGTCCCTCAAGATCAACGCGGCCG
EST: gi|74241229|gb|DT649143.1|DT649143
EST:     GTTGACAGGAAATTTTATTCCAAAATGGGTGAATCGACTTGCTAGAATGG                         GTGCTGTTTGCAACTGCATTCTACCAGAGTCCCTCAAGATCAACGCGGCCC
genomic: GTTGACAGGAAATTTTATTCCAAAATGGGTGAATCGACTTGCTAGAATGGgtaggagttc ... ttatgtgcagGTGCTGTTTGCAACTGCATTCTACCAGAGTCCCTCAAGATCAACGCGGCC-
EST: gi|78109421|gb|DV527837.1|DV527837
EST:     GTTGACAGGAAATTTTATTCCAAAATGGGTGAATCGACTTGCTAGAATGG                         GTGCTGTTTGCAACTGCATTCTACCAGAGTCCCTCAAGATCAACGCGGCCG
genomic: GTTGACAGGAAATTTTATTCCAAAATGGGTGAATCGACTTGCTAGAATGGgtaggagttc ... ttatgtgcagGTGCTGTTTGCAACTGCATTCTACCAGAGTCCCTCAAGATCAACGCGGCCG
EST: gi|76286586|gb|DV026154.1|DV026154
EST:     GTTGACAGGAAATTTTATTCCAAAATGGGTGAATCGACTTGCT-GAATGG                         GTGCTGTTTGCAACTGCATTCTACCAGAGTCCCTCAAGATCAACGCGGCCG
genomic: GTTGACAGGAAATTTTATTCCAAAATGGGTGAATCGACTTGCTAGAATGGgtaggagttc ... ttatgtgcagGTGCTGTTTGCAACTGCATTCTACCAGAGTCCCTCAAGATCAACGCGGCCG
EST: gi|30088173|gb|CB886378.1|CB886378
EST:     GTTGACAGGAAATTTTATTCCAAAATGGGTGAATCGACTTGCTAGAATGG                         GTGCTGTTTGCAACTGCATTCTACCAGAGTCCCTCAAGATCAACGCGGCCG
genomic: GTTGACAGGAAATTTTATTCCAAAATGGGTGAATCGACTTGCTAGAATGGgtaggagttc ... ttatgtgcagGTGCTGTTTGCAACTGCATTCTACCAGAGTCCCTCAAGATCAACGCGGCCG
EST: gi|93014379|gb|EB639899.1|EB639899
EST:     GTTGACAGGAAATTTTATTCCAAAATGGGTGAATCGACTTGCTAGAATGG                         GTGCTGTTTGCAACTGCATTCTACCAGAGTCCCTCAAG
genomic: GTTGACAGGAAATTTTATTCCAAAATGGGTGAATCGACTTGCTAGAATGGgtaggagttc ... ttatgtgcagGTGCTGTTTGCAACTGCATTCTACCAGAGTCCCTCAAG
EST: gi|78109677|gb|DV528093.1|DV528093
EST:     GTTGACAGGAAATTTTATTCCAAAATGGGTGAATCGACTTGCTAGAATGG                         GTGCTGTTTGCAACTGCATTCTACCAGAGTCCCTCAAGATCAACGCGGCCG
genomic: GTTGACAGGAAATTTTATTCCAAAATGGGTGAATCGACTTGCTAGAATGGgtaggagttc ... ttatgtgcagGTGCTGTTTGCAACTGCATTCTACCAGAGTCCCTCAAGATCAACGCGGCCG
EST: gi|37380498|gb|CF627065.1|CF627065
EST:     GTTGACAGGAAATTTTATTCCAAAATGGGTGAATCGACTTGCTAGAATGG                         GTGCTGTTTGCAACTGCATTCTACCAGAGTCCCTCAAGATCAACGCGGCCG
genomic: GTTGACAGGAAATTTTATTCCAAAATGGGTGAATCGACTTGCTAGAATGGgtaggagttc ... ttatgtgcagGTGCTGTTTGCAACTGCATTCTACCAGAGTCCCTCAAGATCAACGCGGCCG
EST: gi|101389925|gb|EB816893.1|EB816893
EST:     GTTGACAGGAAATTTTATTCCAAAATGGGTGAATCGACTTGCT-GAATGG                         GTGCTGTTTGCAACTGCATTCTACCAGAGTCCCTCAAGATCAACGCGGCCG
genomic: GTTGACAGGAAATTTTATTCCAAAATGGGTGAATCGACTTGCTAGAATGGgtaggagttc ... ttatgtgcagGTGCTGTTTGCAACTGCATTCTACCAGAGTCCCTCAAGATCAACGCGGCCG
EST: gi|149081435|gb|EE170555.2|EE170555
EST:     GTTGACAGGAAATTTTATTCCAAAATGGGTGAATCGACTTGCTAGAATGG                         GTGCTGTTTGCAACTGCATTCTACCAGAGTCCCTCAAGATCAACGCGGCCG
genomic: GTTGACAGGAAATTTTATTCCAAAATGGGTGAATCGACTTGCTAGAATGGgtaggagttc ... ttatgtgcagGTGCTGTTTGCAACTGCATTCTACCAGAGTCCCTCAAGATCAACGCGGCCG
EST: gi|94476135|gb|EB705093.1|EB705093
EST:     GTTGACAGGAAATTTTATTCCAAAATGGGTGAATCGACTTGCTAGAATGG                         GTGCTGTTTGCAACTGCATTCTACCAGAGTCCCTCAAGATCAACGCGGCCG
genomic: GTTGACAGGAAATTTTATTCCAAAATGGGTGAATCGACTTGCTAGAATGGgtaggagttc ... ttatgtgcagGTGCTGTTTGCAACTGCATTCTACCAGAGTCCCTCAAGATCAACGCGGCCG
EST: gi|78109676|gb|DV528092.1|DV528092
EST:     GTTGACAGGAAATTTTATTCCAAAATGGGTGAATCGACTTGCTAGAATGG                         GTGCTGTTTGCAACTGCATTCTACCAGAGTCCCTCAAGATCAACGCGGCCG
genomic: GTTGACAGGAAATTTTATTCCAAAATGGGTGAATCGACTTGCTAGAATGGgtaggagttc ... ttatgtgcagGTGCTGTTTGCAACTGCATTCTACCAGAGTCCCTCAAGATCAACGCGGCCG

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), 49 (downstream exon)
Score: 65

CATTTGATAAGTAAAAACTGCAACCATTTCTGTGAGGATATCTGCAAAAGGTTGACAGGAAATTTTATTCCAAAATGGGTGAATCGACTTGCTAGAATGGgtaggagttc ... ttatgtgcagGTGCTGTTTGCAACTGCATTCTACCAGAGTCCCTCAAGATCAACGCGGCCGGTCATGACCCAGCTTCTCGAGCTGAAGATAGCGAGAGAAAAATGCTGAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 57

CATTTGATAAGTAAAAACTGCAACCATTTCTGTGAGGATATCTGCAAAAGGTTGACAGGAAATTTTATTCCAAAATGGGTGAATCGACTTGCTAGAATGGgtaggagttc ... ttatgtgcagGTGCTGTTTGCAACTGCATTCTACCAGAGTCCCTCAAGATCAACGCGGCCGGTCATGACCCAGCTTCTCGAGCTGAAGATAGCGAGAGAAAAATGCTGAC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 57

CATTTGATAAGTAAAAACTGCAACCATTTCTGTGAGGATATCTGCAAAAGGTTGACAGGAAATTTTATTCCAAAATGGGTGAATCGACTTGCTAGAATGGgtaggagttc ... ttatgtgcagGTGCTGTTTGCAACTGCATTCTACCAGAGTCCCTCAAGATCAACGCGGCCGGTCATGACCCAGCTTCTCGAGCTGAAGATAGCGAGAGAAAAATGCTGAC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 44

CATTTGATAAGTAAAAACTGCAACCATTTCTGTGAGGATATCTGCAAAAGGTTGACAGGAAATTTTATTCCAAAATGGGTGAATCGACTTGCTAGAATGGgtaggagttc ... ttatgtgcagGTGCTGTTTGCAACTGCATTCTACCAGAGTCCCTCAAGATCAACGCGGCCGGTCATGACCCAGCTTCTCGAGCTGAAGATAGCGAGAGAAAAATGCTGAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtaacagcttttgttaatgggagccactgagaggcacaaccttttatgtgcagGTGCTGTTTGCAACTGCATTCTACCAGAGTCCCTCAAGATCAACGCGGCCGGTCATGACCCAGCTTCTCGAGCTGAAGATAGCGAGAGAAAAATGCTGAC
             tgttaat  putative branch site (score: 44)
                                         ccttttat  putative PPT
          ttttgttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatgttttgagttgtcatatagtggatggatagctttctaacttgtgtaacagcttttgttaatgggagccactgagaggcacaaccttttatgtgcagGTGCTGTTTGCAACTGCATTCTACCAGAGTCCCTCAAGATCAACGCGGCCGGTCATGACCCAGCTTCTCGAGCTGAAGATAGCGAGAGAAAAATGCTGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG