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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTTAGCTGCTCGAGGTTTGAAGAGTGGCGGTACTGTTCAACAGCGTGCAGATCGTCTTTTCTTGTTGAAGgtgatattaaagacgctagtgctactgctggttcatctattgttcttgcctttttaccattcattttgaactttttgttgattatattttgcag

Basic information

species Zea mays
transcript GRMZM2G178227_T02
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178227_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os03g50850.2 (Oryza sativa), 5'ss of exon 8
GCTTTAGCTGCTCGAGGTTTGAAGAGTGGCGGTACTGTTCAACAGCGTGCAGATCGTCTTTTCTTGTTGAAGgtgatattaaagacgctagtgctactgctggttcatct--attgttcttgcctttttaccattcattttgaactttttgttgattatattttgcag
|||||||||||||| || || || ||||| |||||||||||||||||||| || || ||||||||||||||||| ||    ||    ||  |    |||    |||| ||    | || ||   | |||||||   ||| ||||||| | | ||||||||| ||||||
GCTTTAGCTGCTCGTGGATTAAAAAGTGGTGGTACTGTTCAACAGCGTGCTGAGCGACTTTTCTTGTTGAAGgtaatt---aatgtacttttaaacctggatattcagctcatctttttttaaatatttaccaaatattctgaacttgtcgatgattatatcttgcag
















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|8367537|gb|BE050482.1|BE050482
EST:     AGAGTGGCGGTACTGTTCAACAGCGTGCAGATCGTCTTTTCTTGTTGAAG                         GTTACACCGTTGGAACAACTAGATAGGAAGCATTTTGCCAAAGTTCCACAT
genomic: AGAGTGGCGGTACTGTTCAACAGCGTGCAGATCGTCTTTTCTTGTTGAAGgtgatattaa ... tattttgcagGTTACACCGTTGGAACAACTAGATAGGAAGCATTTTGCCAAAGTTCCACAT
EST: gi|60393978|gb|DN226848.1|DN226848
EST:     AGAGTGGCGGTACTGTTCAACAGCGTGCAGATCGTCTTTTCTTGTTGAAG                         GTTACACCGTTGGAACA
genomic: AGAGTGGCGGTACTGTTCAACAGCGTGCAGATCGTCTTTTCTTGTTGAAGgtgatattaa ... tattttgcagGTTACACCGTTGGAACA
EST: gi|76290494|gb|DV030062.1|DV030062
EST:     GAGTGGCGGTACTGTTCAACAGCGTGCAGATCGTCTTTTCTTGTTGAAAG                         GT-ACACCGTTGGAACAACTAGATAGGAAGCATTTTGC-AAAGTTCCACA
genomic: GAGTGGCGGTACTGTTCAACAGCGTGCAGATCGTCTTTTCTTGTTGAA-Ggtgatattaa ... tattttgcagGTTACACCGTTGGAACAACTAGATAGGAAGCATTTTGCCAAAGTTCCACA
EST: gi|33094832|gb|CF054826.1|CF054826
EST:     ACTGTTCAACAGCGTGCAGATCGGCTTTTCTTGTTGAAG                         GTTACACCGTTGGAACAACTAGATAGGAAGCATTTTGCCAAAGTTCCACAT
genomic: ACTGTTCAACAGCGTGCAGATCGTCTTTTCTTGTTGAAGgtgatattaa ... tattttgcagGTTACACCGTTGGAACAACTAGATAGGAAGCATTTTGCCAAAGTTCCACAT
EST: gi|8367536|gb|BE050481.1|BE050481
EST:     AGAGTGGCGGTACTGTTCAACAGCGTGCAGATCGTCTTTTCTTGTTGAAG                         GTTACACCGTTGGAACAACTAGATAGGAAGCATTTTGCCAAAGTTCCACAT
genomic: AGAGTGGCGGTACTGTTCAACAGCGTGCAGATCGTCTTTTCTTGTTGAAGgtgatattaa ... tattttgcagGTTACACCGTTGGAACAACTAGATAGGAAGCATTTTGCCAAAGTTCCACAT
EST: gi|31358406|gb|CD442763.1|CD442763
EST:     AGAGTGGCGGTACTGTTCAACAGCGTGCAGATCGTCTTTTCTTGTTGAAG                         GTTACACCGTTGGAACAACTAGATAGGAAGCATTTTGCCAAAGTTCCACAT
genomic: AGAGTGGCGGTACTGTTCAACAGCGTGCAGATCGTCTTTTCTTGTTGAAGgtgatattaa ... tattttgcagGTTACACCGTTGGAACAACTAGATAGGAAGCATTTTGCCAAAGTTCCACAT
EST: gi|26456323|gb|CA827906.1|CA827906
EST:     AGAGTGGCGGTACTGTTCAACAGCGTGCAGATCGTCTTTTCTTGTTGAAG                         GTTACACCGTTGGAACAACTAGATAGGAAGCATTTTGCCAAAGTTCCACAT
genomic: AGAGTGGCGGTACTGTTCAACAGCGTGCAGATCGTCTTTTCTTGTTGAAGgtgatattaa ... tattttgcagGTTACACCGTTGGAACAACTAGATAGGAAGCATTTTGCCAAAGTTCCACAT
EST: gi|61117874|gb|DN558835.1|DN558835
EST:     AGAGTGGCGGTACTGTTCAACAGCGTGCAGATCGTCTTTTCTTGTTGAAG                         GTTACACCGTTGGAACAACTAGATAGGAAGCATTTTGCCAAAGTTCCACAT
genomic: AGAGTGGCGGTACTGTTCAACAGCGTGCAGATCGTCTTTTCTTGTTGAAGgtgatattaa ... tattttgcagGTTACACCGTTGGAACAACTAGATAGGAAGCATTTTGCCAAAGTTCCACAT
EST: gi|61117875|gb|DN558836.1|DN558836
EST:     AGAGTGGCGGTACTGTTCAACAGCGTGCAGATCGTCTTTTCTTGTTGAAG                         GTTACACCGTTGGAACAACTAGATAGGAAGCATTTTGCCAAAGTTCCACAT
genomic: AGAGTGGCGGTACTGTTCAACAGCGTGCAGATCGTCTTTTCTTGTTGAAGgtgatattaa ... tattttgcagGTTACACCGTTGGAACAACTAGATAGGAAGCATTTTGCCAAAGTTCCACAT

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: 171

GCTTTAGCTGCTCGAGGTTTGAAGAGTGGCGGTACTGTTCAACAGCGTGCAGATCGTCTTTTCTTGTTGAAGgtgatattaa ... tattttgcagGTTACACCGTTGGAACAACTAGATAGGAAGCATTTTGCCAAAGTTCCACATACTAAAGATGGCTCAAACACAGCTCCTAATGGTAATGCTTTCAAGGAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 203

GCTTTAGCTGCTCGAGGTTTGAAGAGTGGCGGTACTGTTCAACAGCGTGCAGATCGTCTTTTCTTGTTGAAGgtgatattaa ... tattttgcagGTTACACCGTTGGAACAACTAGATAGGAAGCATTTTGCCAAAGTTCCACATACTAAAGATGGCTCAAACACAGCTCCTAATGGTAATGCTTTCAAGGAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 139

GCTTTAGCTGCTCGAGGTTTGAAGAGTGGCGGTACTGTTCAACAGCGTGCAGATCGTCTTTTCTTGTTGAAGgtgatattaa ... tattttgcagGTTACACCGTTGGAACAACTAGATAGGAAGCATTTTGCCAAAGTTCCACATACTAAAGATGGCTCAAACACAGCTCCTAATGGTAATGCTTTCAAGGAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 83

GCTTTAGCTGCTCGAGGTTTGAAGAGTGGCGGTACTGTTCAACAGCGTGCAGATCGTCTTTTCTTGTTGAAGgtgatattaa ... tattttgcagGTTACACCGTTGGAACAACTAGATAGGAAGCATTTTGCCAAAGTTCCACATACTAAAGATGGCTCAAACACAGCTCCTAATGGTAATGCTTTCAAGGAGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTTTAGCTGCTCGAGGTTTGAAGAGTGGCGGTACTGTTCAACAGCGTGCAGATCGTCTTTTCTTGTTGAAGgtgatattaaagacgctagtgctactgctggttcatctattgttcttgcctttttaccattcattttgaactttttgttgattatattttgcag

- - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG