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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGTGGGTTACTTCCATTTCCCTTCAACGAGACACTGGGTGGGACCACTGCAGCTCCGTCCTACTTCAATAACAAGAACAAGGCGGCTGAAGGGCAATATgtagtttcctttttccctgaacttcaacaaggcaatcgtctaataatacactgagtgcaacctgtttttattttccggtgcag

Basic information

species Zea mays
transcript GRMZM2G051262_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G051262_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os01g11070.1 (Oryza sativa), 5'ss of exon 8
CCGTGGGTTACTTCCATTTCCCTTCAACGAGACACTGGGTGGGACCACTGCAGCTCCGTCCTACTTCAATAACAAGAACAAGGCGGCTGAAGGGCAATATgtagtttcctttttccctgaactt--caaca-aggcaatcgtctaataatacactgagtg-caacctgtttttattttccggtgcag
||| ||| | ||||||||||||||||| || || ||||| || |||||||| ||||| || || |||||| |||||||||||||  |||| |  ||||||||| ||||  ||  |  | |||||  || || |     ||   | | ||||| | ||||  ||||||  ||  | ||   | |||||
CCGAGGGCTTCTTCCATTTCCCTTCAATGAAACCCTGGGAGGCACCACTGCTGCTCCATCTTATTTCAATGACAAGAACAAGGCCTCTGATGAACAATATgtattttctcttgcctttaaactttacagcacatattttctcttgacaatactccgagtaacaacctccttgcacttctggttgcag
















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|78083697|gb|DV512090.1|DV512090
EST:     CAGCTCCGTCTTACTTCAATAACAAGAACAAGGCGGCTGAAGGGCAATAT                         CTGAAAGACATTGGAGCATGTAACTTACTGGTGGAACTTGATCTAAGACGG
genomic: CAGCTCCGTCCTACTTCAATAACAAGAACAAGGCGGCTGAAGGGCAATATgtagtttcct ... tccggtgcagCTGAAAGACATTGGAGCATGTAACTTACTGGTGGAACTTGATCTAAGACGG
EST: gi|91054949|gb|EB165367.1|EB165367
EST:     CAGCTCCGTCCTACTTCAATAACAAGAACAAGGCGGCTGAAGGGCAATAT                         CTGAAAGACATTGGAGCATGTAACTTACTGGTGGAACTTGATCTAAGACGG
genomic: CAGCTCCGTCCTACTTCAATAACAAGAACAAGGCGGCTGAAGGGCAATATgtagtttcct ... tccggtgcagCTGAAAGACATTGGAGCATGTAACTTACTGGTGGAACTTGATCTAAGACGG
EST: gi|60395015|gb|DN227884.1|DN227884
EST:     CAGCTCCGTCCTACTTCAATAACAAGAACAAGGCGGCTGAAGGGCAATAT                         CTGAAAGACATTGGAGCATGTAACTTACTGGTGGAACTTGATCTAAGACGG
genomic: CAGCTCCGTCCTACTTCAATAACAAGAACAAGGCGGCTGAAGGGCAATATgtagtttcct ... tccggtgcagCTGAAAGACATTGGAGCATGTAACTTACTGGTGGAACTTGATCTAAGACGG
EST: gi|149100384|gb|EE186456.2|EE186456
EST:     CAGCTCCGTCCTACTTCAATAACAAGAACAAGGCGGCTGAAGGGCAATAT                         CTGAAAGACATTGGAGCATGTAACTTACTGGTGGAACTTGATCTAAGACGG
genomic: CAGCTCCGTCCTACTTCAATAACAAGAACAAGGCGGCTGAAGGGCAATATgtagtttcct ... tccggtgcagCTGAAAGACATTGGAGCATGTAACTTACTGGTGGAACTTGATCTAAGACGG
EST: gi|149109611|gb|EE293398.2|EE293398
EST:     CAGCTCCGTCCTACTTCAATAACAAGAACAAGGCGGCTGAAGGGCAATAT                         CTGAAAGACATTGGAGCATGTAACTTACTGGTGGAACTTGATCTAAGACGG
genomic: CAGCTCCGTCCTACTTCAATAACAAGAACAAGGCGGCTGAAGGGCAATATgtagtttcct ... tccggtgcagCTGAAAGACATTGGAGCATGTAACTTACTGGTGGAACTTGATCTAAGACGG
EST: gi|9731913|gb|BE510665.1|BE510665
EST:     CAGCTCCGTCCTACTTCAATAACAAGAACAAGGCGGCTGAAGGGCAATAT                         CTGAAAGACATTGGAGCATGTAACTTACTGGTGGAACTTGATCTAAGACGG
genomic: CAGCTCCGTCCTACTTCAATAACAAGAACAAGGCGGCTGAAGGGCAATATgtagtttcct ... tccggtgcagCTGAAAGACATTGGAGCATGTAACTTACTGGTGGAACTTGATCTAAGACGG
EST: gi|94477519|gb|EB706477.1|EB706477
EST:     CAGCTCCGTCTTACTTCAATAACAAGAACAAGGCGGCTGAAGGGCAATAT                         CTGAAAGACATTGGAGCATGTAACTTACTGGTGGAACTTGATTTAAGACGG
genomic: CAGCTCCGTCCTACTTCAATAACAAGAACAAGGCGGCTGAAGGGCAATATgtagtttcct ... tccggtgcagCTGAAAGACATTGGAGCATGTAACTTACTGGTGGAACTTGATCTAAGACGG
EST: gi|60352444|gb|DN219417.1|DN219417
EST:     CAGCTCCGTCCTACTTCAATAACAAGAACAAGGCGGCTGAAGGGCAATAT                         CTGAAAGACATTGGAGCATGTAACTTACTGGTGGAACTTGATCTAAGACGG
genomic: CAGCTCCGTCCTACTTCAATAACAAGAACAAGGCGGCTGAAGGGCAATATgtagtttcct ... tccggtgcagCTGAAAGACATTGGAGCATGTAACTTACTGGTGGAACTTGATCTAAGACGG
EST: gi|6538807|gb|AW224946.1|AW224946
EST:     CAGCTCCGTCCTACTTCAATAACAAGAACAAGGCGGCTGAAGGGCAATAT                         CTGAAAGACATTGGAGCATGTAACTTACTGGTGGAACTTGATCTAAGACGG
genomic: CAGCTCCGTCCTACTTCAATAACAAGAACAAGGCGGCTGAAGGGCAATATgtagtttcct ... tccggtgcagCTGAAAGACATTGGAGCATGTAACTTACTGGTGGAACTTGATCTAAGACGG
EST: gi|211283929|gb|FL480867.1|FL480867
EST:     CAGCTCCGTCCTACTTCAATAACAAGAACAAGSCGGCTGAAGGGCAATAT                         CTGAAAGACATTGGAGCATGTAACTTACTGGTGGAACTTGATCTAAGACGG
genomic: CAGCTCCGTCCTACTTCAATAACAAGAACAAGGCGGCTGAAGGGCAATATgtagtttcct ... tccggtgcagCTGAAAGACATTGGAGCATGTAACTTACTGGTGGAACTTGATCTAAGACGG

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), 43 (downstream exon)
Score: 84

CCGTGGGTTACTTCCATTTCCCTTCAACGAGACACTGGGTGGGACCACTGCAGCTCCGTCCTACTTCAATAACAAGAACAAGGCGGCTGAAGGGCAATATgtagtttcct ... tccggtgcagCTGAAAGACATTGGAGCATGTAACTTACTGGTGGAACTTGATCTAAGACGGCCTTACCCCTCGCGCGGGAGTGACTTGTCGACATGGGAG


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 25

CCGTGGGTTACTTCCATTTCCCTTCAACGAGACACTGGGTGGGACCACTGCAGCTCCGTCCTACTTCAATAACAAGAACAAGGCGGCTGAAGGGCAATATgtagtttcct ... tccggtgcagCTGAAAGACATTGGAGCATGTAACTTACTGGTGGAACTTGATCTAAGACGGCCTTACCCCTCGCGCGGGAGTGACTTGTCGACATGGGAG


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 42

CCGTGGGTTACTTCCATTTCCCTTCAACGAGACACTGGGTGGGACCACTGCAGCTCCGTCCTACTTCAATAACAAGAACAAGGCGGCTGAAGGGCAATATgtagtttcct ... tccggtgcagCTGAAAGACATTGGAGCATGTAACTTACTGGTGGAACTTGATCTAAGACGGCCTTACCCCTCGCGCGGGAGTGACTTGTCGACATGGGAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 95

CCGTGGGTTACTTCCATTTCCCTTCAACGAGACACTGGGTGGGACCACTGCAGCTCCGTCCTACTTCAATAACAAGAACAAGGCGGCTGAAGGGCAATATgtagtttcct ... tccggtgcagCTGAAAGACATTGGAGCATGTAACTTACTGGTGGAACTTGATCTAAGACGGCCTTACCCCTCGCGCGGGAGTGACTTGTCGACATGGGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCGTGGGTTACTTCCATTTCCCTTCAACGAGACACTGGGTGGGACCACTGCAGCTCCGTCCTACTTCAATAACAAGAACAAGGCGGCTGAAGGGCAATATgtagtttcctttttccctgaacttcaacaaggcaatcgtctaataatacactgagtgcaacctgtttttattttccggtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG