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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtttccatgccatcaattgttattgtggaatcttccataatggtgtatttcttaactcgtttgcttctttgcatgaaactgcatgtagTTAATGCTCATTGGAAGGGTGATGACAGATGGAAGGCTTAATGCTCGTGTGAAATGTGATTTGACAGACAATCTGACGTTGAAAGTAAATGCACAG

Basic information

species Zea mays
transcript GRMZM2G174696_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174696_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g20750.1 (Oryza sativa), 3'ss of exon 3
gtttgtttccatgccatcaattgttattgtggaatcttccataatggtgtatttcttaactcgtttgcttctttgcatgaaactgcatgtagTTAATGCTCATTGGAAGGGTGATGACAGATGGAAGGCTTAATGCTCGTGTGAAATGTGATTTGACAGACAATCTGACGTTGAAAGTAAATGCACAG
|||||| |  |||  ||  | | ||||    |||| ||    | | ||||||||  ||||| ||     | ||   ||| || ||  |  ||||||| ||  | ||||||||||||||||||||||| || ||||||||||||||||||||| |||||||  |||| ||  ||||| |||||||||||
gtttgtctgtatggaattgaatattat----gaattttttgca-tagtgtattttgtaacttgtga---ttttgaaatggaattgtctacagTTAATTCTTGTAGGAAGGGTGATGACAGATGGAAGACTGAATGCTCGTGTGAAATGTGATCTGACAGATGATCTTACTCTGAAAATAAATGCACAG
















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|51593036|gb|CV072182.1|CV072182
EST:     AAGTTCCAACTGCACATTATGAATTTGGCGCCAATTTTTTAGATCCAAAG                         TTAATGCTCATTGGAAGGGTGATGACAGATGGAAGACTTAATGCTCGTGTG
genomic: AAGTTCCAACTGCACATTATGAATTTGGCGCCAATTTTTTAGATCCAAAGgtttgtttcc ... ctgcatgtagTTAATGCTCATTGGAAGGGTGATGACAGATGGAAGGCTTAATGCTCGTGTG
EST: gi|211089744|gb|FL262762.1|FL262762
EST:     AAGTTCCAACTGCACATTATGAATTTGGCGCCAATTTTTTAGATCCAAAG                         TTAATGCTCATTGGAAGGGTGATGACAGATGGAAGGCTTAATGCTCGTGTG
genomic: AAGTTCCAACTGCACATTATGAATTTGGCGCCAATTTTTTAGATCCAAAGgtttgtttcc ... ctgcatgtagTTAATGCTCATTGGAAGGGTGATGACAGATGGAAGGCTTAATGCTCGTGTG
EST: gi|148937183|gb|EC881364.2|EC881364
EST:     AAGTTCCAACTGCACATTATGAATTTGGCGCCAATTTTTTAGATCCAAAG                         TTAATGCTCATTGGAAGGGTGATGACAGATGGAAGGCTTAATGCTCGTGTG
genomic: AAGTTCCAACTGCACATTATGAATTTGGCGCCAATTTTTTAGATCCAAAGgtttgtttcc ... ctgcatgtagTTAATGCTCATTGGAAGGGTGATGACAGATGGAAGGCTTAATGCTCGTGTG
EST: gi|71428447|gb|DR809497.1|DR809497
EST:     AAGTTCCAACTGCACATTATGAATTTGGCGCCAATTTTTTAGATCCAAAG                         TTAATGCTCATTGGAAGGGTGATGACAGATGGAAGGCTTAATGCTCGTGTG
genomic: AAGTTCCAACTGCACATTATGAATTTGGCGCCAATTTTTTAGATCCAAAGgtttgtttcc ... ctgcatgtagTTAATGCTCATTGGAAGGGTGATGACAGATGGAAGGCTTAATGCTCGTGTG
EST: gi|148944949|gb|EC890114.2|EC890114
EST:     AAGTTCCAACTGCACATTATGAATTTGGCGCCAATTTTTTAGATCCAAAG                         TTAATGCTCATTGGAAGGGTGATGACAGATGGAAGGCTTAATGCTCGTGTG
genomic: AAGTTCCAACTGCACATTATGAATTTGGCGCCAATTTTTTAGATCCAAAGgtttgtttcc ... ctgcatgtagTTAATGCTCATTGGAAGGGTGATGACAGATGGAAGGCTTAATGCTCGTGTG
EST: gi|5268993|gb|AI770957.1|AI770957
EST:     AAGTTCCAACTGCACATTATGAATTTGGCGCCAATTTTTTAGATCCAAAG                         TTAATGCTCATTGGAAGGGTGATGACAGATGGAAGGCTTAATGCTCGTGTG
genomic: AAGTTCCAACTGCACATTATGAATTTGGCGCCAATTTTTTAGATCCAAAGgtttgtttcc ... ctgcatgtagTTAATGCTCATTGGAAGGGTGATGACAGATGGAAGGCTTAATGCTCGTGTG
EST: gi|89762284|gb|DY689955.1|DY689955
EST:     AAGTTCCAACTGCACATTATGAATTTGGCGCCAATTTTTTAGATCCAAAG                         TTAATGCTCATTGGAAGGGTGATGACAGATGGAAGGCTTAATGCTCGTGTG
genomic: AAGTTCCAACTGCACATTATGAATTTGGCGCCAATTTTTTAGATCCAAAGgtttgtttcc ... ctgcatgtagTTAATGCTCATTGGAAGGGTGATGACAGATGGAAGGCTTAATGCTCGTGTG
EST: gi|149090165|gb|EE179465.2|EE179465
EST:     AAGTTCCAACTGCACATTATGAATTTGGCGCCAATTTTTTAGATCCAAAG                         TTAATGCTCATTGGAAGGGTGATGACAGATGGAAGGCTTAATGCTCGTGTG
genomic: AAGTTCCAACTGCACATTATGAATTTGGCGCCAATTTTTTAGATCCAAAGgtttgtttcc ... ctgcatgtagTTAATGCTCATTGGAAGGGTGATGACAGATGGAAGGCTTAATGCTCGTGTG
EST: gi|31353843|gb|CD438200.1|CD438200
EST:     AAGTTCCAACTGCACATTATGAATTTGGCGCCAATTTTTTAGATCCAAAG                         TTAATGCTCATTGGAAGGGTGATGACAGATGGAAGGCTTAATGCTCGTGTG
genomic: AAGTTCCAACTGCACATTATGAATTTGGCGCCAATTTTTTAGATCCAAAGgtttgtttcc ... ctgcatgtagTTAATGCTCATTGGAAGGGTGATGACAGATGGAAGGCTTAATGCTCGTGTG
EST: gi|76294141|gb|DV033709.1|DV033709
EST:     AAGTTCCAACTGCACATTATGAATTTGGCGCCAATTTTTTAGATCCAAAG                         TTAATGCTCATTGGAAGGGTGATGACAGATGGAAGGCTTAATGCTCGTGTG
genomic: AAGTTCCAACTGCACATTATGAATTTGGCGCCAATTTTTTAGATCCAAAGgtttgtttcc ... ctgcatgtagTTAATGCTCATTGGAAGGGTGATGACAGATGGAAGGCTTAATGCTCGTGTG

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: 76

CATTTTTATGGGCTCCTTAGAAGTTCCAGCCCAGGCATCTGAAACTATTAAAGTTCCAACTGCACATTATGAATTTGGCGCCAATTTTTTAGATCCAAAGgtttgtttcc ... ctgcatgtagTTAATGCTCATTGGAAGGGTGATGACAGATGGAAGGCTTAATGCTCGTGTGAAATGTGATTTGACAGACAATCTGACGTTGAAAGTAAATGCACAG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 67

CATTTTTATGGGCTCCTTAGAAGTTCCAGCCCAGGCATCTGAAACTATTAAAGTTCCAACTGCACATTATGAATTTGGCGCCAATTTTTTAGATCCAAAGgtttgtttcc ... ctgcatgtagTTAATGCTCATTGGAAGGGTGATGACAGATGGAAGGCTTAATGCTCGTGTGAAATGTGATTTGACAGACAATCTGACGTTGAAAGTAAATGCACAG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 48

CATTTTTATGGGCTCCTTAGAAGTTCCAGCCCAGGCATCTGAAACTATTAAAGTTCCAACTGCACATTATGAATTTGGCGCCAATTTTTTAGATCCAAAGgtttgtttcc ... ctgcatgtagTTAATGCTCATTGGAAGGGTGATGACAGATGGAAGGCTTAATGCTCGTGTGAAATGTGATTTGACAGACAATCTGACGTTGAAAGTAAATGCACAG


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 80

CATTTTTATGGGCTCCTTAGAAGTTCCAGCCCAGGCATCTGAAACTATTAAAGTTCCAACTGCACATTATGAATTTGGCGCCAATTTTTTAGATCCAAAGgtttgtttcc ... ctgcatgtagTTAATGCTCATTGGAAGGGTGATGACAGATGGAAGGCTTAATGCTCGTGTGAAATGTGATTTGACAGACAATCTGACGTTGAAAGTAAATGCACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccataatggtgtatttcttaactcgtttgcttctttgcatgaaactgcatgtagTTAATGCTCATTGGAAGGGTGATGACAGATGGAAGGCTTAATGCTCGTGTGAAATGTGATTTGACAGACAATCTGACGTTGAAAGTAAATGCACAG
                tcttaac  putative branch site (score: 80)
            tatttcttaa  TA-rich tract