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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgctcattctccttgcctgaaaggatttctctattctgggctactgtggacgcgttgctagtcttaaattgcgagagatttaggatctgtcatttagatttttgtgtgttgtgacatcactatgtgtttgtttgttatatagctgaattatgactcttgcatgcagGGACATCTGCATGCCCTGAGGCGAAATTCTACTGCAAGAATGCAGGCCACACTCCAGTCACGATCTTCTCGTCACGAGTGAATGACGGCATTTGTG

Basic information

species Zea mays
transcript AC213600.3_FGT002
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC213600.3_FGT002 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g16970.2 (Oryza sativa), 3'ss of exon 2
gtactgct-cattctccttgcctgaaagga----------tttctctattctgggctactgtggacgcgttgctagtcttaaattgcgagagatttaggatctgtcatttagatttttgtgtgttgtgacatcactatgtgtttgtttgttatatagc-tgaattatgactcttgcatgcagGGACATCTGCATGCCCTGAGGCGAAATTCTACTGCAAGAATGCAGGCCACACTCCAGTCACGATCTTCTCGTCACGAGTGAATGACGGCATTTGTG
    |||| | ||   || ||||||||             ||| | |    | |  |  || ||| | ||| || || |||  ||         || |     ||   |   || |   |    |  |  |||     | | |  ||  |   || |  |  | | |    ||||   ||||||||||| || ||||| |||| ||| ||||||||| ||||||| || ||  ||||  |||||||||||||||| ||||||||||| || || ||||
--gttgcttccttgctctcgcctgaaaaagattatccctttttttttgccttagctttttgcggaggtgtt-ctggttttaggttctcgtg---tttgtgctagtagctcgaatctacttactgtaggcaatctaagagagctgtttaatcgaattgtgtttactttttgccttg-gcgcagGGACATCGGCGTGCCCGGAGGGGAAGTTCTACTGCCAGAATGCTGGGCATTCTCCCATCACGATCTTCTCGTCGCGAGTGAATGATGGTATCTGTG
















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|15427042|gb|BI542864.1|BI542864
EST:     CCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCG                         GGACATCTGCATGCCCTGAGGCGAAATTCTACTGCAAGAATGCAGGCCACA
genomic: CCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgctca ... ttgcatgcagGGACATCTGCATGCCCTGAGGCGAAATTCTACTGCAAGAATGCAGGCCACA
EST: gi|211470279|gb|FL336879.1|FL336879
EST:     CCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCG                         GGACATCTGCATGCCCTGAGGCGAAATTCTACTGCAAGAATGCAGGCCACA
genomic: CCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgctca ... ttgcatgcagGGACATCTGCATGCCCTGAGGCGAAATTCTACTGCAAGAATGCAGGCCACA
EST: gi|211091911|gb|FL362893.1|FL362893
EST:     CCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCG                         GGACATCTGCATGCCCTGAGGCGAAATTCTACTGCAAGAATGCAGGCCACA
genomic: CCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgctca ... ttgcatgcagGGACATCTGCATGCCCTGAGGCGAAATTCTACTGCAAGAATGCAGGCCACA
EST: gi|211133488|gb|FL236777.1|FL236777
EST:     CCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCG                         GGACATCTGCATGCCCTGAGGCGAAATTCTACTGCAAGAATGCAGGCCACA
genomic: CCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgctca ... ttgcatgcagGGACATCTGCATGCCCTGAGGCGAAATTCTACTGCAAGAATGCAGGCCACA
EST: gi|211391684|gb|FL461159.1|FL461159
EST:     CCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCG                         GGACATCTGCATGCCCTGAGGCGAAATTCTACTGCAAGAATGCAGGCCACA
genomic: CCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgctca ... ttgcatgcagGGACATCTGCATGCCCTGAGGCGAAATTCTACTGCAAGAATGCAGGCCACA
EST: gi|211531444|gb|FL327584.1|FL327584
EST:     CCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCG                         GGACATCTGCATGCCCTGAGGCGAAATTCTACTGCAAGAATGCAGGCCACA
genomic: CCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgctca ... ttgcatgcagGGACATCTGCATGCCCTGAGGCGAAATTCTACTGCAAGAATGCAGGCCACA
EST: gi|32945773|gb|CF050592.1|CF050592
EST:     CCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCG                         GGACATCTGCATGCCCTGAGGCGAAATTCTACTGCAAGAATGCAGGCCACA
genomic: CCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgctca ... ttgcatgcagGGACATCTGCATGCCCTGAGGCGAAATTCTACTGCAAGAATGCAGGCCACA
EST: gi|211389058|gb|FL461157.1|FL461157
EST:     CCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCG                         GGACATCTGCATGCCTTGAGGCGAAATTCTACTGCAAGAATGNAGGCCACA
genomic: CCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgctca ... ttgcatgcagGGACATCTGCATGCCCTGAGGCGAAATTCTACTGCAAGAATGCAGGCCACA
EST: gi|15499427|gb|BI595940.1|BI595940
EST:     CCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCG                         GGACATCTGCATGCCCTGAGGCGAAATTCTACTGCAAGAATGCAGGCCACA
genomic: CCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgctca ... ttgcatgcagGGACATCTGCATGCCCTGAGGCGAAATTCTACTGCAAGAATGCAGGCCACA
EST: gi|60344264|gb|DN211237.1|DN211237
EST:     CCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCG                         GGACATCTGCATGCCCTGAGGCGAAATTCTACTGCAAGAATGCAGGCCACA
genomic: CCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgctca ... ttgcatgcagGGACATCTGCATGCCCTGAGGCGAAATTCTACTGCAAGAATGCAGGCCACA
EST: gi|211237696|gb|FL353195.1|FL353195
EST:     CCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCG                         GGACATCTGCATGCCCTGAGGCGAAATTCTACTGCAAGAATGCAGGCCACA
genomic: CCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgctca ... ttgcatgcagGGACATCTGCATGCCCTGAGGCGAAATTCTACTGCAAGAATGCAGGCCACA
EST: gi|211133487|gb|FL236776.1|FL236776
EST:     CCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCG                         GGACATCTGCATGCCCTGAGGCGAAATTCTACTGCAAGAATGCAGGCCACA
genomic: CCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgctca ... ttgcatgcagGGACATCTGCATGCCCTGAGGCGAAATTCTACTGCAAGAATGCAGGCCACA
EST: gi|211262935|gb|FL345535.1|FL345535
EST:     CCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCG                         GGACATCTGCATGCYCTGANGCGAAATTCTACTGCAAGAATGCAGGCCACA
genomic: CCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgctca ... ttgcatgcagGGACATCTGCATGCCCTGAGGCGAAATTCTACTGCAAGAATGCAGGCCACA

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: 159

ATAGGCGGCGTGATCAAATGCAGGGACGGATCGGGCAGGTTTTCCAGGGACCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgctca ... ttgcatgcagGGACATCTGCATGCCCTGAGGCGAAATTCTACTGCAAGAATGCAGGCCACACTCCAGTCACGATCTTCTCGTCACGAGTGAATGACGGCATTTGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 116

ATAGGCGGCGTGATCAAATGCAGGGACGGATCGGGCAGGTTTTCCAGGGACCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgctca ... ttgcatgcagGGACATCTGCATGCCCTGAGGCGAAATTCTACTGCAAGAATGCAGGCCACACTCCAGTCACGATCTTCTCGTCACGAGTGAATGACGGCATTTGTG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 170

ATAGGCGGCGTGATCAAATGCAGGGACGGATCGGGCAGGTTTTCCAGGGACCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgctca ... ttgcatgcagGGACATCTGCATGCCCTGAGGCGAAATTCTACTGCAAGAATGCAGGCCACACTCCAGTCACGATCTTCTCGTCACGAGTGAATGACGGCATTTGTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 216

ATAGGCGGCGTGATCAAATGCAGGGACGGATCGGGCAGGTTTTCCAGGGACCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgctca ... ttgcatgcagGGACATCTGCATGCCCTGAGGCGAAATTCTACTGCAAGAATGCAGGCCACACTCCAGTCACGATCTTCTCGTCACGAGTGAATGACGGCATTTGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgacatcactatgtgtttgtttgttatatagctgaattatgactcttgcatgcagGGACATCTGCATGCCCTGAGGCGAAATTCTACTGCAAGAATGCAGGCCACACTCCAGTCACGATCTTCTCGTCACGAGTGAATGACGGCATTTGTG
                                          ctcttgc  CT-rich tract
               tttgtttgttatata  TA-rich tract