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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagttcttttatagtttgaatgcattacacatagtttggctattgaagcttccctttctgcttgttttttattagGTACTGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAGGCTTGTTCCAG

Basic information

species Zea mays
transcript GRMZM2G033515_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G033515_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g46610.1 (Oryza sativa), 3'ss of exon 5
gtaaagttcttttatagtttgaatgcattacacatagtttggctattgaagcttccctttct------------------gcttgtttttta----ttagGTACTGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAGGCTTGTTCCAG
|||   |  |   ||   ||  ||  |  ||||| |  |||||| ||||   ||||||||||                  ||||   |||||    | ||| ||||| |||||||| ||||||||||||||||| || ||||||||||||||||
gtatgctggtaccattagtttgatataacacacagaaattggctgttgacatttccctttcttgttacctttgacatttcgctttcgttttacctttcagGCACTGTATTCAGAGAGCCAATTATATGCAAAAATGTCCCAAGGCTTGTTCCAG
















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|67021863|gb|CO450612.1|CO450612
EST:     GAAGCACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG                         GTACTGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAGGCTTGTTC
genomic: GAAGCACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagttct ... tttttattagGTACTGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAGGCTTGTTC
EST: gi|31353696|gb|CD438053.1|CD438053
EST:     GAAGCACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG                         GTACTGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAGGCTTGTTC
genomic: GAAGCACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagttct ... tttttattagGTACTGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAGGCTTGTTC
EST: gi|29130361|gb|CB381065.1|CB381065
EST:     GAAGCACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG                         GTACTGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAG
genomic: GAAGCACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagttct ... tttttattagGTACTGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAG
EST: gi|84980627|gb|DW530976.1|DW530976
EST:     GAAGCACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG                         GTACTGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAGGCTTGTTC
genomic: GAAGCACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagttct ... tttttattagGTACTGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAGGCTTGTTC
EST: gi|61119247|gb|DN560208.1|DN560208
EST:     GAAGCACATGTGGAAGAGCCCAAATGGCACAATTAGAAACATTATAAATG                         GTACTGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAGGCTTGTTC
genomic: GAAGCACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagttct ... tttttattagGTACTGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAGGCTTGTTC
EST: gi|78092177|gb|DV520551.1|DV520551
EST:     GAAGCACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATG                         GTACTGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAGGCTTGTTC
genomic: GAAGCACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagttct ... tttttattagGTACTGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAGGCTTGTTC
EST: gi|211356162|gb|FL188389.1|FL188389
EST:     GAAGCACATGTGGAAGAGCCCAAATCGCACAATTANGAACATTATAARTG                         GTACTGTGTTCAGAGAACCAATTATATG
genomic: GAAGCACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagttct ... tttttattagGTACTGTGTTCAGAGAACCAATTATATG

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: 39 (upstream exon), 41 (downstream exon)
Score: 19

ATGAAACTAGGGTTAAGGAGTTCAATTTGAAGCACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagttct ... tttttattagGTACTGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAGGCTTGTTCCAG


Block sizes: 42 (upstream exon), 45 (downstream exon)
Score: 5

ATGAAACTAGGGTTAAGGAGTTCAATTTGAAGCACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagttct ... tttttattagGTACTGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAGGCTTGTTCCAG


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 19

ATGAAACTAGGGTTAAGGAGTTCAATTTGAAGCACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagttct ... tttttattagGTACTGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAGGCTTGTTCCAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 20

ATGAAACTAGGGTTAAGGAGTTCAATTTGAAGCACATGTGGAAGAGCCCAAATGGCACAATTAGGAACATTATAAATGgtaaagttct ... tttttattagGTACTGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAGGCTTGTTCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcattacacatagtttggctattgaagcttccctttctgcttgttttttattagGTACTGTGTTCAGAGAACCAATTATATGCAAAAACGTTCCAAGGCTTGTTCCAG
                            cttccctttctgcttg  CT-rich tract
                                         ttgttttttatta  TA-rich tract