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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taccttgatctagatgcacgtgtgcctggccactaccctggttattcttcactacagctgatgtgataacctcttaaccagtgcccaatctccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCAGGAGGCTCACATGGATTTGTTGTCGGCCACATATGCCCTGAAGCACAG

Basic information

species Zea mays
transcript AC234528.1_FGT005
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC234528.1_FGT005 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os08g44530.1 (Oryza sativa), 3'ss of exon 11
taccttgatctagatgcacgtgtgcctggccactaccctggttattcttcactacagctgatgtgataacctcttaaccagtgcccaatctccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCAGGAGGCTCACATGGATTTGTTGTCGGCCACATATGCCCTGAAGCACAG
     | |||| | ||  | | ||  || |   || | |      || |    |||||||||   |||     |||||  ||   ||| |  || |||||||||| ||||||||||| ||||| |||||||| ||||| ||||||||||||||||| |||||||| || ||||||||||||
-gtagttatcttgctgt-cttctgaatgtctgataactt------tccttgtgacagctgat-caata----tttaacttgtattcaaacatcactacagGAGTGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTTGTTGTAGGCCACATTTGTCCTGAAGCACAG

upper sequence: AC234528.1_FGT005 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA13G27810.1 (Glycine max), 3'ss of exon 11
taccttgatctagatgcacgtgtgcctggccactaccctggttattcttcactac-agctgatgt--gataacctcttaacca-gtgcccaatctccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCAGGAGGCTCACATGGATTTGTTGTCGGCCACATATGCCCTGAAGCACAG
||  |||    |  || |  |||   |     | | | |  | | || | |  |  | |  |||   |||  | | | || ||  |   |  |    | | |||||    ||  |  |||| ||||| |||||||||||||| |||||||||||||| || ||||| ||||| ||||||||||||
tat-ttgtagaaactgaaaatgtcttt---ttcaagctttatgaatcataataatgaacctatgctggatggcatttcaagcatattgtcttttgatactgcagGAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTTGTGGTTGGCCATATATGTCCTGAAGCACAG

upper sequence: AC234528.1_FGT005 (Zea mays), 3'ss of exon 11
lower sequence: AT3G23940.1 (Arabidopsis thaliana), 3'ss of exon 11
-taccttgatctagatgcacgtgtgcctggcca-ctaccctggttattcttcactacagctgatgtgataacctcttaaccagtgcccaatctccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCAGGAGGCTCACATGGATTTGTTGTCGGCCACATATGCCCTGAAGCACAG
 ||   | ||     || || |    ||    | ||||  ||   ||     |  |||     | | ||||  |   ||   ||  | | |      | ||||| || ||  | ||||| |||||||| || || || || ||||| || |||||||| |||||||| ||||||||||| |||
ttatgcttatggtagtg-acctaaatctttttatctactttgtccatatccgagaacacaccttat-ataaagtgccaatatgttgctattgggtgatgcagGAATGTGCATTACTGACTGATGGTAGGTTCTCTGGTGGGTCACACGGTTTTGTTGTTGGCCACATTTGCCCTGAAGCTCAG

upper sequence: AC234528.1_FGT005 (Zea mays), 3'ss of exon 11
lower sequence: Vv05s0051g00830.t01 (Vitis vinifera), 3'ss of exon 11
taccttgatctagatgcac---gtgtgcctggccactaccctggttattcttcactacagctgatgtgataacctcttaaccagtgcccaatctccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCAGGAGGCTCACATGGATTTGTTGTCGGCCACATATGCCCTGAAGCACAG
||  ||    ||||   |     ||  ||||   |  || |||  ||  |||   | ||  |||||| ||      |     | |        |   |  |||||    ||  || |||| |||||||| ||||||||||| |||||||||| |||||| ||||||||||| ||||||||||| 
tatgttctcttagacatattttatgaacctgctta--acactgagtac-ctttgtttcatttgatgtaatgttacttatggaattttattccttatgtggcagGATGTTGCTTTGTTGACTGATGGTAGGTTTTCAGGAGGTTCACATGGATATGTTGTTGGCCACATATGTCCTGAAGCACAT

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|30031654|gb|CB833505.1|CB833505
EST:     CTGAAATGTTGACTCCAACAAGTGCAATAATGGGTGCTGGTCTCGGAAAG                         GAGTGCGCCCTGCTGACAGATGGTAGATTTTCAGGAGGCTCACATGGATTT
genomic: CTGAAATGTTGACTCCAACAAGTGCAATAATGGGTGCTGGTCTCGGAAAGgtaccactta ... tccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCAGGAGGCTCACATGGATTT
EST: gi|24765717|gb|CA400876.1|CA400876
EST:     CTGAAATGTTGACTCCAACAAGCGCAATAATGGGTGCTGGTCTCGGAAAG                         GAGTGCGCCCTGCTGACAGATGGTAGATTTTCCGGAGGGTCACATGGATTT
genomic: CTGAAATGTTGACTCCAACAAGTGCAATAATGGGTGCTGGTCTCGGAAAGgtaccactta ... tccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCAGGAGGCTCACATGGATTT
EST: gi|71760179|gb|DR958116.1|DR958116
EST:     CTGAAATGTTGACTCCAACAAGTGCAATAATGGGTGCTGGTCTCGGAAAG                         GAGTGCGCCCTGCTGACAGATGGTAGATTTTCAGGAGGCTCACATGGATTT
genomic: CTGAAATGTTGACTCCAACAAGTGCAATAATGGGTGCTGGTCTCGGAAAGgtaccactta ... tccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCAGGAGGCTCACATGGATTT
EST: gi|71320321|gb|DR796908.1|DR796908
EST:     CTGAAATGTTGACTCCAACAAGTGCAATAATGGGTGCTGGTCTCGGAAAG                         GAGTGCGCCCTGCTGACAGATGGTAGATTTTCAGGAGGCTCACATGGATTT
genomic: CTGAAATGTTGACTCCAACAAGTGCAATAATGGGTGCTGGTCTCGGAAAGgtaccactta ... tccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCAGGAGGCTCACATGGATTT
EST: gi|87153700|gb|DY398489.1|DY398489
EST:     CTGAAATGTTGACTCCAACAAGCGCAATAATGGGTGCTGGTCTCGGAAAG                         GAGTGCGCCCTGCTGACAGATGGTAGATTTTCAGGAGGCTCACATGGATTT
genomic: CTGAAATGTTGACTCCAACAAGTGCAATAATGGGTGCTGGTCTCGGAAAGgtaccactta ... tccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCAGGAGGCTCACATGGATTT
EST: gi|18385075|gb|BM418274.1|BM418274
EST:     CTGAAATGTTGACTCCAACAAGCGCAATAATGGGTGCTGGTCTCGGAAAG                         GAGTGCGCCCTGCTGACAGATGGTAGATTTTCAGGAGGCTCACATGGATTT
genomic: CTGAAATGTTGACTCCAACAAGTGCAATAATGGGTGCTGGTCTCGGAAAGgtaccactta ... tccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCAGGAGGCTCACATGGATTT
EST: gi|6695730|gb|AW288808.1|AW288808
EST:     CTGAAATGTTGACTCCAACAAGCGCAATAATGGGTGCTGGTCTCGGAAAG                         GAGTGCGCCCTGCTGACAGATGGTAGATTTTCAGGAGGCTCACATGGATTT
genomic: CTGAAATGTTGACTCCAACAAGTGCAATAATGGGTGCTGGTCTCGGAAAGgtaccactta ... tccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCAGGAGGCTCACATGGATTT
EST: gi|101400106|gb|EB821895.1|EB821895
EST:     CTGAAATGTTGACTCCAACAAGTGCAATAATGGGTGCTGGTCTCGGAAAG                         GAGTGCGCCCTGCTGACAGATGGTAGATTTTCAGGAGGCTCACATGGATTT
genomic: CTGAAATGTTGACTCCAACAAGTGCAATAATGGGTGCTGGTCTCGGAAAGgtaccactta ... tccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCAGGAGGCTCACATGGATTT
EST: gi|31405687|gb|CD484419.1|CD484419
EST:     CTGAAATGTTGACTCCAACAAGTGCAATAATGGGTGCTGGTCTCGGAAAG                         GAGTGCGCCCTGCTGACAGATGGTAGATTTTCAGGAGGCTCACATGGATTT
genomic: CTGAAATGTTGACTCCAACAAGTGCAATAATGGGTGCTGGTCTCGGAAAGgtaccactta ... tccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCAGGAGGCTCACATGGATTT
EST: gi|22489566|gb|BU049489.1|BU049489
EST:     CTGAAATGTTGACTCCAACAAGCGCAATAATGGGTGCTGGTCTCGGAAAG                         GAGTGCGCCCTGCTGACAGATGGTAGATTTTCAGGAGGCTCACATGGATTT
genomic: CTGAAATGTTGACTCCAACAAGTGCAATAATGGGTGCTGGTCTCGGAAAGgtaccactta ... tccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCAGGAGGCTCACATGGATTT
EST: gi|89250573|gb|DY622359.1|DY622359
EST:     CTGAAATGTTGACTCCAACAAGTGCAATAATGGGTGCTGGTCTCGGAAAG                         GAGTGCGCCCTGCTGACAGATGGTAGATTTTCAGGAGGCTCACATGGATTT
genomic: CTGAAATGTTGACTCCAACAAGTGCAATAATGGGTGCTGGTCTCGGAAAGgtaccactta ... tccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCAGGAGGCTCACATGGATTT
EST: gi|31363513|gb|CD447870.1|CD447870
EST:     CTGAAATGTTGACTCCAACAAGCGCAATAATGGGTGCTGGTCTCGGAAAG                         GAGTGCGCCCTGCTGACAGATGGTAGATTTTCCGGAGGGTCACATGGATTT
genomic: CTGAAATGTTGACTCCAACAAGTGCAATAATGGGTGCTGGTCTCGGAAAGgtaccactta ... tccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCAGGAGGCTCACATGGATTT
EST: gi|31358397|gb|CD442754.1|CD442754
EST:     CTGAAATGTTGACTCCAACAAGCGCAATAATGGGTGCTGGTCTCGGAAAG                         GAGTGCGCCCTGCTGACAGATGGTAGATTTTCCGGAGGGTCACATGGATTT
genomic: CTGAAATGTTGACTCCAACAAGTGCAATAATGGGTGCTGGTCTCGGAAAGgtaccactta ... tccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCAGGAGGCTCACATGGATTT
EST: gi|17921817|gb|BM259468.1|BM259468
EST:     CAATAATGGGTGCTGGTCTCGGAAAG                         GAGTGCGCCCTGCTGACAGATGGTAGATTTTCAGGAGGCTCACATGGATTT
genomic: CAATAATGGGTGCTGGTCTCGGAAAGgtaccactta ... tccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCAGGAGGCTCACATGGATTT
EST: gi|24764655|gb|CA399819.1|CA399819
EST:     CTGAAATGTTGACTCCAACAAGCGCAATAATGGGTGCTGGTCTCGGAAAG                         GAGTGCGCCCTGCTGACAGATGGTAGATTTTCCGGAGGGTCACATGGATTT
genomic: CTGAAATGTTGACTCCAACAAGTGCAATAATGGGTGCTGGTCTCGGAAAGgtaccactta ... tccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCAGGAGGCTCACATGGATTT
EST: gi|37395981|gb|CF635277.1|CF635277
EST:     CTGAAATGTTGACTCCAACAAGCGCAATAATGGGTGCTGGTCTCGGAAAG                         GAGTGCGCCCTGCTGACAGATGGTAGATTTTCCGGAGGGTCACATGGATTT
genomic: CTGAAATGTTGACTCCAACAAGTGCAATAATGGGTGCTGGTCTCGGAAAGgtaccactta ... tccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCAGGAGGCTCACATGGATTT
EST: gi|32850063|gb|CD989744.1|CD989744
EST:     CTGAAATGTTGACTCCAACAAGCGCAATAATGGGTGCTGGTCTCGGAAAG                         GAGTGCGCCCTGCTGACAGATGGTAGATTTTCAGGAGGCTCACATGGATTT
genomic: CTGAAATGTTGACTCCAACAAGTGCAATAATGGGTGCTGGTCTCGGAAAGgtaccactta ... tccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCAGGAGGCTCACATGGATTT
EST: gi|60354975|gb|DN221948.1|DN221948
EST:     CTGAAATGTTGACTCCAACAAGTGCAATAATGGGTGCTGGTCTCGGAAAG                         GAGTGCGCCCTGCTGACAGATGGTAGATTTTCAGGAGGCTCACATGGATTT
genomic: CTGAAATGTTGACTCCAACAAGTGCAATAATGGGTGCTGGTCTCGGAAAGgtaccactta ... tccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCAGGAGGCTCACATGGATTT

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), 48 (downstream exon)
Score: 175

AAAGGTAGTAGTAATCCGAGGAGAAGGACCAAAAGGAGGGCCAGGGATGCCTGAAATGTTGACTCCAACAAGTGCAATAATGGGTGCTGGTCTCGGAAAGgtaccactta ... tccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCAGGAGGCTCACATGGATTTGTTGTCGGCCACATATGCCCTGAAGCACAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 118

AAAGGTAGTAGTAATCCGAGGAGAAGGACCAAAAGGAGGGCCAGGGATGCCTGAAATGTTGACTCCAACAAGTGCAATAATGGGTGCTGGTCTCGGAAAGgtaccactta ... tccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCAGGAGGCTCACATGGATTTGTTGTCGGCCACATATGCCCTGAAGCACAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 71

AAAGGTAGTAGTAATCCGAGGAGAAGGACCAAAAGGAGGGCCAGGGATGCCTGAAATGTTGACTCCAACAAGTGCAATAATGGGTGCTGGTCTCGGAAAGgtaccactta ... tccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCAGGAGGCTCACATGGATTTGTTGTCGGCCACATATGCCCTGAAGCACAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 69

AAAGGTAGTAGTAATCCGAGGAGAAGGACCAAAAGGAGGGCCAGGGATGCCTGAAATGTTGACTCCAACAAGTGCAATAATGGGTGCTGGTCTCGGAAAGgtaccactta ... tccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCAGGAGGCTCACATGGATTTGTTGTCGGCCACATATGCCCTGAAGCACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttcactacagctgatgtgataacctcttaaccagtgcccaatctccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCAGGAGGCTCACATGGATTTGTTGTCGGCCACATATGCCCTGAAGCACAG
                          tcttaac  putative branch site (score: 69)
                                           tctccatt  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taccttgatctagatgcacgtgtgcctggccactaccctggttattcttcactacagctgatgtgataacctcttaaccagtgcccaatctccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCAGGAGGCTCACATGGATTTGTTGTCGGCCACATATGCCCTGAAGCACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - -atgcacg
- - - - - - - - - - - tgcctgg
- - - - - - - - - - - - - - - cactacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gctgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccagtgc