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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgaatctacttgtcctgatcttttctctcttgccctgccagtaccatgcatctagtttccatgatcttcagcgaggaggctgtgtgtctctcgtctgtctctccttggcagtgcagtgttaactcccttcatgcttgcttgtgttcccttccctgtgcatttccagGTACGTGTGCTGCGCCGGGTACATGCCGTGCAGCGGCAAGTGCGGCGAGAGCCAGTGCCCGGAAGTATGCCTTGCAACCGAG

Basic information

species Zea mays
transcript GRMZM2G065696_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G065696_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os10g39100.1 (Oryza sativa), 3'ss of exon 3
gtactgaatctacttgtcctgatcttttctctcttgccctgccagtaccatgcatctagtttccatgatcttcagcgaggaggc-tgtgtgtctctcgtctgtctctccttggcagtgcagtgttaactcccttcatgcttgcttgtgttcccttccctgtgcat-ttccagGTACGTGTGCTGCGCCGGGTACATGCCGTGCAGCGGCAAGTGCGGCGAGAGCCAGTGCCCGGAAGTATGCCTTGCAACCGAG
                                                                 |  |||  |   |  |    ||| |||   ||||   |   |   | ||||||||||     |||  ||| |   | | |   ||| |   | ||||  | || ||| || |||||||| || ||||||||||| |||||||| |  |||||||||||| | ||||| ||||| |||||||||||||||
-----------------------------------------------------------------ttctctagaaaaaataaatatgtttgttcatcgtgcatagttaactagcagtgcagtt----ctctgttcttaagtccct---ttcacgcgcgtgtgtgtgtttcagATATGTGTGCTGTGCTGGGTACATGCCATGCAGCGGGAGATGCGGCGAGAGCAACTGCCCCGAAGTGTGCCTTGCAACCGAG
















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|211122993|gb|FL355473.1|FL355473
EST:     TGCGTGTCCTACATGCTGCGCAGACGCGCGCTCTACAATGACATGTCAAG                         GTACGTGTGCTGCGCCGGG
genomic: TGCGTGTCCTACATGCTGCGCAGACGCGCGCTCTACAATGACATGTCAAGgtactgaatc ... gcatttccagGTACGTGTGCTGCGCCGGG
EST: gi|14242658|gb|BG840354.2|BG840354
EST:     TGCGTGTCCTACATGCTGCGCAGACGCGCGCTCTACAATGACATGTCAAG                         GTACGTGTGCTGCGCCGGGTACATGCCGTGCAGCGGCAAGTGCGGCGAGAG
genomic: TGCGTGTCCTACATGCTGCGCAGACGCGCGCTCTACAATGACATGTCAAGgtactgaatc ... gcatttccagGTACGTGTGCTGCGCCGGGTACATGCCGTGCAGCGGCAAGTGCGGCGAGAG
EST: gi|51592771|gb|CV071917.1|CV071917
EST:     TGCGTGTCCTACATGCTGCGCAGACGCGCGCTCTACAATGACATGTCAAG                         GTACGTGTGCTGCGCCGGGTACATGCCGTGCAGCGGCAAGTGCGGCGAGAA
genomic: TGCGTGTCCTACATGCTGCGCAGACGCGCGCTCTACAATGACATGTCAAGgtactgaatc ... gcatttccagGTACGTGTGCTGCGCCGGGTACATGCCGTGCAGCGGCAAGTGCGGCGAGAG
EST: gi|16918930|gb|BM073956.1|BM073956
EST:     ATGCTGCGCAGACGCGCGCTCTACAATGACATGTCAAG                         GTACGTGTGCTGCGCCGGGTACATCCCGTGCAGCGGCAAGTGCGGCGAGAG
genomic: ATGCTGCGCAGACGCGCGCTCTACAATGACATGTCAAGgtactgaatc ... gcatttccagGTACGTGTGCTGCGCCGGGTACATGCCGTGCAGCGGCAAGTGCGGCGAGAG
EST: gi|47961905|gb|CN844614.1|CN844614
EST:     TGCGTGTCCTACATGCTGCGCAGACGCGCGCTCTACAATGACATGTCAAG                         GTACGTGTGCTGCGCCGGGTACATGCCGTGCAGCGGCAAGTGCGGCGAGAG
genomic: TGCGTGTCCTACATGCTGCGCAGACGCGCGCTCTACAATGACATGTCAAGgtactgaatc ... gcatttccagGTACGTGTGCTGCGCCGGGTACATGCCGTGCAGCGGCAAGTGCGGCGAGAG
EST: gi|32919836|gb|CF024648.1|CF024648
EST:     TGCGTGTCCTACATGCTGCGCAGACGCGCGCTCTACAATGACATGTCAAG                         GTACGCGTGCTGCGCCGGGTACATGCCGTGCAGCGGCAAGTGCGGCGAGAG
genomic: TGCGTGTCCTACATGCTGCGCAGACGCGCGCTCTACAATGACATGTCAAGgtactgaatc ... gcatttccagGTACGTGTGCTGCGCCGGGTACATGCCGTGCAGCGGCAAGTGCGGCGAGAG

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 223

CGGCCCGTGCGTGTCCTACATGCTGCGCAGACGCGCGCTCTACAATGACATGTCAAGgtactgaatc ... gcatttccagGTACGTGTGCTGCGCCGGGTACATGCCGTGCAGCGGCAAGTGCGGCGAGAGCCAGTGCCCGGAAGTATGCCTTGCAACCGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 194

CGGCCCGTGCGTGTCCTACATGCTGCGCAGACGCGCGCTCTACAATGACATGTCAAGgtactgaatc ... gcatttccagGTACGTGTGCTGCGCCGGGTACATGCCGTGCAGCGGCAAGTGCGGCGAGAGCCAGTGCCCGGAAGTATGCCTTGCAACCGAG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 5

CGGCCCGTGCGTGTCCTACATGCTGCGCAGACGCGCGCTCTACAATGACATGTCAAGgtactgaatc ... gcatttccagGTACGTGTGCTGCGCCGGGTACATGCCGTGCAGCGGCAAGTGCGGCGAGAGCCAGTGCCCGGAAGTATGCCTTGCAACCGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcagtgttaactcccttcatgcttgcttgtgttcccttccctgtgcatttccagGTACGTGTGCTGCGCCGGGTACATGCCGTGCAGCGGCAAGTGCGGCGAGAGCCAGTGCCCGGAAGTATGCCTTGCAACCGAG
     tgttaac  putative branch site (score: 5)
                                ttcccttccctgtgca  putative PPT