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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtgctttttccttctcaacaacgctttcgttcatgcctcctccgctgtttcgtttgaatggcaagccagcatccttgaccttgagatcctgtgtacatgcagAGACGGAGGAGTCTGCACTCGTCATCACCGGCATCAAGGGAAGGATCAACAGGGCCGTTTGGGGGCCGCTCAACAGGACCATCATCACTGCCGGAGAGGA

Basic information

species Zea mays
transcript GRMZM2G143330_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G143330_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os08g21660.2 (Oryza sativa), 3'ss of exon 1
gtcagtgctttttccttctcaacaacgctttcgttcatgcctcctccgctgtttcgtttgaatggcaagccagcatccttgaccttgagatcctg--tgtacatgcagAGACGGAGGAGTCTGCACTCGTCATCACCGGCATCAAGGGAAGGATCAACAGGGCCGTTTGGGGGCCGCTCAACAGGACCATCATCACTGCCGGAGAGGA
                                    | | | | ||  | || || ||  | | | ||||         ||  ||  ||    ||  |||  |||||||| |||||||||||   ||||| || || ||||||||||| ||||||||||||||||| ||||||||| | |||||||| |||||||| ||||| |||||
----------------------------------gtaagacgcgtctccggtctccttctagttggaagcttctggatgtgttctaaagtgtgtggttgtggatgcagAGTCGGAGGAGTCTCTTCTCGTGATTACTGGCATCAAGGGGAGGATCAACAGGGCCGTGTGGGGGCCGTTGAACAGGACTATCATCACCGCCGGTGAGGA

upper sequence: GRMZM2G143330_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g16660.3 (Oryza sativa), 3'ss of exon 1
-gtcagtgctttttccttctcaacaacgctttcgttcatgc-ctcctccgctgtttcgtttgaatggcaagccagcatccttgaccttgagatcctgtgtacatgcagAGACGGAGGAGTCTGCACTCGTCATCACCGGCATCAAGGGAAGGATCAACAGGGCCGTTTGGGGGCCGCTCAACAGGACCATCATCACTGCCGGAGAGGA
   ||     ||  | |  ||  || | ||     ||||   |  | |      |||     ||   |  |      | ||  |   || | |    |||  ||| |||| |||||||||||   ||||| ||  | ||||||||||| ||||| |||||||| || ||||||||| | ||||||||||||||||| ||||| |||||
aaccaaacaattgacttaatccccacccctcaaactcatattcctccctaacaattccccccaacaacgtgg----gttctgaagtgtgtggt----tgtggatgaagAGTCGGAGGAGTCTCTTCTCGTGATTTCTGGCATCAAGGGGAGGATTAACAGGGCTGTATGGGGGCCGTTGAACAGGACCATCATCACCGCCGGTGAGGA
















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|149043303|gb|EE047366.2|EE047366
EST:     CCACGTCCCCACCGTCCAGGTCAAGCGCATCGCCGAGGACATCGACGACC                         AGACGGAGGAGTCTGCACTCGTCATCACCGGCATCAAGGGAAGGATCAACA
genomic: CCACGTCCCCACCGTCCAGGTCAAGCGCATCGCCGAGGACATCGACGACCgtcagtgctt ... gtacatgcagAGACGGAGGAGTCTGCACTCGTCATCACCGGCATCAAGGGAAGGATCAACA
EST: gi|101401501|gb|EB822430.1|EB822430
EST:     CCACGTCCCCACCGTCCAGGTCAAGCGCATCGCCGAGGACATCGACGACC                         AGACGGAGGAGTCTGCACTCGTCATCACCGGCATCAAGGGAAGGATCAACA
genomic: CCACGTCCCCACCGTCCAGGTCAAGCGCATCGCCGAGGACATCGACGACCgtcagtgctt ... gtacatgcagAGACGGAGGAGTCTGCACTCGTCATCACCGGCATCAAGGGAAGGATCAACA
EST: gi|78119408|gb|DV537792.1|DV537792
EST:     CCACGTCCCCACCGTCCAGGTCAAGCGCATCGCCGAGGACATCGACGACC                         AGACGGAGGAGTCTGCACTCGTCATCACCGGCATCAAGGGAAGGATCAACA
genomic: CCACGTCCCCACCGTCCAGGTCAAGCGCATCGCCGAGGACATCGACGACCgtcagtgctt ... gtacatgcagAGACGGAGGAGTCTGCACTCGTCATCACCGGCATCAAGGGAAGGATCAACA
EST: gi|71440740|gb|DR821790.1|DR821790
EST:     CCACGTCCCCACCGTCCAGGTCAAGCGCATCGCCGAGGACATCGACGACC                         AGACGGAGGAGTCTGCACTCGTCATCACCGGCATCAAGGGAAGGATCAACA
genomic: CCACGTCCCCACCGTCCAGGTCAAGCGCATCGCCGAGGACATCGACGACCgtcagtgctt ... gtacatgcagAGACGGAGGAGTCTGCACTCGTCATCACCGGCATCAAGGGAAGGATCAACA
EST: gi|88751072|gb|DY535213.1|DY535213
EST:     CCACGTCCCCACCGTCCAGGTCAAGCGCATCGCAGAGGACATCGAAGACC                         AGACGGAGGAGTCTGCACTCGTCATCACCGGCATCAAGGGAAGGATCAACA
genomic: CCACGTCCCCACCGTCCAGGTCAAGCGCATCGCCGAGGACATCGACGACCgtcagtgctt ... gtacatgcagAGACGGAGGAGTCTGCACTCGTCATCACCGGCATCAAGGGAAGGATCAACA
EST: gi|31909181|gb|CD650790.1|CD650790
EST:     CCACGTCCCCACCGTCCAGGTCAAGCGCATCGCCGAGGACATCGACGACC                         AGACGGAGGAGTCTGCACTCGTCATCACCGGCATCAAGGGAAGGATCAACA
genomic: CCACGTCCCCACCGTCCAGGTCAAGCGCATCGCCGAGGACATCGACGACCgtcagtgctt ... gtacatgcagAGACGGAGGAGTCTGCACTCGTCATCACCGGCATCAAGGGAAGGATCAACA
EST: gi|93283869|gb|EB676133.1|EB676133
EST:     CCACGTCCCCACCGTCCAGGTCAAGCGCATCGCCGAGGACATCGACGACC                         AGACGGAGGAGTCTGCACTCGTCATCACCGGCATCAAGGGAAGGATCAACA
genomic: CCACGTCCCCACCGTCCAGGTCAAGCGCATCGCCGAGGACATCGACGACCgtcagtgctt ... gtacatgcagAGACGGAGGAGTCTGCACTCGTCATCACCGGCATCAAGGGAAGGATCAACA
EST: gi|91872573|gb|EB402530.1|EB402530
EST:     CCACGTCCCCACCGTCCAGGTCAAGCGCATCGCCGAGGACATCGACGACC                         AGACGGAGGAGTCTGCACTCGTCATCACCGGCATCAAGGGAAGGATCAACA
genomic: CCACGTCCCCACCGTCCAGGTCAAGCGCATCGCCGAGGACATCGACGACCgtcagtgctt ... gtacatgcagAGACGGAGGAGTCTGCACTCGTCATCACCGGCATCAAGGGAAGGATCAACA
EST: gi|148995509|gb|EE034699.2|EE034699
EST:     CCACGTCCCCACCGTCCAGGTCAAGCGCATCGCCGAGGACATCGACGACC                         AGACGGAGGAGTCTGCACTCGTCATCACCGGCATCAAGGGAAGGATCAACA
genomic: CCACGTCCCCACCGTCCAGGTCAAGCGCATCGCCGAGGACATCGACGACCgtcagtgctt ... gtacatgcagAGACGGAGGAGTCTGCACTCGTCATCACCGGCATCAAGGGAAGGATCAACA
EST: gi|74243658|gb|DT651572.1|DT651572
EST:     CCACGTCCCCACCGTCCAGGTCAAGCGCATCGCCGAGGACATCGACGACC                         AGACGGAGGAGTCTGCACTCGTCATCACCGGCATCAAGGGAAGGATCAACA
genomic: CCACGTCCCCACCGTCCAGGTCAAGCGCATCGCCGAGGACATCGACGACCgtcagtgctt ... gtacatgcagAGACGGAGGAGTCTGCACTCGTCATCACCGGCATCAAGGGAAGGATCAACA
EST: gi|148930479|gb|EE285032.2|EE285032
EST:     CCACGTCCCCACCGTCCAGGTCAAGCGCATCGCCGAGGACATCGACGACC                         AGACGGAGGAGTCTGCACTCGTCATCACCGGCATCAAGGGAAGGATCAACA
genomic: CCACGTCCCCACCGTCCAGGTCAAGCGCATCGCCGAGGACATCGACGACCgtcagtgctt ... gtacatgcagAGACGGAGGAGTCTGCACTCGTCATCACCGGCATCAAGGGAAGGATCAACA
EST: gi|78087877|gb|DV516270.1|DV516270
EST:     CCACGTCCCCACCGTCCAGGTCAAGCGCATCGCCGAGGACATCGACGACC                         AGACGGAGGAGTCTGCACTCGTCATCACCGGCATCAAGGGAAGGATCAACA
genomic: CCACGTCCCCACCGTCCAGGTCAAGCGCATCGCCGAGGACATCGACGACCgtcagtgctt ... gtacatgcagAGACGGAGGAGTCTGCACTCGTCATCACCGGCATCAAGGGAAGGATCAACA
EST: gi|211094207|gb|FL010330.1|FL010330
EST:     CCACGTCCC-ACCGTCCAGGTCAAGCGCATCGCCGAGGACATCGACGACC                         AGACGGAGGAGTCTGCACTCGTCATCACCGGCATCAAGGGAAGGATCAACA
genomic: CCACGTCCCCACCGTCCAGGTCAAGCGCATCGCCGAGGACATCGACGACCgtcagtgctt ... gtacatgcagAGACGGAGGAGTCTGCACTCGTCATCACCGGCATCAAGGGAAGGATCAACA
EST: gi|71301123|gb|DR786594.1|DR786594
EST:     CCACGTCCCCACCGTCCAGGTCAAGCGCATCGCCGAGGACATCGACGACC                         AGACGGAGGAGTCTGCACTCGTCATCACCGGCATCAAGGGAAGGATCAACA
genomic: CCACGTCCCCACCGTCCAGGTCAAGCGCATCGCCGAGGACATCGACGACCgtcagtgctt ... gtacatgcagAGACGGAGGAGTCTGCACTCGTCATCACCGGCATCAAGGGAAGGATCAACA

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: 45 (upstream exon), 46 (downstream exon)
Score: 85

TTCGCCATCGGGGACGCGCTCGCCGTCGTCACCACCGACAACTTCATGGACCACGTCCCCACCGTCCAGGTCAAGCGCATCGCCGAGGACATCGACGACCgtcagtgctt ... gtacatgcagAGACGGAGGAGTCTGCACTCGTCATCACCGGCATCAAGGGAAGGATCAACAGGGCCGTTTGGGGGCCGCTCAACAGGACCATCATCACTGCCGGAGAGGA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 100

TTCGCCATCGGGGACGCGCTCGCCGTCGTCACCACCGACAACTTCATGGACCACGTCCCCACCGTCCAGGTCAAGCGCATCGCCGAGGACATCGACGACCgtcagtgctt ... gtacatgcagAGACGGAGGAGTCTGCACTCGTCATCACCGGCATCAAGGGAAGGATCAACAGGGCCGTTTGGGGGCCGCTCAACAGGACCATCATCACTGCCGGAGAGGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 92

TTCGCCATCGGGGACGCGCTCGCCGTCGTCACCACCGACAACTTCATGGACCACGTCCCCACCGTCCAGGTCAAGCGCATCGCCGAGGACATCGACGACCgtcagtgctt ... gtacatgcagAGACGGAGGAGTCTGCACTCGTCATCACCGGCATCAAGGGAAGGATCAACAGGGCCGTTTGGGGGCCGCTCAACAGGACCATCATCACTGCCGGAGAGGA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 71

TTCGCCATCGGGGACGCGCTCGCCGTCGTCACCACCGACAACTTCATGGACCACGTCCCCACCGTCCAGGTCAAGCGCATCGCCGAGGACATCGACGACCgtcagtgctt ... gtacatgcagAGACGGAGGAGTCTGCACTCGTCATCACCGGCATCAAGGGAAGGATCAACAGGGCCGTTTGGGGGCCGCTCAACAGGACCATCATCACTGCCGGAGAGGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcgtttgaatggcaagccagcatccttgaccttgagatcctgtgtacatgcagAGACGGAGGAGTCTGCACTCGTCATCACCGGCATCAAGGGAAGGATCAACAGGGCCGTTTGGGGGCCGCTCAACAGGACCATCATCACTGCCGGAGAGGA
                         ccttgac  putative branch site (score: 71)
     tttgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtgctttttccttctcaacaacgctttcgttcatgcctcctccgctgtttcgtttgaatggcaagccagcatccttgaccttgagatcctgtgtacatgcagAGACGGAGGAGTCTGCACTCGTCATCACCGGCATCAAGGGAAGGATCAACAGGGCCGTTTGGGGGCCGCTCAACAGGACCATCATCACTGCCGGAGAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA