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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAGgtaatggagtcatcacactgatttcctgtatttcaatttgcagtggttctagctgtctggcatttgtttcatgctgctttctctgctatattttcag

Basic information

species Zea mays
transcript GRMZM2G102639_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G102639_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os10g31900.1 (Oryza sativa), 5'ss of exon 7
ATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAGgtaatggagtcatcacactgatttcctgtatttcaatttgcagtggttctagctgtctggcatttgtttcatgctgctttctctgctata--ttttcag
|||||||||||||||||||| ||||||||  ||||||||||||||||||||||||| ||||||||||||||||| ||||| ||||||||||   | |   |||| | | ||| | |||||   ||        ||| |  | |   | || |||||||     | || | ||| | |  ||| |||
ATAATGCGAGATCCTGAAACTGGAAATTCACGAGGCTTTGGCTTTGTGAGCTATGACTCCTTTGAATCATCTGATCAAGCTATAGAGgtaacacaattgccacaataagttc-tatattttgtttc-------ttccatttatt--gaatgtgtttca-----ccttatgtgccacaattttccag

upper sequence: GRMZM2G102639_T02 (Zea mays), 5'ss of exon 5
lower sequence: Vv04s0023g01470.t01 (Vitis vinifera), 5'ss of exon 7
ATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAGgtaatggagtcatcacactgatttcctgtatttcaatttgcagtggttctagctgtctggcatttgtttcatgctgctttctctgctatattttcag---
|||||| |||||||||| |||||||||||| | || ||||| || || |||||||| || |||||  |||||||   ||| || ||||||      || | |   |  |||| | |  || |  | |   |   | |     |  |  ||  |   ||   | |  | | ||   || |    |   
ATAATGAGAGATCCTGATACAGGAAATTCTCGTGGTTTTGGTTTCGTTAGCTATGACTCTTTTGAGGCATCTGATGCAGCTATTGAGgtatatatctcttgatgatattttcatatcatttaggtggttttaactttctgcttaagctatgagaaacacaattcagtatttggattaatgattggct
















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|26558877|gb|CA831112.1|CA831112
EST:     TTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAG                         GGCATGAACAACCAACATTTGTGC
genomic: TTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAGgtaatggagt ... atattttcagGCCATGAACAACCAACATTTGTGC
EST: gi|78090866|gb|DV519240.1|DV519240
EST:     TTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAG                         GCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCT
genomic: TTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAGgtaatggagt ... atattttcagGCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCT
EST: gi|91056510|gb|EB166928.1|EB166928
EST:     TTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAG                         GCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCT
genomic: TTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAGgtaatggagt ... atattttcagGCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCT
EST: gi|76015741|gb|DT942911.1|DT942911
EST:     GACCAAGCAATAGAG                         GCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCT
genomic: GACCAAGCAATAGAGgtaatggagt ... atattttcagGCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCT
EST: gi|71319024|gb|DR796257.1|DR796257
EST:     TTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAG                         GCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCT
genomic: TTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAGgtaatggagt ... atattttcagGCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCT
EST: gi|148943004|gb|EC888052.2|EC888052
EST:     TTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAG                         GCCATGAACAACAAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCT
genomic: TTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAGgtaatggagt ... atattttcagGCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCT
EST: gi|87157489|gb|DY402278.1|DY402278
EST:     TTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAG                         GCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCT
genomic: TTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAGgtaatggagt ... atattttcagGCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCT
EST: gi|33467168|gb|CF244217.1|CF244217
EST:     TTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAG                         GCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCT
genomic: TTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAGgtaatggagt ... atattttcagGCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCT
EST: gi|148956981|gb|EC902927.2|EC902927
EST:     TTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAG                         GCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCT
genomic: TTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAGgtaatggagt ... atattttcagGCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCT
EST: gi|148933043|gb|EE285938.2|EE285938
EST:     TTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAG                         GCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCT
genomic: TTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAGgtaatggagt ... atattttcagGCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCT
EST: gi|78124664|gb|DV543048.1|DV543048
EST:     CTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAG                         GCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCT
genomic: TTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAGgtaatggagt ... atattttcagGCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCT
EST: gi|50322326|gb|CO517452.1|CO517452
EST:     TTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAG                         GCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCT
genomic: TTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAGgtaatggagt ... atattttcagGCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCT
EST: gi|211005558|gb|FL032308.1|FL032308
EST:     TTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAG                         GCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCT
genomic: TTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAGgtaatggagt ... atattttcagGCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCT
EST: gi|89762379|gb|DY689990.1|DY689990
EST:     TTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAG                         GCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCT
genomic: TTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAGgtaatggagt ... atattttcagGCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCT
EST: gi|94477767|gb|EB706725.1|EB706725
EST:     TTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAG                         GCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCT
genomic: TTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAGgtaatggagt ... atattttcagGCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCT
EST: gi|76288123|gb|DV027691.1|DV027691
EST:     TTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAG                         GCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCT
genomic: TTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAGgtaatggagt ... atattttcagGCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCT
EST: gi|71425499|gb|DR806709.1|DR806709
EST:     TTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAG                         GCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCT
genomic: TTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAGgtaatggagt ... atattttcagGCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCT
EST: gi|31355533|gb|CD439890.1|CD439890
EST:     TTGGCTTTGTGAGCTATGAGTCCTTTGTTTCATCTGACCAAGCAATAGAG                         GCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCT
genomic: TTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAGgtaatggagt ... atattttcagGCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCT
EST: gi|76291455|gb|DV031023.1|DV031023
EST:     TTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAG                         GCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCT
genomic: TTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAGgtaatggagt ... atattttcagGCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCT
EST: gi|76015742|gb|DT942912.1|DT942912
EST:     TTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAG                         GCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCT
genomic: TTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAGgtaatggagt ... atattttcagGCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCT
EST: gi|76290093|gb|DV029661.1|DV029661
EST:     TTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAG                         GCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCT
genomic: TTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAGgtaatggagt ... atattttcagGCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCT
EST: gi|78124734|gb|DV543118.1|DV543118
EST:     TTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAG                         GCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCT
genomic: TTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAGgtaatggagt ... atattttcagGCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCT
EST: gi|148938096|gb|EC882358.2|EC882358
EST:     TTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAG                         GCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCT
genomic: TTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAGgtaatggagt ... atattttcagGCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCT

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: 46 (upstream exon), 48 (downstream exon)
Score: 58

ATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAGgtaatggagt ... atattttcagGCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 52

ATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAGgtaatggagt ... atattttcagGCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 40

ATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAGgtaatggagt ... atattttcagGCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 23

ATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAGgtaatggagt ... atattttcagGCCATGAACAACCAACATTTGTGCAACCGCCCAATCACTGTCTCTTATGCTTACAAGAAAGACACGAAAGGAGAACGCCATGGCACACCAGCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAGgtaatggagtcatcacactgatttcctgtatttcaatttgcagtggttctagctgtctggcatttgtttcatgctgctttctctgctatattttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA