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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgcctcattctccttatttgaatggatttctctattcatcgtgtagatttcttgtttttgtgtgtgtgtcatgacatcactatgtgtttgttgttgttggaactgtaggaatacagatacagttatgtagctgaattatgactcttgcatgcagGGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACACTCCAGTCACGATCTTCTCATCACGAGTGAATGACGGCATTTGTG

Basic information

species Zea mays
transcript GRMZM2G052875_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052875_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g16970.2 (Oryza sativa), 3'ss of exon 2
gtactgcctcattctccttatttgaatggatttctc---tattcatcgtgtagatttcttgtttttgtgtgtgtgtcatgacatcactatgtgtttgtt-gttgttggaa--------ctgtaggaatacagatacagttatgtagctgaattatgact----cttgc----atgcagGGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACACTCCAGTCACGATCTTCTCATCACGAGTGAATGACGGCATTTGTG
    ||| || ||   ||    ||||     || ||   | ||  | |  |    || |||     |||| | ||   | |  |     ||| | || | || | | |||        ||||||| |  |  | | || | | ||   ||||| ||  |     ||||      ||||||||||| |||||||| |||| ||||||||||||| ||||||| || ||  ||||  ||||||||||||| || ||||||||||| || || ||||
--gttgcttccttgctctcgcctgaaaaagattatccctttttttttgccttagctttttgcggaggtgt-tctggttttaggttctcgtgtttgtgctagtagctcgaatctacttactgtaggcaatctaagagagctgtttaatcgaattgtgtttactttttgccttggcgcagGGACATCGGCGTGCCCGGAGGGGAAGTTCTACTGCCAGAATGCTGGGCATTCTCCCATCACGATCTTCTCGTCGCGAGTGAATGATGGTATCTGTG
















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|87153726|gb|DY398515.1|DY398515
EST:     GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCG                         GGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
genomic: GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgcctc ... ttgcatgcagGGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
EST: gi|211215768|gb|FL437214.1|FL437214
EST:     CGACTTCTGCGACTGCCCCGACGGGCACCGACGAGCCCG                         GGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
genomic: CGACTTCTGCGACTGCCCCGAC-GGCACCGACGAGCCCGgtactgcctc ... ttgcatgcagGGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
EST: gi|22490637|gb|BU050560.1|BU050560
EST:     GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCG                         GGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
genomic: GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgcctc ... ttgcatgcagGGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
EST: gi|211322390|gb|FL223767.1|FL223767
EST:     GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCG                         GGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
genomic: GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgcctc ... ttgcatgcagGGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
EST: gi|19057817|gb|BM736484.1|BM736484
EST:     GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCG                         GGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
genomic: GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgcctc ... ttgcatgcagGGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
EST: gi|31612130|gb|CD568752.1|CD568752
EST:     GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCG                         GGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
genomic: GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgcctc ... ttgcatgcagGGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
EST: gi|19058293|gb|BM736960.1|BM736960
EST:     GCAGCTCAACGACGACTTCTGCGACTGCCCCGCCGGCACCGCCGAGCCCG                         GGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
genomic: GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgcctc ... ttgcatgcagGGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
EST: gi|211320224|gb|FL223759.1|FL223759
EST:     GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCG                         GGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGGAGGCCACA
genomic: GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgcctc ... ttgcatgcagGGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
EST: gi|211322386|gb|FL223763.1|FL223763
EST:     GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCG                         GGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
genomic: GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgcctc ... ttgcatgcagGGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
EST: gi|211457195|gb|FL323091.1|FL323091
EST:     GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCG                         GGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
genomic: GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgcctc ... ttgcatgcagGGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
EST: gi|211322388|gb|FL223765.1|FL223765
EST:     GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCG                         GGACATCTGCGTGCCCTGAGGCGGAGTTCTACTGCAAGAATGCAGGCCACA
genomic: GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgcctc ... ttgcatgcagGGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
EST: gi|211322389|gb|FL223766.1|FL223766
EST:     GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCG                         GGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
genomic: GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgcctc ... ttgcatgcagGGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
EST: gi|32847353|gb|CD987034.1|CD987034
EST:     GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCG                         GGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
genomic: GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgcctc ... ttgcatgcagGGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
EST: gi|211320227|gb|FL223762.1|FL223762
EST:     GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCG                         GGACATCTGCCNTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCAC
genomic: GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgcctc ... ttgcatgcagGGACATCTGCG-TGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCAC
EST: gi|211320225|gb|FL223760.1|FL223760
EST:     GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCG                         GGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
genomic: GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgcctc ... ttgcatgcagGGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
EST: gi|211320223|gb|FL223758.1|FL223758
EST:     GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCG                         GGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA
genomic: GCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgcctc ... ttgcatgcagGGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACA

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: 87

AGAGGCGGCGTGATTAAATGCAGGGACGGATCAGGCAGGTTCTCCCGGGAGCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgcctc ... ttgcatgcagGGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACACTCCAGTCACGATCTTCTCATCACGAGTGAATGACGGCATTTGTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 122

AGAGGCGGCGTGATTAAATGCAGGGACGGATCAGGCAGGTTCTCCCGGGAGCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgcctc ... ttgcatgcagGGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACACTCCAGTCACGATCTTCTCATCACGAGTGAATGACGGCATTTGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 86

AGAGGCGGCGTGATTAAATGCAGGGACGGATCAGGCAGGTTCTCCCGGGAGCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgcctc ... ttgcatgcagGGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACACTCCAGTCACGATCTTCTCATCACGAGTGAATGACGGCATTTGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 155

AGAGGCGGCGTGATTAAATGCAGGGACGGATCAGGCAGGTTCTCCCGGGAGCAGCTCAACGACGACTTCTGCGACTGCCCCGACGGCACCGACGAGCCCGgtactgcctc ... ttgcatgcagGGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACACTCCAGTCACGATCTTCTCATCACGAGTGAATGACGGCATTTGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaactgtaggaatacagatacagttatgtagctgaattatgactcttgcatgcagGGACATCTGCGTGCCCTGAGGCGAAGTTCTACTGCAAGAATGCAGGCCACACTCCAGTCACGATCTTCTCATCACGAGTGAATGACGGCATTTGTG
                                          ctcttgc  CT-rich tract
                                tgaattat  TA-rich tract