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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATCCAGGAACTACAGTTGTGACAGATAGTGTGACTTCAGATGGATTGACTGTATTTATTGAAAATAAACTTGgtatgtactgttcacattgtcgtgctttgtttgagtaaataatcatttacttatctatttttttttcttaag

Basic information

species Zea mays
transcript GRMZM2G069676_T03
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069676_T02 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os07g26610.2 (Oryza sativa), 5'ss of exon 11
CATCCAGGAACTACAGTTGTGACAGATAGTGTGACTTCAGATGGATTGACTGTATTTATTGAAAATAAACTTGgtatgtactgttcacattgtcgtgctttgtttgagtaaataatcatttacttatctatttttttttcttaag
|| ||||| |||||| ||||||||||||| |||||||| |||||  |||||  ||||||||||||||||||||||| ||| |  | | ||||  || || ||||  | |   | |||  || || || | || | |  |   |||
CACCCAGGCACTACAATTGTGACAGATAGCGTGACTTCTGATGGGCTGACTACATTTATTGAAAATAAACTTGgtaggtatttgttagattg--gtcctctgttctatttgtttatcggttgctcatttgttctatgata--aag

upper sequence: GRMZM2G069676_T02 (Zea mays), 5'ss of exon 11
lower sequence: Vv13s0019g04370.t01 (Vitis vinifera), 5'ss of exon 12
CATCCAGGAACTACAGTTGTGACAGATAGTGTGACTTCAGATGGATTGACTGTATTTATTGAAAATAAACTTGgtatgtactgttcacattgtcgtgctttgtttgagtaaataatcatttacttatctatttttt-----tttcttaag-
||||||||||| ||  | || || |||||||| |||||||||||  |||||  ||| |||||||| |||||||||||||         | || | |  | |   | |  | ||||| ||  | || |   |   |      || ||||   
CATCCAGGAACAACCATAGTCACGGATAGTGTAACTTCAGATGGCCTGACTACATTCATTGAAAAGAAACTTGgtatgttgaaactgaaatggcataatgtccat-atcatataatgatgaatttgttcttaactcaagggttccttatag
















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|211441851|gb|FL182588.1|FL182588
EST:     AGATAGTGTGACTTCAGATGGATTGACTGTATTTATTGAAAATAAACTTG                         GAGGGAAGCATCACCGTTTCAAACGAGGGTACAAGAATGTAATAGACGAGG
genomic: AGATAGTGTGACTTCAGATGGATTGACTGTATTTATTGAAAATAAACTTGgtatgtactg ... ttttcttaagGAGGGAAGCATCACCGTTTCAAACGAGGGTACAAGAATGTAATAGACGAGG
EST: gi|32933693|gb|CF038505.1|CF038505
EST:     AGATAGTGTGACTTCAGATGGATTGACTGTATTTATTGAAAATAAACTTG                         GAGGGAAGCATCACCGTTTCAAACGAGGGT
genomic: AGATAGTGTGACTTCAGATGGATTGACTGTATTTATTGAAAATAAACTTGgtatgtactg ... ttttcttaagGAGGGAAGCATCACCGTTTCAAACGAGGGT
EST: gi|60341753|gb|DN208726.1|DN208726
EST:     AGATAGTGTGACTTCAGATGGATTGACTGTATTTATTGAAAATAAACTTG                         GAGGGAAGCATCACCGTTTCAAACGAGGGTACAAGAATGTAATAGACGAGG
genomic: AGATAGTGTGACTTCAGATGGATTGACTGTATTTATTGAAAATAAACTTGgtatgtactg ... ttttcttaagGAGGGAAGCATCACCGTTTCAAACGAGGGTACAAGAATGTAATAGACGAGG
EST: gi|32832812|gb|CD972490.1|CD972490
EST:     AGATAGTGTGACTTCAGATGGATTGACTGTATTTATTGAAAATAAACTTG                         GAGGGAAGCATCACCGTTTCAAACGAGGGTA
genomic: AGATAGTGTGACTTCAGATGGATTGACTGTATTTATTGAAAATAAACTTGgtatgtactg ... ttttcttaagGAGGGAAGCATCACCGTTTCAAACGAGGGTA
EST: gi|33094155|gb|CF054149.1|CF054149
EST:     AGATAGTGTGACTTCAGATGGATTGACTGTATTTATTGAAAATAAACTTG                         GAGGGAAGCATCACCGTTTCAAACGAGGGTAC
genomic: AGATAGTGTGACTTCAGATGGATTGACTGTATTTATTGAAAATAAACTTGgtatgtactg ... ttttcttaagGAGGGAAGCATCACCGTTTCAAACGAGGGTAC

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: 48 (upstream exon), 46 (downstream exon)
Score: 49

CATCCAGGAACTACAGTTGTGACAGATAGTGTGACTTCAGATGGATTGACTGTATTTATTGAAAATAAACTTGgtatgtactg ... ttttcttaagGAGGGAAGCATCACCGTTTCAAACGAGGGTACAAGAATGTAATAGACGAGGCTATTCGTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 109

CATCCAGGAACTACAGTTGTGACAGATAGTGTGACTTCAGATGGATTGACTGTATTTATTGAAAATAAACTTGgtatgtactg ... ttttcttaagGAGGGAAGCATCACCGTTTCAAACGAGGGTACAAGAATGTAATAGACGAGGCTATTCGTCTG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 70

CATCCAGGAACTACAGTTGTGACAGATAGTGTGACTTCAGATGGATTGACTGTATTTATTGAAAATAAACTTGgtatgtactg ... ttttcttaagGAGGGAAGCATCACCGTTTCAAACGAGGGTACAAGAATGTAATAGACGAGGCTATTCGTCTG


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 112

CATCCAGGAACTACAGTTGTGACAGATAGTGTGACTTCAGATGGATTGACTGTATTTATTGAAAATAAACTTGgtatgtactg ... ttttcttaagGAGGGAAGCATCACCGTTTCAAACGAGGGTACAAGAATGTAATAGACGAGGCTATTCGTCTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATCCAGGAACTACAGTTGTGACAGATAGTGTGACTTCAGATGGATTGACTGTATTTATTGAAAATAAACTTGgtatgtactgttcacattgtcgtgctttgtttgagtaaataatcatttacttatctatttttttttcttaag

- - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - -  GATGGA