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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagtcggttcaactctctgcaagtttgtttagccccgcatttctcacatggaacttagtttgataaagtcagggtttcttcagcatgatctcaggatcccccccaaaagcatcgctgtcagtaaccaaacacttgaatgacttccgaacgttttccttatcttggtttattttcagGATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTG

Basic information

species Zea mays
transcript GRMZM2G090087_T03
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G090087_T03 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os05g45960.1 (Oryza sativa), 3'ss of exon 13
gcaagtcggttcaactctctgcaagtttgtttagccccgcatttctcacatggaacttagtttgataaagtcagggtttcttcagcatgatctcaggatcccccccaaaagcatcgctgtcagtaaccaaacacttgaat------gacttccgaacgttttc--cttatcttggtttattttcagGATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTG
                                                                                     |||  | | || |   | | |  |    | ||   ||  ||   |||||||||||      | ||     || | | |  |  |   |  |   ||||||||| ||||||||| |||| |||||||||||||| || ||||| || ||||| ||||| || || |||||||||||||||||
-------------------------------------------------------------------------------------catcttgt-agcaatactcacgcagcttttgccaccaacaattgaacacttgaatccaatcggctcagtgacttatccaacacacactcatcggttttcagGAAGTACTTGGGCGATCAGTTAACGGGACAACATATGCCGGCATCCGAGCAAGGACAACTGGTGCTCCACAGAACCACTG
















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|18383619|gb|BM416819.1|BM416819
EST:     ATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAG                         GATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCG
genomic: ATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAGgcaagtcggt ... ttattttcagGATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCG
EST: gi|211120257|gb|FL200678.1|FL200678
EST:     ATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAG                         GATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCG
genomic: ATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAGgcaagtcggt ... ttattttcagGATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCG
EST: gi|67020094|gb|CO448843.1|CO448843
EST:     ATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAG                         GATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCG
genomic: ATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAGgcaagtcggt ... ttattttcagGATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCG
EST: gi|27769727|gb|CB042906.1|CB042906
EST:     ATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAG                         GATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCG
genomic: ATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAGgcaagtcggt ... ttattttcagGATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCG
EST: gi|6827469|gb|AW331112.1|AW331112
EST:     ATGCGCATCTGACGGCTGCAGTTGTCTCGAACGACCCGCTATTCCTGCAG                         GATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCG
genomic: ATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAGgcaagtcggt ... ttattttcagGATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCG
EST: gi|18659076|gb|BM500142.1|BM500142
EST:     ATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAG                         GATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAAT
genomic: ATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAGgcaagtcggt ... ttattttcagGATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAAT
EST: gi|27576018|gb|CA998712.1|CA998712
EST:     ATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAG                         GATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCG
genomic: ATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAGgcaagtcggt ... ttattttcagGATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCG
EST: gi|30088118|gb|CB886323.1|CB886323
EST:     ATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAG                         GATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCG
genomic: ATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAGgcaagtcggt ... ttattttcagGATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCG
EST: gi|24773212|gb|CA408466.1|CA408466
EST:     ATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAG                         GATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAAT
genomic: ATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAGgcaagtcggt ... ttattttcagGATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAAT
EST: gi|29544968|gb|CB605146.1|CB605146
EST:     ATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAG                         GATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCG
genomic: ATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAGgcaagtcggt ... ttattttcagGATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCG
EST: gi|28422820|gb|CB251998.1|CB251998
EST:     ATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAG                         GATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCG
genomic: ATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAGgcaagtcggt ... ttattttcagGATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCG
EST: gi|4966653|gb|AI691509.1|AI691509
EST:     TGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAG                         GATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCG
genomic: TGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAGgcaagtcggt ... ttattttcagGATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCG
EST: gi|67025872|gb|CO454621.1|CO454621
EST:     ATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAG                         GATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCG
genomic: ATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAGgcaagtcggt ... ttattttcagGATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCG
EST: gi|67023454|gb|CO452203.1|CO452203
EST:     ATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAG                         GATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCG-AATTCGAGCG
genomic: ATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAGgcaagtcggt ... ttattttcagGATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCG
EST: gi|37380563|gb|CF627102.1|CF627102
EST:     ATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAG                         GATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCG
genomic: ATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAGgcaagtcggt ... ttattttcagGATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCG
EST: gi|27521928|gb|CA989034.1|CA989034
EST:     ATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAG                         GATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCG
genomic: ATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAGgcaagtcggt ... ttattttcagGATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCG
EST: gi|30306480|gb|CD001153.1|CD001153
EST:     ATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAG                         GATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCG
genomic: ATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAGgcaagtcggt ... ttattttcagGATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCG
EST: gi|60340281|gb|DN207254.1|DN207254
EST:     ATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAG                         GATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCG
genomic: ATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAGgcaagtcggt ... ttattttcagGATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCG
EST: gi|67018698|gb|CO447447.1|CO447447
EST:     ATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAG                         GATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCG
genomic: ATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAGgcaagtcggt ... ttattttcagGATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCG
EST: gi|211507628|gb|FL212141.1|FL212141
EST:     ATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAG                         GATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCG
genomic: ATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAGgcaagtcggt ... ttattttcagGATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCG
EST: gi|67014372|gb|CO443121.1|CO443121
EST:     ATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAG                         GATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCG
genomic: ATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAGgcaagtcggt ... ttattttcagGATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCG
EST: gi|211301793|gb|FL438947.1|FL438947
EST:     ATGCGCATCTGACAGCTGCAGTTGTCTMAAACGACCCGCTATTCCTGCAG                         GATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCG
genomic: ATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAGgcaagtcggt ... ttattttcagGATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCG
EST: gi|60349947|gb|DN216920.1|DN216920
EST:     ATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAG                         GATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCG
genomic: ATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAGgcaagtcggt ... ttattttcagGATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCG
EST: gi|211342162|gb|FL434432.1|FL434432
EST:     ATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAG                         GATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCG
genomic: ATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAGgcaagtcggt ... ttattttcagGATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCG
EST: gi|71440457|gb|DR821507.1|DR821507
EST:     CTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAG                         GATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCG
genomic: CTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAGgcaagtcggt ... ttattttcagGATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCG
EST: gi|211507626|gb|FL212139.1|FL212139
EST:     ATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAG                         GATSTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCG
genomic: ATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAGgcaagtcggt ... ttattttcagGATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCG

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: 469

ATACTCTGAGGATCAGCTTGAGTTGGTCTTAGAAGCCTGCGAAAGGATGAATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAGgcaagtcggt ... ttattttcagGATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 285

ATACTCTGAGGATCAGCTTGAGTTGGTCTTAGAAGCCTGCGAAAGGATGAATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAGgcaagtcggt ... ttattttcagGATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 98

ATACTCTGAGGATCAGCTTGAGTTGGTCTTAGAAGCCTGCGAAAGGATGAATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAGgcaagtcggt ... ttattttcagGATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 333

ATACTCTGAGGATCAGCTTGAGTTGGTCTTAGAAGCCTGCGAAAGGATGAATGCGCATCTGACAGCTGCAGTTGTCTCAAACGACCCGCTATTCCTGCAGgcaagtcggt ... ttattttcagGATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaccaaacacttgaatgacttccgaacgttttccttatcttggtttattttcagGATGTACTTGGGAGATCCGTTAACGGGACAACCTACGCCGGAATTCGAGCGAGGACCACGGGCGCTCCACAGAACCACTG
 cagtaac  putative branch site (score: 333)
                                            tttattttc  putative PPT
                                            tttattttca  TA-rich tract