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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcgttccctgattgtggcaatggattgatttttttaaaagaaaccactattcagtgagctacttatttttgtggtctgatggagctacttaaatttcagGTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAG

Basic information

species Zea mays
transcript GRMZM2G053767_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G053767_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os04g56670.1 (Oryza sativa), 3'ss of exon 3
gtcgttccctgattgtggcaatggattgatttttttaaaag--aaaccactattcagtgagctacttatt-tttgtggtctgatggagctacttaaatttcagGTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAG-------------------------
   |  | || | | | | |     ||  | |||  |   |   | ||| |      |    ||||  |  | ||| || ||||| || |  | |||||||||||| || |||||||||||| |||||||| ||||| ||||||  ||||| ||||||||||||||| |||| |||||                         
---gcactcttaattttgtatgcttttcttgtttccagttgtctagccatttccagattttgtactactcatgtgtagtttgatgaagttcatgaaatttcagGTACAACATGGGTGTAATTCCAACAAAAAAGAGCCTGTTAACATGTGAAAAACTTTCAGTGAGCTCCTTTTGCAGGTCCTTTCTCTCTCTCTCTCTCTCT

upper sequence: GRMZM2G053767_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os04g56670.2 (Oryza sativa), 3'ss of exon 3
gtcgttccctgattgtggcaatggattgatttttttaaaag--aaaccactattcagtgagctacttatt-tttgtggtctgatggagctacttaaatttcagGTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAG
   |  | || | | | | |     ||  | |||  |   |   | ||| |      |    ||||  |  | ||| || ||||| || |  | |||||||||||| || |||||||||||| |||||||| ||||| ||||||  ||||| ||||||||||||||| |||| |||||
---gcactcttaattttgtatgcttttcttgtttccagttgtctagccatttccagattttgtactactcatgtgtagtttgatgaagttcatgaaatttcagGTACAACATGGGTGTAATTCCAACAAAAAAGAGCCTGTTAACATGTGAAAAACTTTCAGTGAGCTCCTTTTGCAG
















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|60342340|gb|DN209313.1|DN209313
EST:     CCAAGAGACCCTTTCAGAATCCAGATGACAGACTTGATTCTCGATAAGCT                         GTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAA
genomic: CCAAGAGACCCTTTCAGAATCCAGATGACAGACTTGATTCTCGATAAGCTgtaagactgc ... taaatttcagGTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAA
EST: gi|50324650|gb|CO519776.1|CO519776
EST:     CCAAGAGACCCTTTCAGAATCCAGATGACAGACTTGATTCTCGATAAGCT                         GTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAA
genomic: CCAAGAGACCCTTTCAGAATCCAGATGACAGACTTGATTCTCGATAAGCTgtaagactgc ... taaatttcagGTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAA
EST: gi|211018457|gb|FL453049.1|FL453049
EST:     TTCTCGATAAGCT                         GTATAATATGGGTGTAATTTCAACAAAARAGAGCTTGTTAAAGTGTGAGAA
genomic: TTCTCGATAAGCTgtaagactgc ... taaatttcagGTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAA
EST: gi|50324261|gb|CO519387.1|CO519387
EST:     CCAAGAGACCCTTTCAGAATCCAGATGACAGACTTGATTCTCGATAAGCT                         GTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAA
genomic: CCAAGAGACCCTTTCAGAATCCAGATGACAGACTTGATTCTCGATAAGCTgtaagactgc ... taaatttcagGTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAA
EST: gi|60395364|gb|DN228233.1|DN228233
EST:     CCAAGAGACCCTTTCAGAATCCAGATGACAGGCTTGATTCTCGATAAGCT                         GTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAA
genomic: CCAAGAGACCCTTTCAGAATCCAGATGACAGACTTGATTCTCGATAAGCTgtaagactgc ... taaatttcagGTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAA
EST: gi|71438629|gb|DR819679.1|DR819679
EST:     CCAAGAGACCCTTTCAGAATCCAGATGACAGACTTGATTCTCGATAAGCT                         GTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAA
genomic: CCAAGAGACCCTTTCAGAATCCAGATGACAGACTTGATTCTCGATAAGCTgtaagactgc ... taaatttcagGTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAA
EST: gi|211245445|gb|FK950833.1|FK950833
EST:     CCAAGAGACCCTTTCAGAATCCAGATGACAGACTTGATTCTCGATAAGCT                         GTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAA
genomic: CCAAGAGACCCTTTCAGAATCCAGATGACAGACTTGATTCTCGATAAGCTgtaagactgc ... taaatttcagGTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAA
EST: gi|31611944|gb|CD568566.1|CD568566
EST:     CCAAGAGACCCTTTCAGAATCCAGATGACAGACTTGATTCTCGATAAGCT                         GTATAATATGGGTGTAATTTCAACAAAAGAGAG
genomic: CCAAGAGACCCTTTCAGAATCCAGATGACAGACTTGATTCTCGATAAGCTgtaagactgc ... taaatttcagGTATAATATGGGTGTAATTTCAACAAAAGAGAG
EST: gi|211430616|gb|FL465154.1|FL465154
EST:     CCAAGAGACCCTTTCAGAATCCAGATGACAGACTTGATTCTCGATAAGCT                         GTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAA
genomic: CCAAGAGACCCTTTCAGAATCCAGATGACAGACTTGATTCTCGATAAGCTgtaagactgc ... taaatttcagGTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAA
EST: gi|31664102|gb|CD573282.1|CD573282
EST:     CCAAGAGACCCTTTCAGAATCCAGATGACAGACTTGATTCTCGATAAGCT                         GTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAA
genomic: CCAAGAGACCCTTTCAGAATCCAGATGACAGACTTGATTCTCGATAAGCTgtaagactgc ... taaatttcagGTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAA
EST: gi|211245444|gb|FK950832.1|FK950832
EST:     CCAAGAGACCCTTTCAGAATCCAGATGACAGACTTGATTCTCGATAAGCT                         GTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAA
genomic: CCAAGAGACCCTTTCAGAATCCAGATGACAGACTTGATTCTCGATAAGCTgtaagactgc ... taaatttcagGTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAA
EST: gi|211526429|gb|FL471796.1|FL471796
EST:     CCTTTCAGAATCCAGATGACAGACTTGATTCTCGATAAGCT                         GTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAA
genomic: CCTTTCAGAATCCAGATGACAGACTTGATTCTCGATAAGCTgtaagactgc ... taaatttcagGTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAA
EST: gi|78122122|gb|DV540506.1|DV540506
EST:     CCAAGAGACCCTTTCAGAATCCAGATGACAGACTTGATTCTCGATAAGCT                         GTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAA
genomic: CCAAGAGACCCTTTCAGAATCCAGATGACAGACTTGATTCTCGATAAGCTgtaagactgc ... taaatttcagGTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAA
EST: gi|60343595|gb|DN210568.1|DN210568
EST:     CCAAGAGACCCTTTCAGAATCCAGATGACAGACTTGATTCTCGATAAGCT                         GTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAA
genomic: CCAAGAGACCCTTTCAGAATCCAGATGACAGACTTGATTCTCGATAAGCTgtaagactgc ... taaatttcagGTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAA
EST: gi|6431873|gb|AW172077.1|AW172077
EST:     CCAAGAGACCCTTTCAGAATCCAGATGACAGACTTGATTCTCGATAAGCT                         GTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAA
genomic: CCAAGAGACCCTTTCAGAATCCAGATGACAGACTTGATTCTCGATAAGCTgtaagactgc ... taaatttcagGTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAA
EST: gi|6342793|gb|AW165617.1|AW165617
EST:     CCAAGAGCCCCTTTCAGAATCCAGATGCCAGACTTGATTCTCGATAAGCT                         GTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAA
genomic: CCAAGAGACCCTTTCAGAATCCAGATGACAGACTTGATTCTCGATAAGCTgtaagactgc ... taaatttcagGTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAA
EST: gi|33103763|gb|CF063723.1|CF063723
EST:     CCAAGAGACCCTTTCAGAATCCAGATGACAGACTTGATTCTCGATAAGCT                         GTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAA
genomic: CCAAGAGACCCTTTCAGAATCCAGATGACAGACTTGATTCTCGATAAGCTgtaagactgc ... taaatttcagGTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAA
EST: gi|32945068|gb|CF049887.1|CF049887
EST:     CCAAGAGACCCTTTCAGAATCCAGATGACAGACTTGATTCTCGATAAGCT                         GTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAA
genomic: CCAAGAGACCCTTTCAGAATCCAGATGACAGACTTGATTCTCGATAAGCTgtaagactgc ... taaatttcagGTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAA
EST: gi|71759525|gb|DR957462.1|DR957462
EST:     CCAAGAGACCCTTTCAGAATCCAGATGACAGACTTGATTCTCGATAAGCT                         GTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAA
genomic: CCAAGAGACCCTTTCAGAATCCAGATGACAGACTTGATTCTCGATAAGCTgtaagactgc ... taaatttcagGTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAA
EST: gi|213172151|gb|FM193873.1|FM193873
EST:     ATTCTCGATAAGCT                         GTATAATANNNNNGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAA
genomic: ATTCTCGATAAGCTgtaagactgc ... taaatttcagGTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAA
EST: gi|50325006|gb|CO520132.1|CO520132
EST:     CCAAGAGACCCTTTCAGAATCCAGATGACAGACTTGATTCTCGATAAGCT                         GTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAA
genomic: CCAAGAGACCCTTTCAGAATCCAGATGACAGACTTGATTCTCGATAAGCTgtaagactgc ... taaatttcagGTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAA

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: 143

GGATATGCTTAATGGTGCAAAAGCTCGTTAACATCATAAAGCAGATGGACCCAAGAGACCCTTTCAGAATCCAGATGACAGACTTGATTCTCGATAAGCTgtaagactgc ... taaatttcagGTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAG


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

GGATATGCTTAATGGTGCAAAAGCTCGTTAACATCATAAAGCAGATGGACCCAAGAGACCCTTTCAGAATCCAGATGACAGACTTGATTCTCGATAAGCTgtaagactgc ... taaatttcagGTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 85

GGATATGCTTAATGGTGCAAAAGCTCGTTAACATCATAAAGCAGATGGACCCAAGAGACCCTTTCAGAATCCAGATGACAGACTTGATTCTCGATAAGCTgtaagactgc ... taaatttcagGTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 62

GGATATGCTTAATGGTGCAAAAGCTCGTTAACATCATAAAGCAGATGGACCCAAGAGACCCTTTCAGAATCCAGATGACAGACTTGATTCTCGATAAGCTgtaagactgc ... taaatttcagGTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactattcagtgagctacttatttttgtggtctgatggagctacttaaatttcagGTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAG
                             gtctgat  putative branch site (score: 62)
               tacttattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcgttccctgattgtggcaatggattgatttttttaaaagaaaccactattcagtgagctacttatttttgtggtctgatggagctacttaaatttcagGTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG