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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactttatatctgttcgctgaagcatttattgtctatagctttatgttggtagcattttaacttcatcttttttcttcggcatttaaccttattaagAGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCGGACACGGCTCCTAGGAAGGCACACACGGCTAATCAG

Basic information

species Zea mays
transcript GRMZM5G864266_T01
intron # 33
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G864266_T01 (Zea mays), 3'ss of exon 33
lower sequence: LOC_Os07g06950.1 (Oryza sativa), 3'ss of exon 31
gtactttatatc--tgttcgctgaagcatttattgtctatagctttatgttggtagcattttaacttcatcttttttcttcggcatttaaccttattaagAGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCGGACACGGCTCCTAGGAAGGCACACACGGCTAATCAG
||||  ||| |   || | ||| || || | | |||   | |||| || | | |  ||||| |||||    ||||| |||           |||||| || ||||||||||||||||||||||||| |||||||||||||| ||||| |||||||||||||| ||| ||||||  |||||||||
gtacaatattttcttgcttgctaaa-caatcactgttagt-gcttaatttggttcacatttaaactt----tttttgcttg----------cttatttagCGAAACATGTATGGAGCTTGGGAGCAATATCTTGGACTGGAGCATCCAGACACGGCTCCTAGAAAGACACACAACGCTAATCAG
















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|211450914|gb|FL439857.1|FL439857
EST:     TGAAGATTCAGATACTGTAGCCCTAAAATTCCAG                         AGAAACATGTATGGAGCTTGGGASCAGTATCTTGGACTGGAACATCCGGAC
genomic: TGAAGATTCAGATACTGTAGCCCTAAAATTCCAGgtactttata ... ccttattaagAGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCGGAC
EST: gi|60348260|gb|DN215233.1|DN215233
EST:     GTCGTCCTGACTATTTTGAAGATTCAGATACTGTAGCCCTAAAATTCCAG                         AGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCGGAC
genomic: GTCGTCCTGACTATTTTGAAGATTCAGATACTGTAGCCCTAAAATTCCAGgtactttata ... ccttattaagAGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCGGAC
EST: gi|61118763|gb|DN559724.1|DN559724
EST:     GTCGTCCTGACTATTTTGAAGATTCAGATACTGTAGCACTAAAATTCCAG                         AGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCGGAC
genomic: GTCGTCCTGACTATTTTGAAGATTCAGATACTGTAGCCCTAAAATTCCAGgtactttata ... ccttattaagAGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCGGAC
EST: gi|60400274|gb|DN233081.1|DN233081
EST:     GTCGTCCTGACTATTTTGAAGATTCAGATACTGTAGCCCTAAAATTCCAG                         AGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCGGAC
genomic: GTCGTCCTGACTATTTTGAAGATTCAGATACTGTAGCCCTAAAATTCCAGgtactttata ... ccttattaagAGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCGGAC
EST: gi|78106266|gb|DV524684.1|DV524684
EST:     GTCGTCCTGACTATTTTGAAGATTCAGATACTGTAGCCCTAAAATTCCAG                         AGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCGGAC
genomic: GTCGTCCTGACTATTTTGAAGATTCAGATACTGTAGCCCTAAAATTCCAGgtactttata ... ccttattaagAGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCGGAC
EST: gi|60394863|gb|DN227732.1|DN227732
EST:     GTCGTCCTGACTATTTTGAAGATTCAGATACTGTAGCCCTAAAATTCCAG                         AGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCGGAC
genomic: GTCGTCCTGACTATTTTGAAGATTCAGATACTGTAGCCCTAAAATTCCAGgtactttata ... ccttattaagAGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCGGAC
EST: gi|211112821|gb|FL033799.1|FL033799
EST:     TGAAGATTCAGATACTGTAGCCCTAAAATTCCAG                         AGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCGGAC
genomic: TGAAGATTCAGATACTGTAGCCCTAAAATTCCAGgtactttata ... ccttattaagAGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCGGAC
EST: gi|67014431|gb|CO443180.1|CO443180
EST:     GTCGTCCTGACTATTTTGAAGATTCAGATACTGTAGCCCTAAAATTCCAG                         AGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCGGAC
genomic: GTCGTCCTGACTATTTTGAAGATTCAGATACTGTAGCCCTAAAATTCCAGgtactttata ... ccttattaagAGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCGGAC
EST: gi|67020350|gb|CO449099.1|CO449099
EST:     GTCGTCCTGACTATTTTGAAGATTCAGATACTGTAGCCCTAAAATTCCAG                         AGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCGGAC
genomic: GTCGTCCTGACTATTTTGAAGATTCAGATACTGTAGCCCTAAAATTCCAGgtactttata ... ccttattaagAGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCGGAC

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), 49 (downstream exon)
Score: 96

TGGAAGTTTGCATACATTTCACTCGGTCGTCCTGACTATTTTGAAGATTCAGATACTGTAGCCCTAAAATTCCAGgtactttata ... ccttattaagAGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCGGACACGGCTCCTAGGAAGGCACACACGGCTAATCAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 37

TGGAAGTTTGCATACATTTCACTCGGTCGTCCTGACTATTTTGAAGATTCAGATACTGTAGCCCTAAAATTCCAGgtactttata ... ccttattaagAGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCGGACACGGCTCCTAGGAAGGCACACACGGCTAATCAG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 70

TGGAAGTTTGCATACATTTCACTCGGTCGTCCTGACTATTTTGAAGATTCAGATACTGTAGCCCTAAAATTCCAGgtactttata ... ccttattaagAGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCGGACACGGCTCCTAGGAAGGCACACACGGCTAATCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 63

TGGAAGTTTGCATACATTTCACTCGGTCGTCCTGACTATTTTGAAGATTCAGATACTGTAGCCCTAAAATTCCAGgtactttata ... ccttattaagAGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCGGACACGGCTCCTAGGAAGGCACACACGGCTAATCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgttggtagcattttaacttcatcttttttcttcggcatttaaccttattaagAGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCGGACACGGCTCCTAGGAAGGCACACACGGCTAATCAG
                                             ccttatt  CT-rich tract
                                       atttaaccttattaa  TA-rich tract