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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCCATGGAAGGTGATGCTGATGCAAATGATCCAGGGAAAGAATGTGTTATTTGCCTCTCAGAACCAAGGGATACTACTGTCCTGCCATGTAGGCATATGgtaagtctgctggtaatctattcaaggattgcattttgtgtgtgtgtagaaactaacgatctattcttgaagaaacttggtataagttttcattatttaa...

Basic information

species Zea mays
transcript GRMZM2G036697_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G036697_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g15000.1 (Oryza sativa), 5'ss of exon 2
CTCCATGGAAGGTGATGCTGATGCAAATGATCCAGGGAAAGAATGTGTTATTTGCCTCTCAGAACCAAGGGATACTACTGTCCTGCCATGTAGGCATATGgtaagtctgctggtaatctattcaaggattgcattttgtgtgtgtgtagaaactaacgatctattcttgaagaaacttggtataagttttcattatttaa-------
|||  ||||||| ||||||||||| |||||||| |||||||||||||||||||||||||| || |||||||||||||| || || ||||||||||||||||||||| | |   |  | ||||    || |   |  ||||      |||      | |||| | |  | || |||  |   | |  | |||  | | |||       
CTCGGTGGAAGGCGATGCTGATGCCAATGATCCTGGGAAAGAATGTGTTATTTGCCTCTCGGAGCCAAGGGATACTACCGTTCTCCCATGTAGGCATATGgtaagtatccgatttgtgtatt----gactagttcatgtgcagcattaggggtccatgatcaagt--taaataaagcta-caaagttattctgtttctaaaaccata

upper sequence: GRMZM2G036697_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv08s0040g01940.t01 (Vitis vinifera), 5'ss of exon 2
CTCCATGGAAGGTGATGCTGATGCAAATGATCCAGGGAAAGAATGTGTTATTTGCCTCTCAGAACCAAGGGATACTACTGTCCTGCCATGTAGGCATATGgtaagtctgctgg-taatctattcaaggattgcattttgtgtgtgtgtagaaacta-acgatctattcttgaagaaacttggtataagttttcattatttaa---
|||  | || ||||||  |||    ||||||||||| |||||||||||||| ||| | || |||||  |||| || |||||||| || ||| | ||||||||||||    |   |  | ||||   ||  ||  | |  |     ||  ||| | | | |  |||   | |   ||   |||| ||  |   || ||||      
CTCTGTTGATGGTGATTTTGACAGCAATGATCCAGGAAAAGAATGTGTTATCTGCTTGTCGGAACCTCGGGACACAACTGTCCTTCCCTGTCGACATATGgtaagtgcattatcttgtttatttttgggatggctgtaata-aaatgaggaagcgagaagggctaaaatagcccaa---tggt-tagctgcccagtattccttga
















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|211058673|gb|FL451742.1|FL451742
EST:     TTTGCCTCTCAGAACCAAGGGATACTACTGTCCTGCCATGTAGGCATATG                         TGCATGTGCAGTGAGTGCGCCAAGGTCCTGAGGTACCAAACCACTCGGTGC
genomic: TTTGCCTCTCAGAACCAAGGGATACTACTGTCCTGCCATGTAGGCATATGgtaagtctgc ... tttaccgcagTGCATGTGCAGTGAGTGCGCCAAGGTCCTGAGGTACCAAACCACTCGGTGC
EST: gi|16379508|gb|BI992994.1|BI992994
EST:     ACCAAGGAATACTACTGTCCTGCCATGTAGGCATATG                         TGCATGTGCAGTGAGTGCGCCAAGGTCCTGAGGTACCAACCCACTCGGTGC
genomic: ACCAAGGGATACTACTGTCCTGCCATGTAGGCATATGgtaagtctgc ... tttaccgcagTGCATGTGCAGTGAGTGCGCCAAGGTCCTGAGGTACCAAACCACTCGGTGC
EST: gi|32803883|gb|CD956119.1|CD956119
EST:     TTTGCCTCTCAGAACCAAGGGATACTACTGTCCTGCCATGTAGGCATATG                         TGCATGTGCAGTGAGTGCGCCAAGGTCCTGAGGTACCAAACCACTCGGTGC
genomic: TTTGCCTCTCAGAACCAAGGGATACTACTGTCCTGCCATGTAGGCATATGgtaagtctgc ... tttaccgcagTGCATGTGCAGTGAGTGCGCCAAGGTCCTGAGGTACCAAACCACTCGGTGC
EST: gi|74238793|gb|DT646707.1|DT646707
EST:     TTTGCCTCTCAGAACCAAGGGATACTACTGTCCTGCCATGTAGGCATATG                         TGCATGTGCAGTGAGTGCGCCAAGGTCCTGAGGTACCAAACCACTCGGTGC
genomic: TTTGCCTCTCAGAACCAAGGGATACTACTGTCCTGCCATGTAGGCATATGgtaagtctgc ... tttaccgcagTGCATGTGCAGTGAGTGCGCCAAGGTCCTGAGGTACCAAACCACTCGGTGC
EST: gi|33771308|gb|CF272854.1|CF272854
EST:     TTTGCCTCTCAGAACCAAGGGATACTACTGTCCTGCCATGTAGGCATATG                         TGCATGTGCAGTGAGTGCGCCAAGGTCCTGAGGTACCAAACCACTCGGTGC
genomic: TTTGCCTCTCAGAACCAAGGGATACTACTGTCCTGCCATGTAGGCATATGgtaagtctgc ... tttaccgcagTGCATGTGCAGTGAGTGCGCCAAGGTCCTGAGGTACCAAACCACTCGGTGC
EST: gi|24768542|gb|CA403671.1|CA403671
EST:     TTTGCCTCTCAGAACCAAGGGATACTACTGTCCTGCCATGTAGGCATATG                         TGCATGTGCAGTGAGTGCGCCAAGGTCCTGAGGTACCAAACCACTCGGTGC
genomic: TTTGCCTCTCAGAACCAAGGGATACTACTGTCCTGCCATGTAGGCATATGgtaagtctgc ... tttaccgcagTGCATGTGCAGTGAGTGCGCCAAGGTCCTGAGGTACCAAACCACTCGGTGC
EST: gi|74035321|gb|DT535810.1|DT535810
EST:     TTTGCCTCTCAGAACCAAGGGATACTACTGTCCTGCCATGTAGGCATATG                         TGCATGTGCAGTGAGTGCGCCAAGGTCCTGAGGTACCAAACCACTCGGTGC
genomic: TTTGCCTCTCAGAACCAAGGGATACTACTGTCCTGCCATGTAGGCATATGgtaagtctgc ... tttaccgcagTGCATGTGCAGTGAGTGCGCCAAGGTCCTGAGGTACCAAACCACTCGGTGC
EST: gi|31353447|gb|CD437804.1|CD437804
EST:     TTTGCCTCTCAGAACCAAGGGATACTACTGTCCTGCCATGTAGGCATATG                         TGCATGTGCAGTGAGTGCGCCAAGGTCCTGAGGTACCAAACCACTCGGTGC
genomic: TTTGCCTCTCAGAACCAAGGGATACTACTGTCCTGCCATGTAGGCATATGgtaagtctgc ... tttaccgcagTGCATGTGCAGTGAGTGCGCCAAGGTCCTGAGGTACCAAACCACTCGGTGC
EST: gi|76011615|gb|DT938785.1|DT938785
EST:     TTTGCCTCTCAGAACCAAGGGATACTACTGTCCTGCCATGTAGGCATATG                         TGCATGTGCAGTGAGTGCGCCAAGGTCCTGAGGTACCAAACCACTCGGTGC
genomic: TTTGCCTCTCAGAACCAAGGGATACTACTGTCCTGCCATGTAGGCATATGgtaagtctgc ... tttaccgcagTGCATGTGCAGTGAGTGCGCCAAGGTCCTGAGGTACCAAACCACTCGGTGC
EST: gi|24767726|gb|CA402866.1|CA402866
EST:     TTTGCCTCTCAGAACCAAGGGATACTACTGTCCTGCCATGTAGGCATATG                         TGCATGTGCAGTGAGTGCGCCAAGGTCCTGAGGTACCAAACCACTCGGTGC
genomic: TTTGCCTCTCAGAACCAAGGGATACTACTGTCCTGCCATGTAGGCATATGgtaagtctgc ... tttaccgcagTGCATGTGCAGTGAGTGCGCCAAGGTCCTGAGGTACCAAACCACTCGGTGC
EST: gi|76011616|gb|DT938786.1|DT938786
EST:     TTTGCCTCTCAGAACCAAGGGATACTACTGTCCTGCCATGTAGGCATATG                         TGCATGTGCAGTGAGTGCGCCAAGGTCCTGAGGTACCAAACCACTCGGTGC
genomic: TTTGCCTCTCAGAACCAAGGGATACTACTGTCCTGCCATGTAGGCATATGgtaagtctgc ... tttaccgcagTGCATGTGCAGTGAGTGCGCCAAGGTCCTGAGGTACCAAACCACTCGGTGC
EST: gi|74238794|gb|DT646708.1|DT646708
EST:     TTTGCCTCTCAGAACCAAGGGATACTACTGTCCTGCCATGTAGGCATATG                         TGCATGTGCAGTGAGTGCGCCAAGGTCCTGAGGTNAC-AAACCACTCGGTG
genomic: TTTGCCTCTCAGAACCAAGGGATACTACTGTCCTGCCATGTAGGCATATGgtaagtctgc ... tttaccgcagTGCATGTGCAGTGAGTGCGCCAAGGTCCTGAGGT-ACCAAACCACTCGGTG
EST: gi|71449569|gb|DR830619.1|DR830619
EST:     TTTGCCTCTCAGAACCAAGGGATACTACTGTCCTGCCATGTAGGCATATG                         TGCATGTGCAGTGAGTGCGCCAAGGTCCTGAGGTACCAAACCACTCGGTGC
genomic: TTTGCCTCTCAGAACCAAGGGATACTACTGTCCTGCCATGTAGGCATATGgtaagtctgc ... tttaccgcagTGCATGTGCAGTGAGTGCGCCAAGGTCCTGAGGTACCAAACCACTCGGTGC
EST: gi|13490509|gb|BG517273.1|BG517273
EST:     TGCCATGTAGGCATATG                         TGCATGTGCAGTGAGTGCGCCAAGGTCCTGAGGTACCAAACCACTCGGTGC
genomic: TGCCATGTAGGCATATGgtaagtctgc ... tttaccgcagTGCATGTGCAGTGAGTGCGCCAAGGTCCTGAGGTACCAAACCACTCGGTGC
EST: gi|32850522|gb|CD990203.1|CD990203
EST:     TTTGCCTCTCAGAACCAAGGGATACTACTGTCCTGCCATGTAGGCATATG                         TGCATGTGCAGTGAGTGCGCCAAGGTCCTGAGGT
genomic: TTTGCCTCTCAGAACCAAGGGATACTACTGTCCTGCCATGTAGGCATATGgtaagtctgc ... tttaccgcagTGCATGTGCAGTGAGTGCGCCAAGGTCCTGAGGT

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: 47 (upstream exon), 48 (downstream exon)
Score: 86

CTCCATGGAAGGTGATGCTGATGCAAATGATCCAGGGAAAGAATGTGTTATTTGCCTCTCAGAACCAAGGGATACTACTGTCCTGCCATGTAGGCATATGgtaagtctgc ... tttaccgcagTGCATGTGCAGTGAGTGCGCCAAGGTCCTGAGGTACCAAACCACTCGGTGCCCCATCTGCAGGCAGCCTGTGGAGCGTCTCCTGGAGATCAAAGTGAACA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 122

CTCCATGGAAGGTGATGCTGATGCAAATGATCCAGGGAAAGAATGTGTTATTTGCCTCTCAGAACCAAGGGATACTACTGTCCTGCCATGTAGGCATATGgtaagtctgc ... tttaccgcagTGCATGTGCAGTGAGTGCGCCAAGGTCCTGAGGTACCAAACCACTCGGTGCCCCATCTGCAGGCAGCCTGTGGAGCGTCTCCTGGAGATCAAAGTGAACA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 160

CTCCATGGAAGGTGATGCTGATGCAAATGATCCAGGGAAAGAATGTGTTATTTGCCTCTCAGAACCAAGGGATACTACTGTCCTGCCATGTAGGCATATGgtaagtctgc ... tttaccgcagTGCATGTGCAGTGAGTGCGCCAAGGTCCTGAGGTACCAAACCACTCGGTGCCCCATCTGCAGGCAGCCTGTGGAGCGTCTCCTGGAGATCAAAGTGAACA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 112

CTCCATGGAAGGTGATGCTGATGCAAATGATCCAGGGAAAGAATGTGTTATTTGCCTCTCAGAACCAAGGGATACTACTGTCCTGCCATGTAGGCATATGgtaagtctgc ... tttaccgcagTGCATGTGCAGTGAGTGCGCCAAGGTCCTGAGGTACCAAACCACTCGGTGCCCCATCTGCAGGCAGCCTGTGGAGCGTCTCCTGGAGATCAAAGTGAACA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCCATGGAAGGTGATGCTGATGCAAATGATCCAGGGAAAGAATGTGTTATTTGCCTCTCAGAACCAAGGGATACTACTGTCCTGCCATGTAGGCATATGgtaagtctgctggtaatctattcaaggattgcattttgtgtgtgtgtagaaactaacgatctattcttgaagaaacttggtataagttttcattatttaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaagaaac