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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcgtcacgcccccgccgccgccgcttaaaccctaaccccgccgaatccatctaatccgcggcgcgtgcttgcgtctggctgctgtgtccaatcggatggcagAGGCGGCGAATGGCGGCGCCGACGGGGAAGGCGACGGTGACGACAAGGAGGCTGTGAAGCGCGCGGTGCCGGTGTTCAGGGAGTTTGCTCTGGCCGAGCT

Basic information

species Zea mays
transcript GRMZM2G054634_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G054634_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os10g42110.1 (Oryza sativa), 3'ss of exon 1
gtaagcgtcac-gcccccgccgccgccg-cttaaaccctaaccccgccgaatccatctaatccgcggcgcgtgcttgc--gtctgg-ctgctgtgtccaatcggatg--gcagAGGCGGC------GAATGGCGGCGCCGAC---------GGGGAAGGCGACGGTGACGACAAGGAGGCTGTGAAGCGCGCGGTGCCGGTGTTCAGGGAGTTTGCTCTGGCCGAGCT
||||||  ||| ||| ||   ||||||  | |||||||||||||| ||    |||    | || | || | ||||| |   |||   || ||        | || ||  | |||||||||      |||||||||||| |||         |  || |||| ||| ||||||||||| || |  ||||||||||| |||||||||||||||||               
gtaagccccaccgccgccattgccgccctcctaaaccctaacccc-ccatccccacacca-ccaccgctcttgcttcctaatctaatctactcctattgcttggttgttgtagAGGCGGCGGCCGCGAATGGCGGCGCTGACTCCGCGGCGGCCGACGGCGGCGGCGACGACAAGGACGCCGCCAAGCGCGCGGTCCCGGTGTTCAGGGAGTT---------------
















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|211341380|gb|FL170565.1|FL170565
EST:     GCCGCCCAACGACGCCGCCGCTCTCCCCGCCGACAAGCCTGCAGATCCTG                         AGGCGGCGAATGGCGGCGCCGACGGGGAAGGCGACGGTGACGACNAGGAGG
genomic: GCCGCCCAACGACGCCGCCGCTCTCCCCGCCGACAAGCCTGCAGATCCTGgtaagcgtca ... cggatggcagAGGCGGCGAATGGCGGCGCCGACGGGGAAGGCGACGGTGACGACAAGGAGG
EST: gi|211336403|gb|FL381835.1|FL381835
EST:     GCCGCCCAACGACGCCGCCGCTCTCCCCGCCGACAAGCCTGCAGATCCTG                         AGGCGGCGAATGGCGGCGC-GACGGGGAAGGCGACGGTGACGACAAGGAGG
genomic: GCCGCCCAACGACGCCGCCGCTCTCCCCGCCGACAAGCCTGCAGATCCTGgtaagcgtca ... cggatggcagAGGCGGCGAATGGCGGCGCCGACGGGGAAGGCGACGGTGACGACAAGGAGG
EST: gi|211341381|gb|FL170566.1|FL170566
EST:     GCCGCCCAACGACGCCGCCGCTCTCCCCGCCGACAAGCCTGCAGATCCTG                         AGGCGGCGAATGGCGGCGCCGACGGGGAAGGCGACGGTGACGACAAGGAGG
genomic: GCCGCCCAACGACGCCGCCGCTCTCCCCGCCGACAAGCCTGCAGATCCTGgtaagcgtca ... cggatggcagAGGCGGCGAATGGCGGCGCCGACGGGGAAGGCGACGGTGACGACAAGGAGG
EST: gi|211341383|gb|FL170568.1|FL170568
EST:     GCCGCCCAACGACGCCGCCGCTCTCCCCGCCGACAAGCCTGCAGATCCTG                         AGGCGGCGAATGGCGGCGC-GACGGGGAAGGCGACGGTGACGACAAGGAGG
genomic: GCCGCCCAACGACGCCGCCGCTCTCCCCGCCGACAAGCCTGCAGATCCTGgtaagcgtca ... cggatggcagAGGCGGCGAATGGCGGCGCCGACGGGGAAGGCGACGGTGACGACAAGGAGG
EST: gi|211343762|gb|FL170571.1|FL170571
EST:     GCCGCCCAACGACGCCGCCGCTCTCCCCGCCGACAAGMCTGCAGATCCTG                         AGGCGGCGAATGGCGGCGC-GACGGGGAAKGCGACGGTGACGACAAGGAGG
genomic: GCCGCCCAACGACGCCGCCGCTCTCCCCGCCGACAAGCCTGCAGATCCTGgtaagcgtca ... cggatggcagAGGCGGCGAATGGCGGCGCCGACGGGGAAGGCGACGGTGACGACAAGGAGG
EST: gi|211343761|gb|FL170570.1|FL170570
EST:     GCCGCCCAACGACGCCGCCGCTCTCCCCGCCGACAAGCCTGCAGATCCTG                         AGGCGGCGAATGGCGGCGC-GACGGGGAAGGCGACGGTGACGACAAGGAGG
genomic: GCCGCCCAACGACGCCGCCGCTCTCCCCGCCGACAAGCCTGCAGATCCTGgtaagcgtca ... cggatggcagAGGCGGCGAATGGCGGCGCCGACGGGGAAGGCGACGGTGACGACAAGGAGG
EST: gi|211341382|gb|FL170567.1|FL170567
EST:     GCCGCCCAACGACGCCGCCGCTCTCCCCGCCGACAAGCCTGCAGATCCTG                         AGGCGGCGAATGGCGGCGCCGACGGGGAAGGCGACGGTCACGACAAGGAGG
genomic: GCCGCCCAACGACGCCGCCGCTCTCCCCGCCGACAAGCCTGCAGATCCTGgtaagcgtca ... cggatggcagAGGCGGCGAATGGCGGCGCCGACGGGGAAGGCGACGGTGACGACAAGGAGG
EST: gi|211341384|gb|FL170569.1|FL170569
EST:     GCCGCCCAACGACGCCGCCGCTCTCCCCGCCGACAAGCCTGCAGATCCTG                         AGGCGGCGAATGGCGGCGC-GACGGGGAAGGCGACGGTGACGACAAGGAGG
genomic: GCCGCCCAACGACGCCGCCGCTCTCCCCGCCGACAAGCCTGCAGATCCTGgtaagcgtca ... cggatggcagAGGCGGCGAATGGCGGCGCCGACGGGGAAGGCGACGGTGACGACAAGGAGG

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: 305

TCTCCATTCCCGCCCATGGGATGCTTCCAGTCGAAGGTGGCGGGGCCCCTGCCGCCCAACGACGCCGCCGCTCTCCCCGCCGACAAGCCTGCAGATCCTGgtaagcgtca ... cggatggcagAGGCGGCGAATGGCGGCGCCGACGGGGAAGGCGACGGTGACGACAAGGAGGCTGTGAAGCGCGCGGTGCCGGTGTTCAGGGAGTTTGCTCTGGCCGAGCT


Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 40

TCTCCATTCCCGCCCATGGGATGCTTCCAGTCGAAGGTGGCGGGGCCCCTGCCGCCCAACGACGCCGCCGCTCTCCCCGCCGACAAGCCTGCAGATCCTGgtaagcgtca ... cggatggcagAGGCGGCGAATGGCGGCGCCGACGGGGAAGGCGACGGTGACGACAAGGAGGCTGTGAAGCGCGCGGTGCCGGTGTTCAGGGAGTTTGCTCTGGCCGAGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 36

TCTCCATTCCCGCCCATGGGATGCTTCCAGTCGAAGGTGGCGGGGCCCCTGCCGCCCAACGACGCCGCCGCTCTCCCCGCCGACAAGCCTGCAGATCCTGgtaagcgtca ... cggatggcagAGGCGGCGAATGGCGGCGCCGACGGGGAAGGCGACGGTGACGACAAGGAGGCTGTGAAGCGCGCGGTGCCGGTGTTCAGGGAGTTTGCTCTGGCCGAGCT


Block sizes: 49 (upstream exon), 36 (downstream exon)
Score: 28

TCTCCATTCCCGCCCATGGGATGCTTCCAGTCGAAGGTGGCGGGGCCCCTGCCGCCCAACGACGCCGCCGCTCTCCCCGCCGACAAGCCTGCAGATCCTGgtaagcgtca ... cggatggcagAGGCGGCGAATGGCGGCGCCGACGGGGAAGGCGACGGTGACGACAAGGAGGCTGTGAAGCGCGCGGTGCCGGTGTTCAGGGAGTTTGCTCTGGCCGAGCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catctaatccgcggcgcgtgcttgcgtctggctgctgtgtccaatcggatggcagAGGCGGCGAATGGCGGCGCCGACGGGGAAGGCGACGGTGACGACAAGGAGGCTGTGAAGCGCGCGGTGCCGGTGTTCAGGGAGTTTGCTCTGGCCGAGCT
 atctaat  putative branch site (score: 28)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcgtcacgcccccgccgccgccgcttaaaccctaaccccgccgaatccatctaatccgcggcgcgtgcttgcgtctggctgctgtgtccaatcggatggcagAGGCGGCGAATGGCGGCGCCGACGGGGAAGGCGACGGTGACGACAAGGAGGCTGTGAAGCGCGCGGTGCCGGTGTTCAGGGAGTTTGCTCTGGCCGAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC