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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCACACAGCTGCAATTGCTGCTGGAAACAATGGGGTCCCAGTGCGAATGCATGGTCACGAATTTGGCAAGGCAAGTGGTATGGCCCCACGTGCTAGgtaagctataatttctgggacatgcatttttggggggggaatgttatagcttcacccatgtacaatcaatatcatgatactttgtgagtttgagaaagcaactttgcttttgcttacttgtcttgtgcttgttag

Basic information

species Zea mays
transcript GRMZM2G114394_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G114394_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os06g48650.3 (Oryza sativa), 5'ss of exon 4
TCACACAGCTGCAATTGCTGCTGGAAACAATGGGGTCCCAGTGCGAATGCATGGTCACGAATTTGGCAAGGCAAGTGGTATGGCCCCACGTGCTAGgtaagctataatttctgggacatgcatttttggggggggaatgttatagcttcacccatgtacaatcaatatcatgatactttgtgagtttgagaaagcaactttgcttttgcttacttgtcttgtgcttgttag
||| ||||| ||||||||||||||||| |||||| | ||||| |||||||||||||||||||||||||| |||||||||||||| |||||||||||||||| |   ||||||    |||   ||| |         || | || |   || | | | | |||  | |  |     ||   ||| | ||||       ||                                
TCATACAGCAGCAATTGCTGCTGGAAATAATGGGATTCCAGTACGAATGCATGGTCACGAATTTGGCAAAGCAAGTGGTATGGCTCCACGTGCTAGgtaagtttccatttcttcagcat---tttctaatttcaagatctcattgaa-caactaagaataatgcacaaaaatcacctcaatgaatgtgagccttgtgcta-------------------------------

upper sequence: GRMZM2G114394_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA13G00580.1 (Glycine max), 5'ss of exon 4
TCACACAGCTGCAATTGCTGCTGGAAACAATGGGGTCCCAGTGCGAATGCATGGTCACGAATTTGGCAAGGCAAGTGGTATGGCCCCACGTGCTAGgtaagctataatttctgggacatgcatttttggggggggaatgttatagcttcacccatgtacaatcaatatcatgatactttgtgagtttgagaaagcaactttgcttttgcttacttgtcttgtgcttgttag
||| |||||  | ||||| |||||||| |||||  | || ||| |||||||||| ||||||||||| |  || ||||| ||||| || |||||||||| ||  |||||  |       ||   ||||      || |  ||| ||      |  | | || |  | ||  || |   |  |   ||| ||                                         
TCATACAGCCTCTATTGCGGCTGGAAATAATGGAATTCCTGTGAGAATGCATGGCCACGAATTTGGGAGAGCGAGTGGGATGGCTCCTCGTGCTAGgtgaggaataataacc---ctttgttgttttaaaactggga-attacagtcctttctgt-tgcattagacatt-tggtgtatcct---tttcag-----------------------------------------
















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|31354263|gb|CD438620.1|CD438620
EST:     AAGTGGTATGGCCCCACGTGCTAG                         GGTAGCTGTC-CCTAA-GAACTTTACAGGCTTTTTGGTGGTTACATAGCTG
genomic: AAGTGGTATGGCCCCACGTGCTAGgtaagctata ... tgcttgttagGGTAGCTGTCTAC-AAGGTTCTTTACAGGCTTTTTGGTGGTTACATAGCTG
EST: gi|67043292|gb|CO469547.1|CO469547
EST:     TTTGGCAAGGCAAGTGGTATGGCCCCACGTGCTAG                         GGTAGCTGTCTACAATGTTCTTTACAGGCTTTTTGGTGGTTACATAGCTGA
genomic: TTTGGCAAGGCAAGTGGTATGGCCCCACGTGCTAGgtaagctata ... tgcttgttagGGTAGCTGTCTACAAGGTTCTTTACAGGCTTTTTGGTGGTTACATAGCTGA
EST: gi|31351455|gb|CD435812.1|CD435812
EST:     ATGCATGGTCACGAATTTGGCAAGGCAAGTGGTATGGCCCCACGTGCTAG                         GGTAGCTGTCTACAAGGTTCTTTACAGGCTTTTTGGTGGTTACATAGCTGA
genomic: ATGCATGGTCACGAATTTGGCAAGGCAAGTGGTATGGCCCCACGTGCTAGgtaagctata ... tgcttgttagGGTAGCTGTCTACAAGGTTCTTTACAGGCTTTTTGGTGGTTACATAGCTGA

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: 44 (upstream exon), 49 (downstream exon)
Score: 136

TCACACAGCTGCAATTGCTGCTGGAAACAATGGGGTCCCAGTGCGAATGCATGGTCACGAATTTGGCAAGGCAAGTGGTATGGCCCCACGTGCTAGgtaagctata ... tgcttgttagGGTAGCTGTCTACAAGGTTCTTTACAGGCTTTTTGGTGGTTACATAGCTGATGTTGTGGCAGCTATTGATCAG


Block sizes: 47 (upstream exon), 40 (downstream exon)
Score: 28

TCACACAGCTGCAATTGCTGCTGGAAACAATGGGGTCCCAGTGCGAATGCATGGTCACGAATTTGGCAAGGCAAGTGGTATGGCCCCACGTGCTAGgtaagctata ... tgcttgttagGGTAGCTGTCTACAAGGTTCTTTACAGGCTTTTTGGTGGTTACATAGCTGATGTTGTGGCAGCTATTGATCAG


Block sizes: 47 (upstream exon), 16 (downstream exon)
Score: 32

TCACACAGCTGCAATTGCTGCTGGAAACAATGGGGTCCCAGTGCGAATGCATGGTCACGAATTTGGCAAGGCAAGTGGTATGGCCCCACGTGCTAGgtaagctata ... tgcttgttagGGTAGCTGTCTACAAGGTTCTTTACAGGCTTTTTGGTGGTTACATAGCTGATGTTGTGGCAGCTATTGATCAG


Block sizes: 42 (upstream exon), 44 (downstream exon)
Score: 33

TCACACAGCTGCAATTGCTGCTGGAAACAATGGGGTCCCAGTGCGAATGCATGGTCACGAATTTGGCAAGGCAAGTGGTATGGCCCCACGTGCTAGgtaagctata ... tgcttgttagGGTAGCTGTCTACAAGGTTCTTTACAGGCTTTTTGGTGGTTACATAGCTGATGTTGTGGCAGCTATTGATCAG