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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgggtgcatttaattttttttcttctaattcttctaagccccttcatagagtttactaactagtgcttactttcagGCATGCGCATCCCTAGAACCAAATTACCAGCCTCCTGTAACATTTGTGGTGGTTCAAAAACGTCATCATACGAGACTATTTACAAACAATCACAAAGACA

Basic information

species Zea mays
transcript AC189879.3_FGT003
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 17
gttgggtgcatttaattttttttcttctaattcttctaagccccttcatagagtttactaactag-tgcttactttcagGCATGCGCATCCCTAGAACCAAATTACCAGCCTCCTGTAACATTTGTGGTGGTTCAAAAACGTCATCATACGAGACTATTTACAAACAATCACAAAGACA
||| | |||||||   |||| ||     |  | || |   || ||| ||   |||  || || |  || || |||| ||||||| ||||| |||||||||||||| ||||||||||||||||| ||||| || ||||| ||||| ||||| ||||| ||  ||||||||||||||||||
gttagatgcatttgtattttctttactcagatattttgt-ccactttattaggttgcctgacgaaatgttttcttttagGCATGTGCATCTCTAGAACCAAATTATCAGCCTCCTGTAACATTCGTGGTTGTCCAAAAGCGTCACCATACAAGACTCTTCGCAAACAATCACAAAGACA

upper sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA06G23920.1 (Glycine max), 3'ss of exon 17
--gttgggtgcatttaattttttttc----ttctaattcttctaa--gccccttcatagagtttactaactagtgcttactttcagGCATGCGCATCCCTAGAACCAAATTACCAGCCTCCTGTAACATTTGTGGTGGTTCAAAAACGTCATCATACGAGACTATTTACAAACAATCACAAAGACA
      ||   |   ||   |||  |    || ||||| || | |  |   | |     | | | || | |  |  ||   |  |||| || |||||  | ||||| | |||||| ||||| |||||||||||  | ||||||||||| ||||| || ||||| ||  ||||||||||  | ||||
gtacctggaaaaaaaaacaatttagcaaagttataatttttattactgtggcattcctcaatattcttattctt-tttgtgtatagGCTTGTGCATCTTTGGAACCTAGTTACCAACCTCCAGTAACATTTGTTATTGTTCAAAAACGGCATCACACTAGACTCTTCGCAAACAATCATGATGACA

upper sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA17G12850.1 (Glycine max), 3'ss of exon 17
---gttgggtgcatttaattttttttcttctaattcttctaagccccttcatagagtttactaactagtgcttactttcagGCATGCGCATCCCTAGAACCAAATTACCAGCCTCCTGTAACATTTGTGGTGGTTCAAAAACGTCATCATACGAGACTATTTACAAACAATCACAAAGACA
    ||||    |||  | || | ||  | ||  | |  || | |  |||  |  | ||| |  ||     | |  |  |||| || |||||  | ||||| | |||||| ||||| ||||||||||| ||||||||||| || ||||| || ||||| ||  ||||||||||  | ||||
gtacttggacaaattacagttatatttatttatatttattatgacatttcccaatgcttaatttct-----taatgtgtagGCTTGTGCATCTTTGGAACCTAGTTACCAACCTCCGGTAACATTTGTTGTGGTTCAAAAGCGACATCACACTAGACTCTTCTCAAACAATCATGACGACA

upper sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 18
gttgggtgcatttaattttttttcttctaattcttctaagccccttcatagagtttactaactagtgcttacttt-cagGCATGCGCATCCCTAGAACCAAATTACCAGCCTCCTGTAACATTTGTGGTGGTTCAAAAACGTCATCATACGAGACTATTTACAAACAATCACAAAGACA
||  ||  || ||  | |  ||         | |||| |     |  |     | | || |  |||  |  || |  ||||||| || ||| |||||||||| ||||||||||| ||||||||  | || || |||||| | ||||||||  |  ||||| |||||||  |||  ||||
gtcaggatcactttctctcattatacacttgttttcttattatgtcaaagatatgttctgagaagttatatctgtgtagGCATGTGCTTCCTTAGAACCAAACTACCAGCCTCCAGTAACATTCATAGTTGTGCAAAAAAGACATCATACCCGGTTATTTGCAAACAACTACAGGGACA

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|91877156|gb|EB407113.1|EB407113
EST:     AAGGCCAGTTCTATCAAGTTCTCCTTTACGAGTTAGATGCCATCCGTAAG                         GCATGCGCATCCCTAGAACCAAATTACCAGCCTCCTGTAACATTTGTGGTG
genomic: AAGGCCAGTTCTATCAAGTTCTCCTTTACGAGTTAGATGCCATCCGTAAGgttgggtgca ... ttactttcagGCATGCGCATCCCTAGAACCAAATTACCAGCCTCCTGTAACATTTGTGGTG
EST: gi|211241581|gb|FL211915.1|FL211915
EST:     AAGGCCAGTTCTATCAAGTTCTCCTTTACGAGTTAGATGCCATCCGTAAG                         GCATGCGCATCCCTAGAACCAAATTACCAGCCTCCTGTAACATTTGTGGTG
genomic: AAGGCCAGTTCTATCAAGTTCTCCTTTACGAGTTAGATGCCATCCGTAAGgttgggtgca ... ttactttcagGCATGCGCATCCCTAGAACCAAATTACCAGCCTCCTGTAACATTTGTGGTG
EST: gi|9566493|gb|BE476002.1|BE476002
EST:     AAGGCCAGTTCTATCAAGTTCTCCTTTACGAGTTAGATGCCATCCGTAAG                         GCATGCGCATCCCTAGAACCAAATTACCAGCCTCCTGTAACATTTGTGGTG
genomic: AAGGCCAGTTCTATCAAGTTCTCCTTTACGAGTTAGATGCCATCCGTAAGgttgggtgca ... ttactttcagGCATGCGCATCCCTAGAACCAAATTACCAGCCTCCTGTAACATTTGTGGTG
EST: gi|20301316|gb|BQ164259.1|BQ164259
EST:     AAGGCCAGTTCTATCAAGTTCTCCTTTACGAGTTAGATGCCATCCGTAAG                         GCATGCGCATCCCTAGAACCAAATTACCAGCCTCCTGTAACATTTGTGGTG
genomic: AAGGCCAGTTCTATCAAGTTCTCCTTTACGAGTTAGATGCCATCCGTAAGgttgggtgca ... ttactttcagGCATGCGCATCCCTAGAACCAAATTACCAGCCTCCTGTAACATTTGTGGTG

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: 962

GGACGGTGTTAGTGAAGGCCAGTTCTATCAAGTTCTCCTTTACGAGTTAGATGCCATCCGTAAGgttgggtgca ... ttactttcagGCATGCGCATCCCTAGAACCAAATTACCAGCCTCCTGTAACATTTGTGGTGGTTCAAAAACGTCATCATACGAGACTATTTACAAACAATCACAAAGACA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 178

GGACGGTGTTAGTGAAGGCCAGTTCTATCAAGTTCTCCTTTACGAGTTAGATGCCATCCGTAAGgttgggtgca ... ttactttcagGCATGCGCATCCCTAGAACCAAATTACCAGCCTCCTGTAACATTTGTGGTGGTTCAAAAACGTCATCATACGAGACTATTTACAAACAATCACAAAGACA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 82

GGACGGTGTTAGTGAAGGCCAGTTCTATCAAGTTCTCCTTTACGAGTTAGATGCCATCCGTAAGgttgggtgca ... ttactttcagGCATGCGCATCCCTAGAACCAAATTACCAGCCTCCTGTAACATTTGTGGTGGTTCAAAAACGTCATCATACGAGACTATTTACAAACAATCACAAAGACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 219

GGACGGTGTTAGTGAAGGCCAGTTCTATCAAGTTCTCCTTTACGAGTTAGATGCCATCCGTAAGgttgggtgca ... ttactttcagGCATGCGCATCCCTAGAACCAAATTACCAGCCTCCTGTAACATTTGTGGTGGTTCAAAAACGTCATCATACGAGACTATTTACAAACAATCACAAAGACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctaattcttctaagccccttcatagagtttactaactagtgcttactttcagGCATGCGCATCCCTAGAACCAAATTACCAGCCTCCTGTAACATTTGTGGTGGTTCAAAAACGTCATCATACGAGACTATTTACAAACAATCACAAAGACA
                                            cttactttc  CT-rich tract
                              tttactaa  TA-rich tract