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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgataaattaacaaaaactgcgtgaaaggaggatataaattgttttccgtaggagggtggttggtgcgttttactgatgaaatgcgcaatacgatttcagTTCATGACATCTGATCACTCATATGTATCACGGAAGCATGAGGAGGATAAGGTGATCATCTTTGAGAGAGGAGATTTGGTCTTCGTGTTCAACTTCCACT

Basic information

species Zea mays
transcript GRMZM2G073054_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|32836879|gb|CD976557.1|CD976557
EST:     GTATGCAAGAGTTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAA                         TTCATGACATCTGATCACTCATATGTATCACGGAAGCATGAGGAGGATAAG
genomic: GTATGCAAGAGTTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAAgtatgtcact ... acgatttcagTTCATGACATCTGATCACTCATATGTATCACGGAAGCATGAGGAGGATAAG
EST: gi|60347950|gb|DN214923.1|DN214923
EST:     GTATGCAAGAGTTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAA                         TTCATGACATCTGATCACTCATATGTATCACGGAAGCATGAGGAGGATAAG
genomic: GTATGCAAGAGTTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAAgtatgtcact ... acgatttcagTTCATGACATCTGATCACTCATATGTATCACGGAAGCATGAGGAGGATAAG
EST: gi|32934500|gb|CF039312.1|CF039312
EST:     GTATGCAAGAGTTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAA                         TTCATGACATCTGATCACTCATATGTATCACGGAAGCATGAGGAGGATAAG
genomic: GTATGCAAGAGTTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAAgtatgtcact ... acgatttcagTTCATGACATCTGATCACTCATATGTATCACGGAAGCATGAGGAGGATAAG
EST: gi|60338294|gb|DN205267.1|DN205267
EST:     GTATGCAAGAGTTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAA                         TTCATGACATCTGATCACTCATATGTATCACGGAAGCATGAGGAGGATAAG
genomic: GTATGCAAGAGTTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAAgtatgtcact ... acgatttcagTTCATGACATCTGATCACTCATATGTATCACGGAAGCATGAGGAGGATAAG
EST: gi|32837113|gb|CD976791.1|CD976791
EST:     GTATGCAAGAGTTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAA                         TTCATGACATCTGATCACTCATATGTATCACGGAAGCATGAGGAGGATAAG
genomic: GTATGCAAGAGTTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAAgtatgtcact ... acgatttcagTTCATGACATCTGATCACTCATATGTATCACGGAAGCATGAGGAGGATAAG
EST: gi|32920624|gb|CF025436.1|CF025436
EST:     GTATGCAAGAGTTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAA                         TTCATGACATCTGATCACTCATATGTATCACGGAAGCATGAGGAGGATAAG
genomic: GTATGCAAGAGTTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAAgtatgtcact ... acgatttcagTTCATGACATCTGATCACTCATATGTATCACGGAAGCATGAGGAGGATAAG
EST: gi|78024920|gb|DV493307.1|DV493307
EST:     GTATGCAAGAGTTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAA                         TTCATGACATCTGATCACTCATATGTATCACGGAAGCATGAGGAGGATAAG
genomic: GTATGCAAGAGTTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAAgtatgtcact ... acgatttcagTTCATGACATCTGATCACTCATATGTATCACGGAAGCATGAGGAGGATAAG
EST: gi|60394366|gb|DN227236.1|DN227236
EST:     GTATGCAAGAGTTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAA                         TTCATGACATCTGATCACTCATATGTATCACGGAAGCATGAGGAGGATAAG
genomic: GTATGCAAGAGTTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAAgtatgtcact ... acgatttcagTTCATGACATCTGATCACTCATATGTATCACGGAAGCATGAGGAGGATAAG
EST: gi|91878000|gb|EB407957.1|EB407957
EST:     GTATGCAAGAGTTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAA                         TTCATGACATCTGATCACTCATATGTATCACGGAAGCATGAGGAGGATAAG
genomic: GTATGCAAGAGTTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAAgtatgtcact ... acgatttcagTTCATGACATCTGATCACTCATATGTATCACGGAAGCATGAGGAGGATAAG
EST: gi|60345781|gb|DN212754.1|DN212754
EST:     GTATGCAAGAGTTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAA                         TTCATGACATCTGATCACTCATATGTATCACGGAAGCATGAGGAGGATAAG
genomic: GTATGCAAGAGTTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAAgtatgtcact ... acgatttcagTTCATGACATCTGATCACTCATATGTATCACGGAAGCATGAGGAGGATAAG
EST: gi|211026372|gb|FL004586.1|FL004586
EST:     GTATGCAAGAGTTNGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAA                         TTCATGACATCTGATCACTCATATGTATCACGGAAGCATGAGGAGGATAAG
genomic: GTATGCAAGAGTTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAAgtatgtcact ... acgatttcagTTCATGACATCTGATCACTCATATGTATCACGGAAGCATGAGGAGGATAAG
EST: gi|32864974|gb|CF004656.1|CF004656
EST:     GTATGCAAGAGTTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAA                         TTCATGACATCTGATCACTCATATGTATCACGGAAGCATGAGGAGGATAAA
genomic: GTATGCAAGAGTTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAAgtatgtcact ... acgatttcagTTCATGACATCTGATCACTCATATGTATCACGGAAGCATGAGGAGGATAA-
EST: gi|101386687|gb|EB815360.1|EB815360
EST:     TTTGACCAGGCAATGCAGCACC-TGAGGGAAAATATGAA                         TTCATGACATCTGATCACTCATATGTATCACGGAAGCATGAGGAGGATAAG
genomic: TTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAAgtatgtcact ... acgatttcagTTCATGACATCTGATCACTCATATGTATCACGGAAGCATGAGGAGGATAAG
EST: gi|32930900|gb|CF035712.1|CF035712
EST:     GTATGCAAGAGTTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAA                         TTCATGACATCTGATCACTCATATGTATCACGGAAGCATGAGGAGGATAAG
genomic: GTATGCAAGAGTTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAAgtatgtcact ... acgatttcagTTCATGACATCTGATCACTCATATGTATCACGGAAGCATGAGGAGGATAAG
EST: gi|32837751|gb|CD977429.1|CD977429
EST:     GTATGCAAGAGTTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAA                         TTCATGACATCTGATCACTCATATGTATCACGGAAGCATGAGGAGGATAAG
genomic: GTATGCAAGAGTTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAAgtatgtcact ... acgatttcagTTCATGACATCTGATCACTCATATGTATCACGGAAGCATGAGGAGGATAAG
EST: gi|32921787|gb|CF026599.1|CF026599
EST:     GTATGCAAGAGTTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAA                         TTCATGACATCTGATCACTCATATGTATCACGGAAGCATGAGGAGGATAAG
genomic: GTATGCAAGAGTTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAAgtatgtcact ... acgatttcagTTCATGACATCTGATCACTCATATGTATCACGGAAGCATGAGGAGGATAAG
EST: gi|17921780|gb|BM259431.1|BM259431
EST:     ACCAGGCAATGCAGCACCTTGAGGGAAAATATGAA                         TTCATGACATCTGATCACTCATATGTATCACGGAAGCATGAGGAGGATAAG
genomic: ACCAGGCAATGCAGCACCTTGAGGGAAAATATGAAgtatgtcact ... acgatttcagTTCATGACATCTGATCACTCATATGTATCACGGAAGCATGAGGAGGATAAG
EST: gi|32931179|gb|CF035991.1|CF035991
EST:     GTATGCAAGAGTTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAA                         TTCATGACATCTGATCACTCATATGTATCACGGAAGCATGAGGAGGATAAG
genomic: GTATGCAAGAGTTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAAgtatgtcact ... acgatttcagTTCATGACATCTGATCACTCATATGTATCACGGAAGCATGAGGAGGATAAG
EST: gi|32933816|gb|CF038628.1|CF038628
EST:     GTATGCAAGAGTTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAA                         TTCATGACATCTGATCACTCATATGTATCACGGAAGCATGAGGAGGATAAG
genomic: GTATGCAAGAGTTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAAgtatgtcact ... acgatttcagTTCATGACATCTGATCACTCATATGTATCACGGAAGCATGAGGAGGATAAG

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: 834

GGAGATGCAGATTATCTTAGATATCGTGGTATGCAAGAGTTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAAgtatgtcact ... acgatttcagTTCATGACATCTGATCACTCATATGTATCACGGAAGCATGAGGAGGATAAGGTGATCATCTTTGAGAGAGGAGATTTGGTCTTCGTGTTCAACTTCCACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 219

GGAGATGCAGATTATCTTAGATATCGTGGTATGCAAGAGTTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAAgtatgtcact ... acgatttcagTTCATGACATCTGATCACTCATATGTATCACGGAAGCATGAGGAGGATAAGGTGATCATCTTTGAGAGAGGAGATTTGGTCTTCGTGTTCAACTTCCACT


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 28

GGAGATGCAGATTATCTTAGATATCGTGGTATGCAAGAGTTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAAgtatgtcact ... acgatttcagTTCATGACATCTGATCACTCATATGTATCACGGAAGCATGAGGAGGATAAGGTGATCATCTTTGAGAGAGGAGATTTGGTCTTCGTGTTCAACTTCCACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 257

GGAGATGCAGATTATCTTAGATATCGTGGTATGCAAGAGTTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAAgtatgtcact ... acgatttcagTTCATGACATCTGATCACTCATATGTATCACGGAAGCATGAGGAGGATAAGGTGATCATCTTTGAGAGAGGAGATTTGGTCTTCGTGTTCAACTTCCACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccgtaggagggtggttggtgcgttttactgatgaaatgcgcaatacgatttcagTTCATGACATCTGATCACTCATATGTATCACGGAAGCATGAGGAGGATAAGGTGATCATCTTTGAGAGAGGAGATTTGGTCTTCGTGTTCAACTTCCACT
                          tactgat  putative branch site (score: 257)
                       ttttact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgataaattaacaaaaactgcgtgaaaggaggatataaattgttttccgtaggagggtggttggtgcgttttactgatgaaatgcgcaatacgatttcagTTCATGACATCTGATCACTCATATGTATCACGGAAGCATGAGGAGGATAAGGTGATCATCTTTGAGAGAGGAGATTTGGTCTTCGTGTTCAACTTCCACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - -aacaaaa
- - - - - - - - -ctgcgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgatga