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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcctctttacctcgtgtcctccttttcttctgcatgcggcgtacttaccagtatcaccaatattgctgcaaccaaaatatatttggttcctttctgtttgacgtggatctcctgtgtaactgcagATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGATGGCTTCATCACACGTTTGAGGGAGGAAATCGCAGCCTTCAAATGATTTT

Basic information

species Zea mays
transcript GRMZM2G553314_T01
intron # 19
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|6952479|gb|AW424547.1|AW424547
EST:     AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAAT                         ATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
genomic: AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAATgtaagtcctc ... gtaactgcagATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
EST: gi|166638170|gb|EG314081.1|EG314081
EST:     AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAAT                         ATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTC
genomic: AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAATgtaagtcctc ... gtaactgcagATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTC
EST: gi|113703092|gb|EE680596.1|EE680596
EST:     AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAAT                         ATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
genomic: AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAATgtaagtcctc ... gtaactgcagATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
EST: gi|60353902|gb|DN220875.1|DN220875
EST:     AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAAT                         ATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
genomic: AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAATgtaagtcctc ... gtaactgcagATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
EST: gi|113633353|gb|DW791645.1|DW791645
EST:     CGAGACTGGAAAT                         ATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
genomic: CGAGACTGGAAATgtaagtcctc ... gtaactgcagATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
EST: gi|211228557|gb|FL433549.1|FL433549
EST:     AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAAT                         ATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
genomic: AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAATgtaagtcctc ... gtaactgcagATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
EST: gi|60398537|gb|DN231353.1|DN231353
EST:     AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAAT                         ATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
genomic: AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAATgtaagtcctc ... gtaactgcagATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
EST: gi|211470957|gb|FL472665.1|FL472665
EST:     AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAAT                         ATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
genomic: AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAATgtaagtcctc ... gtaactgcagATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
EST: gi|60338498|gb|DN205471.1|DN205471
EST:     AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAAT                         ATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
genomic: AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAATgtaagtcctc ... gtaactgcagATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
EST: gi|33098241|gb|CF058201.1|CF058201
EST:     AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAAT                         ATATGCGTTAGGGTAAGAGACAATGCTGACCTGGCCACAATGAGTGTAGAT
genomic: AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAATgtaagtcctc ... gtaactgcagATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
EST: gi|149089739|gb|EE179010.2|EE179010
EST:     AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAAT                         ATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
genomic: AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAATgtaagtcctc ... gtaactgcagATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
EST: gi|78092216|gb|DV520590.1|DV520590
EST:     AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAAT                         ATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
genomic: AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAATgtaagtcctc ... gtaactgcagATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
EST: gi|4314687|gb|AI438596.2|AI438596
EST:     AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAAT                         ATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
genomic: AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAATgtaagtcctc ... gtaactgcagATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
EST: gi|60339876|gb|DN206849.1|DN206849
EST:     AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAAT                         ATATGCGTTAGGGTAAGAGACAATGCTGACCTGGCCACAATGAGTGTAGAT
genomic: AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAATgtaagtcctc ... gtaactgcagATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
EST: gi|166421299|gb|EG291044.1|EG291044
EST:     TGTCGTAGGTGCACAAGAGGCCGAGACTGGAAAT                         ATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
genomic: TGTCGTAGGTGCACAAGAGGCCGAGACTGGAAATgtaagtcctc ... gtaactgcagATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
EST: gi|60339654|gb|DN206627.1|DN206627
EST:     AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAAT                         ATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
genomic: AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAATgtaagtcctc ... gtaactgcagATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
EST: gi|211470956|gb|FL472664.1|FL472664
EST:     AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAAT                         ATATGCGTTAGGGTAARAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
genomic: AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAATgtaagtcctc ... gtaactgcagATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
EST: gi|37388666|gb|CF631544.1|CF631544
EST:     AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAAT                         ATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
genomic: AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAATgtaagtcctc ... gtaactgcagATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
EST: gi|211228558|gb|FL433550.1|FL433550
EST:     AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAAT                         ATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
genomic: AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAATgtaagtcctc ... gtaactgcagATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
EST: gi|5069904|gb|AI737869.1|AI737869
EST:     AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAAT                         ATATGCGTTAGGGTAAGAGACAATGCTGACCTGGCCACAATGAGTGTAGAT
genomic: AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAATgtaagtcctc ... gtaactgcagATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
EST: gi|16378424|gb|BI992438.1|BI992438
EST:     AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAAT                         ATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
genomic: AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAATgtaagtcctc ... gtaactgcagATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
EST: gi|13249712|gb|BG360617.1|BG360617
EST:     AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAAT                         ATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
genomic: AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAATgtaagtcctc ... gtaactgcagATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
EST: gi|60346740|gb|DN213713.1|DN213713
EST:     AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAAT                         ATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
genomic: AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAATgtaagtcctc ... gtaactgcagATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
EST: gi|8665943|gb|BE186759.1|BE186759
EST:     AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAAT                         ATATGCGTTAGGGTAAGAGACAATGCTGACCTGGCCACAATGAGTGTAGAT
genomic: AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAATgtaagtcctc ... gtaactgcagATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
EST: gi|76021643|gb|DT948813.1|DT948813
EST:     AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAAT                         ATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCCCAACGAGTGTAGAT
genomic: AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAATgtaagtcctc ... gtaactgcagATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
EST: gi|78544270|gb|DV621768.1|DV621768
EST:     AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAAT                         ATATGCGTTAGGGTAAGAGACAATGCTGACCTGGCCACAATGAGTGTAGAT
genomic: AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAATgtaagtcctc ... gtaactgcagATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
EST: gi|60338142|gb|DN205115.1|DN205115
EST:     AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAAT                         ATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
genomic: AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAATgtaagtcctc ... gtaactgcagATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
EST: gi|60344806|gb|DN211779.1|DN211779
EST:     AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAAT                         ATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
genomic: AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAATgtaagtcctc ... gtaactgcagATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
EST: gi|50334017|gb|CO529143.1|CO529143
EST:     AATTCAACTCCATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAAT                         ATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
genomic: AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAATgtaagtcctc ... gtaactgcagATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
EST: gi|60343958|gb|DN210931.1|DN210931
EST:     AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAAT                         ATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT
genomic: AATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAATgtaagtcctc ... gtaactgcagATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGAT

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: 235

GTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAATgtaagtcctc ... gtaactgcagATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGATGGCTTCATCACACGTTTGAGGGAGGAAATCGCAGCCTTCAAATGATTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 217

GTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAATgtaagtcctc ... gtaactgcagATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGATGGCTTCATCACACGTTTGAGGGAGGAAATCGCAGCCTTCAAATGATTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 206

GTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAATgtaagtcctc ... gtaactgcagATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGATGGCTTCATCACACGTTTGAGGGAGGAAATCGCAGCCTTCAAATGATTTT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 167

GTACGGGAAGCTCAACTGGCCCAATTCAACTACATTCTTGTCGTAGGTGCACAAGAGGCCGAGACTGGAAATgtaagtcctc ... gtaactgcagATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGATGGCTTCATCACACGTTTGAGGGAGGAAATCGCAGCCTTCAAATGATTTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accaaaatatatttggttcctttctgtttgacgtggatctcctgtgtaactgcagATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGATGGCTTCATCACACGTTTGAGGGAGGAAATCGCAGCCTTCAAATGATTTT
                                           gtgtaac  putative branch site (score: 167)
     aatatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcctctttacctcgtgtcctccttttcttctgcatgcggcgtacttaccagtatcaccaatattgctgcaaccaaaatatatttggttcctttctgtttgacgtggatctcctgtgtaactgcagATATGCGTTAGGGTAAGAGACAATGCTGACCTGGTCACAACGAGTGTAGATGGCTTCATCACACGTTTGAGGGAGGAAATCGCAGCCTTCAAATGATTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA