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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCGTATTGCTGCCGGGTTGCCATGTGGTAGTGAAAGCTTCCTCTTGATGTTTGCCAGATGGAGAAAACTTGAGAGGGATTTATACAATGAAAGAAAGGAgtaaagtgtttaacctctggatgtttagaaatcaatatagtgttttattctacttttgttaaagtcactcatgatgctttatttcataatgcag

Basic information

species Zea mays
transcript GRMZM2G022997_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G022997_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g48300.3 (Oryza sativa), 5'ss of exon 22
CTCGTATTGCTGCCGGGTTGCCATGTGGTAGTGAAAGCTTCCTCTTGATGTTTGCCAGATGGAGAAAACTTGAGAGGGATTTATACAATGAAAGAAAGGAg----taaagtgtttaacctctggatgttt-------agaaatcaatatagtgttttattctacttttgtta--aagtcactcat--gatgctttatt--tcataatgcag
|||||||||||||||||||||| ||||||||||| ||||||||||||||||||||  |||||| ||||||||||||||||||||| |||||||||||||||    |||| ||||| || | | ||  | |       |||||||| | || |     | | ||  ||  ||    | ||||| ||    ||||  ||   |  || |||||
CTCGTATTGCTGCCGGGTTGCCTTGTGGTAGTGAGAGCTTCCTCTTGATGTTTGCTCGATGGAAAAAACTTGAGAGGGATTTATATAATGAAAGAAAGGAgtgagtaaaatgtttcacttttagacttcttgatgtcagaaatcattttattaaccaagtataacttccttctccaatcacttatatagtgctccataaattttactgcag

upper sequence: GRMZM2G022997_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT5G15070.2 (Arabidopsis thaliana), 5'ss of exon 23
CTCGTATTGCTGCCGGGTTGCCATGTGGTAGTGAAAGCTTCCTCTTGATGTTTGCCAGATGGAGAAAACTTGAGAGGGATTTATACAATGAAAGAAAGGAgtaaagtgtttaacctctggatgtttagaaatcaatatagtgttttattctacttttgttaaagtcactcatgatgctttatttcataatgcag
 ||| ||||||||||| || || |||||||||||| | ||||| |||||||||||| | ||||||||||| || |||||| | ||||| |||||||  ||||||     | ||   |   ||| |          | |  |  | | ||  | ||||   || | |||| ||   | |  | ||   |||||||
GTCGGATTGCTGCCGGATTACCTTGTGGTAGTGAAGGGTTCCTTTTGATGTTTGCCCGGTGGAGAAAACTCGAAAGGGATCTCTACAACGAAAGAAGAGAgtaag----taaatggccatatgctc---------tcttattctctgtttgagttttagaaatggcactgat--cgttggaattg--aatgcag

upper sequence: GRMZM2G022997_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT3G01310.2 (Arabidopsis thaliana), 5'ss of exon 23
CTCGTATTGCTGCCGGGTTGCCATGTGGTAGTGAAAGCTTCCTCTTGATGTTTGCCAGATGGAGAAAACTTGAGAGGGATTTATACAATGAAAGAAAGGAgtaaagtgtttaacc--tctggatgtttagaaatcaatat--agtgttttat---tctacttttgttaaagtcactca--------tgatgctttatttcataatgcag
 ||| |||||| | || || ||||||||||||||| | |||||  ||||||||||  | |||| ||||||||  |||||| | |||||||||||||| ||||||  |  | | |   | ||||| |||||  ||   | |  |   ||| ||   | |  ||    ||||||              ||||  || |||| | | |||||
ATCGGATTGCTTCTGGATTACCATGTGGTAGTGAAGGATTCCTTCTGATGTTTGCTCGGTGGATAAAACTTGCTAGGGATCTCTACAATGAAAGAAAAGAgtaagtttatcatcggatttggat-tttagcgatgcttctcaaaattttcatctctttgtttccagtaaagttttgtgagtagcactgatagttaatttta-attgcag

upper sequence: GRMZM2G022997_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv14s0066g02540.t01 (Vitis vinifera), 5'ss of exon 22
CTCGTATTGCTGCCGGGTTGCCATGTGGTAGTGAAAGCTTCCTCTTGATGTTTGCCAGATGGAGAAAACTTGAGAGGGATTTATACAATGAAAGAAAGGAgtaaa-gtgtttaacctctgg-atgtttagaaatcaatata----gtgttttattctacttttgttaaagtcactcatgatgctttatttcataatgcag-
  ||||||||||| || || ||||||||||||||  | ||||| |||||||||||  | ||||||||||||||||| || |||||||||||| | || ||||||   | | |||  | |   |||| |    ||   | ||    | |      |   |   ||||    | | |  |    | |||| | |   |  |  
ACCGTATTGCTGCTGGATTACCATGTGGTAGTGAGGGATTCCTTTTGATGTTTGCTCGCTGGAGAAAACTTGAGAGAGACTTATACAATGAACGCAAAGAgtaagcatctataattttttacatgtatcagtatggttgtatgaggagccaagattctcaactgtttgctttaattttttccccttatctga-ggtataat

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|211061721|gb|FL342304.1|FL342304
EST:     TTTGCCAGATGGAGAAAACTTGAGAGGGATTTATACAATGAAAGAAAGGA                         CCGTTTTGACATTACACAGATCCCAGATGTATATGATTCCTGCAA
genomic: TTTGCCAGATGGAGAAAACTTGAGAGGGATTTATACAATGAAAGAAAGGAgtaaagtgtt ... cataatgcagCCGTTTTGACATTACACAGATCCCAGATGTATATGATTCCTGCAA
EST: gi|211058621|gb|FL339128.1|FL339128
EST:     TTTGCCAGATGGAGAAAACTTGAGAGGGATTTATACAATGAAAGAAAGGA                         CCGTTTCGACATTACACAGATCCCAGATGTATATGATTCCTGCAA
genomic: TTTGCCAGATGGAGAAAACTTGAGAGGGATTTATACAATGAAAGAAAGGAgtaaagtgtt ... cataatgcagCCGTTTTGACATTACACAGATCCCAGATGTATATGATTCCTGCAA
EST: gi|51592786|gb|CV071932.1|CV071932
EST:     TTTGCCAGATGGAGAAAACTTGAGAGGGATTTATACAATGAAAGAAAGGA                         CCGTTTTGACATTACACAGATCCCAGATGTATATGATTCCTGCAA
genomic: TTTGCCAGATGGAGAAAACTTGAGAGGGATTTATACAATGAAAGAAAGGAgtaaagtgtt ... cataatgcagCCGTTTTGACATTACACAGATCCCAGATGTATATGATTCCTGCAA
EST: gi|211197623|gb|FL318610.1|FL318610
EST:     TTTGCCAGATGGAGAAAACTTGAGAGGGATTTATACAATGAAAGAAAGGA                         CCGTTTTGACATTACACAGATCCCAGATGTATATGATTCCTGCAA
genomic: TTTGCCAGATGGAGAAAACTTGAGAGGGATTTATACAATGAAAGAAAGGAgtaaagtgtt ... cataatgcagCCGTTTTGACATTACACAGATCCCAGATGTATATGATTCCTGCAA
EST: gi|211467194|gb|FL319591.1|FL319591
EST:     TTTGCCAGATGGAGAAAACTTGAGAGGGATTTATACAATGAAAGAAAGGA                         CCGTTTTGACATTACACAGATCCCAGATGTATATGATTCCTGCAA
genomic: TTTGCCAGATGGAGAAAACTTGAGAGGGATTTATACAATGAAAGAAAGGAgtaaagtgtt ... cataatgcagCCGTTTTGACATTACACAGATCCCAGATGTATATGATTCCTGCAA
EST: gi|211302287|gb|FL347329.1|FL347329
EST:     TTTGCCAGATGGAGAAAACTTGAGAGGGATTTATACAATGAAAGAAAGGA                         CCGTTTTGACATTACACAGATCCTAGATGTATATGATTCCTGCAA
genomic: TTTGCCAGATGGAGAAAACTTGAGAGGGATTTATACAATGAAAGAAAGGAgtaaagtgtt ... cataatgcagCCGTTTTGACATTACACAGATCCCAGATGTATATGATTCCTGCAA
EST: gi|211459419|gb|FL313798.1|FL313798
EST:     TTTGCCAGATGGAGAAAACTTGAGAGGGATTTATACAATGAAAGAAAGGA                         CCGTTTTGACATTACACAGATCCCAGATGTATATGATTCCTGCAA
genomic: TTTGCCAGATGGAGAAAACTTGAGAGGGATTTATACAATGAAAGAAAGGAgtaaagtgtt ... cataatgcagCCGTTTTGACATTACACAGATCCCAGATGTATATGATTCCTGCAA

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), 45 (downstream exon)
Score: 49

CTCGTATTGCTGCCGGGTTGCCATGTGGTAGTGAAAGCTTCCTCTTGATGTTTGCCAGATGGAGAAAACTTGAGAGGGATTTATACAATGAAAGAAAGGAgtaaagtgtt ... cataatgcagCCGTTTTGACATTACACAGATCCCAGATGTATATGATTCCTGCAA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 29

CTCGTATTGCTGCCGGGTTGCCATGTGGTAGTGAAAGCTTCCTCTTGATGTTTGCCAGATGGAGAAAACTTGAGAGGGATTTATACAATGAAAGAAAGGAgtaaagtgtt ... cataatgcagCCGTTTTGACATTACACAGATCCCAGATGTATATGATTCCTGCAA


Block sizes: 42 (upstream exon), 45 (downstream exon)
Score: 23

CTCGTATTGCTGCCGGGTTGCCATGTGGTAGTGAAAGCTTCCTCTTGATGTTTGCCAGATGGAGAAAACTTGAGAGGGATTTATACAATGAAAGAAAGGAgtaaagtgtt ... cataatgcagCCGTTTTGACATTACACAGATCCCAGATGTATATGATTCCTGCAA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 106

CTCGTATTGCTGCCGGGTTGCCATGTGGTAGTGAAAGCTTCCTCTTGATGTTTGCCAGATGGAGAAAACTTGAGAGGGATTTATACAATGAAAGAAAGGAgtaaagtgtt ... cataatgcagCCGTTTTGACATTACACAGATCCCAGATGTATATGATTCCTGCAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCGTATTGCTGCCGGGTTGCCATGTGGTAGTGAAAGCTTCCTCTTGATGTTTGCCAGATGGAGAAAACTTGAGAGGGATTTATACAATGAAAGAAAGGAgtaaagtgtttaacctctggatgtttagaaatcaatatagtgttttattctacttttgttaaagtcactcatgatgctttatttcataatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA