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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTTTCTGAGACTGGTGGCATTCCCATTGGTATTGGGAAAAATTCACATATCAGAAAAGCAATCATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAGgtatttcaaatatactgaatttgccttaacctgataatgttttgtatctattggctattctttaactatagggattaatcaaatatcttatttatgtaaa...

Basic information

species Zea mays
transcript GRMZM2G106213_T02
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G106213_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os09g12660.2 (Oryza sativa), 5'ss of exon 8
CCTTTCTGAGACTGGTGGCATTCCCATTGGTATTGGGAAAAATTCACATATCAGAAAAGCAATCATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAGgtatttcaaatatactgaatttgccttaacctgataatgttttgtatctattggctattctttaactatagggattaatcaaatatcttatttatgtaaa---------
|||||||||||||||||||||||||||||||||||| || ||| |||| |||||||||||||| |||||||| |||||||| |||||||||||||| ||||||||||| ||||| | |   | | ||    ||  ||| |  || |  | |    | |   ||||||     ||| ||  |   ||    |  | | |||         
CCTTTCTGAGACTGGTGGCATTCCCATTGGTATTGGAAAGAATGCACACATCAGAAAAGCAATAATTGACAAGAATGCTCGTATTGGAGAAAATGTTAAGgtatttcatatatattta---tacttttggttgtcaatctgatgaag-tgtgccttctgtattaact-----gatcaactattcattacttgaaagaaaagagagggac

upper sequence: GRMZM2G106213_T02 (Zea mays), 5'ss of exon 8
lower sequence: PP1S76_105V6.1 (Physcomitrella patens), 5'ss of exon 8
CCTTTCTGAGACTGGTGGCATTCCCATTGGTATTGGGAAAAATTCACATATCAGAAAAGCAATCATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAGgtatttcaaat---atactgaatttgccttaacctgataatgttttgtatctattggctattctttaactatagggattaatcaaatatcttatttatgtaaa
  | |  |  || |||||||||||||| |||||||| |||||||||  | | | || |||||| || ||||| ||||| || || ||||||||||||||||||    |  |   ||  |  |  |  || ||    || | |   |||     || |         |  | |     ||  ||||||       |   |    
GTTGTTAGCCACAGGTGGCATTCCCATGGGTATTGGCAAAAATTCAGTTGTGAAAAGAGCAATTATCGACAAGAATGCACGAATCGGAGAAAATGTGAAGgtaggctatgttagatgttagaagttactgaatggaatcaaggcgtgttgtctttcgtgcacacaaatttgttcatgttgttcaaatccaactctatcgc---

upper sequence: GRMZM2G106213_T02 (Zea mays), 5'ss of exon 8
lower sequence: PP1S2_392V6.1 (Physcomitrella patens), 5'ss of exon 8
CCTTTCTGAGACTGGTGGCATTCCCATTGGTATTGGGAAAAATTCACATATCAGAAAAGCAATCATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAGgtat--ttcaaatatactgaatttgccttaacctgataatgttttgtatctattggctattctttaact---atagggattaatcaaatatcttatttatgtaaa-----------------------------------
  |    |   | |||||||| ||||| || ||||| | ||| ||     | | || ||||||||||||||||||||| || |||||||| ||||| |||||||  ||       |||    |   ||  |  |  || |  | || |  || ||  | |  |    ||   |||     ||     |  | |||    | | ||                                   
GTTGCTAGCCTCAGGTGGCATACCCATGGGCATTGGAAGAAACTCTGTAGTGAAAAGAGCAATCATTGACAAAAATGCACGAATTGGAGAGAATGTTAAGgtatgctttgttctcactttggtaagctgcaagtagtattcatatgcacataatgagtttcataagtcttgtataatacatacatggaagtattaccattttgaatatggattaatggtcggacgttatcctttgtgtag

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|60337923|gb|DN204896.1|DN204896
EST:     TCAGAAAAGCAATCATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAG                         ATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATAT
genomic: TCAGAAAAGCAATCATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAGgtatttcaaa ... tgttttacagATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATAT
EST: gi|31356186|gb|CD440543.1|CD440543
EST:     TCAGAAAAGCAATAATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAG                         ATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATAT
genomic: TCAGAAAAGCAATCATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAGgtatttcaaa ... tgttttacagATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATAT
EST: gi|6538829|gb|AW224968.1|AW224968
EST:     TCAGAAAAGCAATAATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAG                         ATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATAT
genomic: TCAGAAAAGCAATCATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAGgtatttcaaa ... tgttttacagATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATAT
EST: gi|31357016|gb|CD441373.1|CD441373
EST:     TCAGAAAAGCAATAATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAG                         ATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATAT
genomic: TCAGAAAAGCAATCATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAGgtatttcaaa ... tgttttacagATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATAT
EST: gi|32929383|gb|CF034195.1|CF034195
EST:     TCAGAAAAGCAATCATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAG                         ATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATAT
genomic: TCAGAAAAGCAATCATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAGgtatttcaaa ... tgttttacagATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATAT
EST: gi|211487577|gb|FL154404.1|FL154404
EST:     TCAGARAAGCAATAATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAG                         ATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATAT
genomic: TCAGAAAAGCAATCATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAGgtatttcaaa ... tgttttacagATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATAT
EST: gi|6918703|gb|AW400233.1|AW400233
EST:     TCAGAAAAGCAATAATTGGCAAAAATGCTCGCATTGGAGAAAATGTGAAG                         ATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATAT
genomic: TCAGAAAAGCAATCATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAGgtatttcaaa ... tgttttacagATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATAT
EST: gi|32934685|gb|CF039497.1|CF039497
EST:     TCAGAAAAGCAATCATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAG                         ATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATAT
genomic: TCAGAAAAGCAATCATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAGgtatttcaaa ... tgttttacagATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATAT
EST: gi|32933844|gb|CF038656.1|CF038656
EST:     TCAGAAAAGCAATCATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAG                         ATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATAT
genomic: TCAGAAAAGCAATCATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAGgtatttcaaa ... tgttttacagATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATAT
EST: gi|67042108|gb|CO468363.1|CO468363
EST:     TCAGAAAAGCAATAATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAG                         ATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATAT
genomic: TCAGAAAAGCAATCATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAGgtatttcaaa ... tgttttacagATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATAT
EST: gi|71301127|gb|DR786596.1|DR786596
EST:     TCAGAAAAGCAATCATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAG                         ATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATAT
genomic: TCAGAAAAGCAATCATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAGgtatttcaaa ... tgttttacagATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATAT
EST: gi|32846616|gb|CD986297.1|CD986297
EST:     TCAGAAAAGCAATCATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAG                         ATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATAT
genomic: TCAGAAAAGCAATCATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAGgtatttcaaa ... tgttttacagATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATAT
EST: gi|6918472|gb|AW400002.1|AW400002
EST:     TCAGAAAAGCAATAATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAG                         ATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATAT
genomic: TCAGAAAAGCAATCATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAGgtatttcaaa ... tgttttacagATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATAT
EST: gi|110511027|gb|EE019293.1|EE019293
EST:     TCAGAAAAGCAATCATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAG                         ATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATAT
genomic: TCAGAAAAGCAATCATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAGgtatttcaaa ... tgttttacagATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATAT
EST: gi|148950460|gb|EC896030.2|EC896030
EST:     TCAGAAAAGCAATCATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAG                         ATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATAT
genomic: TCAGAAAAGCAATCATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAGgtatttcaaa ... tgttttacagATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATAT
EST: gi|78180055|gb|DV550428.1|DV550428
EST:     TCAGAAAAGCAATAATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAG                         ATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATAT
genomic: TCAGAAAAGCAATCATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAGgtatttcaaa ... tgttttacagATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATAT
EST: gi|60352415|gb|DN219388.1|DN219388
EST:     TCAGAAAAGCAATCATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAG                         ATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATAT
genomic: TCAGAAAAGCAATCATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAGgtatttcaaa ... tgttttacagATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATAT
EST: gi|37381963|gb|CF627890.1|CF627890
EST:     TCAGAAAAGCAATAATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAG                         ATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATAT
genomic: TCAGAAAAGCAATCATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAGgtatttcaaa ... tgttttacagATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATAT
EST: gi|32856251|gb|CD995932.1|CD995932
EST:     TCAGAAAAGCAATCATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAG                         ATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATAT
genomic: TCAGAAAAGCAATCATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAGgtatttcaaa ... tgttttacagATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATAT
EST: gi|32929486|gb|CF034298.1|CF034298
EST:     TCAGAAAAGCAATCATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAG                         ATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATAT
genomic: TCAGAAAAGCAATCATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAGgtatttcaaa ... tgttttacagATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATAT
EST: gi|211241905|gb|FL451944.1|FL451944
EST:     TCAGAAAAGCAATAATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAG                         ATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATAT
genomic: TCAGAAAAGCAATCATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAGgtatttcaaa ... tgttttacagATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATAT
EST: gi|12046285|gb|BF728424.1|BF728424
EST:     TCAGAAAAGCAATAATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAG                         ATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATAT
genomic: TCAGAAAAGCAATCATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAGgtatttcaaa ... tgttttacagATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATAT
EST: gi|211186265|gb|FL114940.1|FL114940
EST:     TCAGAAAAGCAATAATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAG                         ATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATAT
genomic: TCAGAAAAGCAATCATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAGgtatttcaaa ... tgttttacagATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATAT

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: 653

CCTTTCTGAGACTGGTGGCATTCCCATTGGTATTGGGAAAAATTCACATATCAGAAAAGCAATCATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAGgtatttcaaa ... tgttttacagATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATATTTTATCAAAAGTGGAATTGTCACGGTGATTAAAGATGCTTTAATTCCTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 229

CCTTTCTGAGACTGGTGGCATTCCCATTGGTATTGGGAAAAATTCACATATCAGAAAAGCAATCATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAGgtatttcaaa ... tgttttacagATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATATTTTATCAAAAGTGGAATTGTCACGGTGATTAAAGATGCTTTAATTCCTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 23

CCTTTCTGAGACTGGTGGCATTCCCATTGGTATTGGGAAAAATTCACATATCAGAAAAGCAATCATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAGgtatttcaaa ... tgttttacagATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATATTTTATCAAAAGTGGAATTGTCACGGTGATTAAAGATGCTTTAATTCCTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 229

CCTTTCTGAGACTGGTGGCATTCCCATTGGTATTGGGAAAAATTCACATATCAGAAAAGCAATCATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAGgtatttcaaa ... tgttttacagATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATATTTTATCAAAAGTGGAATTGTCACGGTGATTAAAGATGCTTTAATTCCTA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTTTCTGAGACTGGTGGCATTCCCATTGGTATTGGGAAAAATTCACATATCAGAAAAGCAATCATTGACAAAAATGCTCGCATTGGAGAAAATGTGAAGgtatttcaaatatactgaatttgccttaacctgataatgttttgtatctattggctattctttaactatagggattaatcaaatatcttatttatgtaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA