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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcaagttaaccatttatttggtctgtacaattttagtgaatcagaataataagttcatttacagcttttaagagtccaccacatgtttaatattgcagGTTCACCCTGTTCTTATGCTTATCGGTTATGTTATTATCGGCGGTGAAG

Basic information

species Zea mays
transcript GRMZM2G060357_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G060357_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g42890.1 (Oryza sativa), 3'ss of exon 1
tttcaagttaaccatttatttggtctgtacaattttagtgaatcagaataataa-gttcatttacagcttttaagagtccaccacatgtttaat--------attgcagGTTCACCCTGTTCTTATGCTTATCGGTTATGTTATTATCGGCGGTGAAG
        ||| |||||   |  ||  ||| | |  ||| | |||| ||| ||  || ||||  |   |   |   ||   ||| || | ||||        |||||||||||||||||||||||||||||| || ||| | ||  | ||| ||||||
-------ctaatcatttgcatattccttactact--agtaattcaggatactactgtacattagcgtttcaaatcggttgcccatatctctaatgttgagacattgcagGTTCACCCTGTTCTTATGCTTATTGGCTATATAATCCTAGGCAGTGAAG
















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|211354977|gb|FL245102.1|FL245102
EST:     TCCGCGGCGGGCTCGCCATCGAGTCCACCAACAAGAACCTCATCTTCAAC                         GTTCACCCTGTTCTTATGCTTATCGGTTATGTTATTATCGGCGGTGAAG
genomic: TCCGCGGTGGGCTCGCCATCGAGTCCACCAACAAGAACCTCATCTTCAACgtgagtactc ... aatattgcagGTTCACCCTGTTCTTATGCTTATCGGTTATGTTATTATCGGCGGTGAAG
EST: gi|211354978|gb|FL245103.1|FL245103
EST:     TCCGCGGCGGGCTCGCCATCGAGTCCACCAACAAGAACCTCATCTTCAAC                         GTTCACCCTGTTCTTATGCTTATCGGTTATGTTATTATCGGCGGTGAAG
genomic: TCCGCGGTGGGCTCGCCATCGAGTCCACCAACAAGAACCTCATCTTCAACgtgagtactc ... aatattgcagGTTCACCCTGTTCTTATGCTTATCGGTTATGTTATTATCGGCGGTGAAG
EST: gi|211273672|gb|FL301554.1|FL301554
EST:     TCCGCGGCGGGCTCGCCATCGAGTCCACCAACAAGAACCTCATCTTCAAC                         GTTCACCCTGTTCTTATGCTTATCGGTTATGTTATTATCGGCGGTGAAG
genomic: TCCGCGGTGGGCTCGCCATCGAGTCCACCAACAAGAACCTCATCTTCAACgtgagtactc ... aatattgcagGTTCACCCTGTTCTTATGCTTATCGGTTATGTTATTATCGGCGGTGAAG
EST: gi|211275485|gb|FL301566.1|FL301566
EST:     TCCGCGGCGGGCTCGCCATCGAGTCCACCAACAAGAACCTCATCTTCAAC                         GTTCACCCTGTTCTTATGCTTATCGGTTATGTTATTATCGGCGGTGAAG
genomic: TCCGCGGTGGGCTCGCCATCGAGTCCACCAACAAGAACCTCATCTTCAACgtgagtactc ... aatattgcagGTTCACCCTGTTCTTATGCTTATCGGTTATGTTATTATCGGCGGTGAAG
EST: gi|211273675|gb|FL301557.1|FL301557
EST:     TCCGCGGCGGGCTCGCCATCGAGTCCACCAACAAGAACCTCATCTTCAAC                         GTTCACCCTGTTCTTATGCTTATCGGTTATGTTATTATCGGCGGTGAAG
genomic: TCCGCGGTGGGCTCGCCATCGAGTCCACCAACAAGAACCTCATCTTCAACgtgagtactc ... aatattgcagGTTCACCCTGTTCTTATGCTTATCGGTTATGTTATTATCGGCGGTGAAG
EST: gi|28187673|gb|CB179283.1|CB179283
EST:     TCCGCGGCGGGCTCGCCATCGAGTCCACCAACAAGAACCTCATCTTCAAC                         GTTCACCCTGTTCTTATGCTTATCGGTTATGTTATTATCGGCGGTGAAG
genomic: TCCGCGGTGGGCTCGCCATCGAGTCCACCAACAAGAACCTCATCTTCAACgtgagtactc ... aatattgcagGTTCACCCTGTTCTTATGCTTATCGGTTATGTTATTATCGGCGGTGAAG
EST: gi|211352579|gb|FL245097.1|FL245097
EST:     TCCGCGGCGGGCTCGCCATCGAGTCCACCAACAAGAACCTCATCTTCAAC                         GTTCACCCTGTTCTTATGCTTATCGGTTATGTTATTATCGGCGGTGAAG
genomic: TCCGCGGTGGGCTCGCCATCGAGTCCACCAACAAGAACCTCATCTTCAACgtgagtactc ... aatattgcagGTTCACCCTGTTCTTATGCTTATCGGTTATGTTATTATCGGCGGTGAAG
EST: gi|211273676|gb|FL301558.1|FL301558
EST:     TCCGCGGCGGGCTCG-CATCGAGTCCACCAACAAGAACCTCATCTTCAAC                         GTTCACCCTGTTCTTATGCTTATCGGTTATGTTATTATCGGCGGTGAAG
genomic: TCCGCGGTGGGCTCGCCATCGAGTCCACCAACAAGAACCTCATCTTCAACgtgagtactc ... aatattgcagGTTCACCCTGTTCTTATGCTTATCGGTTATGTTATTATCGGCGGTGAAG
EST: gi|71435569|gb|DR816619.1|DR816619
EST:     TCCGCGGTGGGCTCGCCATCGAGTCCACCAACAAGAACCTCATCTTCAAC                         GTTCACCCTGTTCTTATGCTTATCGGTTATGTTATTATCGGCGGTGAAG
genomic: TCCGCGGTGGGCTCGCCATCGAGTCCACCAACAAGAACCTCATCTTCAACgtgagtactc ... aatattgcagGTTCACCCTGTTCTTATGCTTATCGGTTATGTTATTATCGGCGGTGAAG
EST: gi|211352577|gb|FL245095.1|FL245095
EST:     TCCGCGGCGGGCTCGCCATCGAGTCCACCAACAAGAACCTCATCTTCAAC                         GTTCACCCTGTTCTTATGCTTATCGGTTATGTTATTATCGGCGGTGAAG
genomic: TCCGCGGTGGGCTCGCCATCGAGTCCACCAACAAGAACCTCATCTTCAACgtgagtactc ... aatattgcagGTTCACCCTGTTCTTATGCTTATCGGTTATGTTATTATCGGCGGTGAAG
EST: gi|1366564|gb|W59826.1|W59826
EST:     AAGAACCTCATCTTCAAC                         GTTCACCCTGTTCTTATGCTTATCGGTTATGTTATTATCGGCGGTGAAG
genomic: AAGAACCTCATCTTCAACgtgagtactc ... aatattgcagGTTCACCCTGTTCTTATGCTTATCGGTTATGTTATTATCGGCGGTGAAG
EST: gi|211354976|gb|FL245101.1|FL245101
EST:     TCCGCGGCGGGCTCG-CATCGAGTCCACCAACAAGAACCTCATCTTCAAC                         GTTCACCCTGTTCTTATGCTTATCGGTTATGTTATTATCGGCGGTGAAG
genomic: TCCGCGGTGGGCTCGCCATCGAGTCCACCAACAAGAACCTCATCTTCAACgtgagtactc ... aatattgcagGTTCACCCTGTTCTTATGCTTATCGGTTATGTTATTATCGGCGGTGAAG
EST: gi|211352575|gb|FL245093.1|FL245093
EST:     TCCGCGGCGGGCTCGCCATCGAGTCCACCAACAAGAACCTCATCTTCAAC                         GTTCACCCTGTTCTTATGCTTATCGGTTATGTTATTATCGGCGGTGAAG
genomic: TCCGCGGTGGGCTCGCCATCGAGTCCACCAACAAGAACCTCATCTTCAACgtgagtactc ... aatattgcagGTTCACCCTGTTCTTATGCTTATCGGTTATGTTATTATCGGCGGTGAAG
EST: gi|211275490|gb|FL301571.1|FL301571
EST:     TCCGCGGCGGGCTCGCCATCGAGTCCACCAACAAGAACCTCATCTTCAAC                         GTTCACCCTGTTCTTATGCTTATCGGTTATGTTATTATCGGCGGTGAAG
genomic: TCCGCGGTGGGCTCGCCATCGAGTCCACCAACAAGAACCTCATCTTCAACgtgagtactc ... aatattgcagGTTCACCCTGTTCTTATGCTTATCGGTTATGTTATTATCGGCGGTGAAG
EST: gi|211273673|gb|FL301555.1|FL301555
EST:     TCCGCGGCGGGCTCGCCATCGAGTCCACCAACAAGAACCTCATCTTCAAC                         GTTCACCCTGTTCTTATGCTTATCGGTTATGTTATTATCGGCGGTGAAG
genomic: TCCGCGGTGGGCTCGCCATCGAGTCCACCAACAAGAACCTCATCTTCAACgtgagtactc ... aatattgcagGTTCACCCTGTTCTTATGCTTATCGGTTATGTTATTATCGGCGGTGAAG
EST: gi|211275484|gb|FL301565.1|FL301565
EST:     TCCGCGGCGGGCTCGCCATCGAGTCCACCAACAAGAACCTCATCTTCAAC                         GTTCACCCTGTTCTTATGCTTATCGGTTATGTTATTATCGGCGGTGAAG
genomic: TCCGCGGTGGGCTCGCCATCGAGTCCACCAACAAGAACCTCATCTTCAACgtgagtactc ... aatattgcagGTTCACCCTGTTCTTATGCTTATCGGTTATGTTATTATCGGCGGTGAAG
EST: gi|12047248|gb|BF729387.1|BF729387
EST:     TCCGCGGCGGGCTCGCCATCGAGTCCACCAACAAGAACCTCATCTTCAAC                         GTTCACCCTGTTCTTATGCTTATCGGTTATGTTATTATCGGCGGTGAAG
genomic: TCCGCGGTGGGCTCGCCATCGAGTCCACCAACAAGAACCTCATCTTCAACgtgagtactc ... aatattgcagGTTCACCCTGTTCTTATGCTTATCGGTTATGTTATTATCGGCGGTGAAG
EST: gi|149078706|gb|EE167504.2|EE167504
EST:     TCCGCGGTGGGCTCGCCATCGAGTCCACCAACAAGAACCTCATCTTCAAC                         GTTCACCCTGTTCTTATGCTTATCGGTTATGTTATTATCGGCGGTGAAG
genomic: TCCGCGGTGGGCTCGCCATCGAGTCCACCAACAAGAACCTCATCTTCAACgtgagtactc ... aatattgcagGTTCACCCTGTTCTTATGCTTATCGGTTATGTTATTATCGGCGGTGAAG
EST: gi|211275489|gb|FL301570.1|FL301570
EST:     TCCGCGGCGGGCTCGCCATCGAGTCCACCAACAAGAACCTCATCTTCAAC                         GTTCACCCTGTTCTTATGCTTATCGGTTATGTTATTATCGGCGGTGAAG
genomic: TCCGCGGTGGGCTCGCCATCGAGTCCACCAACAAGAACCTCATCTTCAACgtgagtactc ... aatattgcagGTTCACCCTGTTCTTATGCTTATCGGTTATGTTATTATCGGCGGTGAAG

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: 47 (upstream exon), 45 (downstream exon)
Score: 127

CGCACTGGCCGTCGCGGCGGCGGCCATGGTTCTCGTCTGGTCCATCCAGTTCCGCGGTGGGCTCGCCATCGAGTCCACCAACAAGAACCTCATCTTCAACgtgagtactc ... aatattgcagGTTCACCCTGTTCTTATGCTTATCGGTTATGTTATTATCGGCGGTGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 542

CGCACTGGCCGTCGCGGCGGCGGCCATGGTTCTCGTCTGGTCCATCCAGTTCCGCGGTGGGCTCGCCATCGAGTCCACCAACAAGAACCTCATCTTCAACgtgagtactc ... aatattgcagGTTCACCCTGTTCTTATGCTTATCGGTTATGTTATTATCGGCGGTGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 469

CGCACTGGCCGTCGCGGCGGCGGCCATGGTTCTCGTCTGGTCCATCCAGTTCCGCGGTGGGCTCGCCATCGAGTCCACCAACAAGAACCTCATCTTCAACgtgagtactc ... aatattgcagGTTCACCCTGTTCTTATGCTTATCGGTTATGTTATTATCGGCGGTGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 415

CGCACTGGCCGTCGCGGCGGCGGCCATGGTTCTCGTCTGGTCCATCCAGTTCCGCGGTGGGCTCGCCATCGAGTCCACCAACAAGAACCTCATCTTCAACgtgagtactc ... aatattgcagGTTCACCCTGTTCTTATGCTTATCGGTTATGTTATTATCGGCGGTGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaataataagttcatttacagcttttaagagtccaccacatgtttaatattgcagGTTCACCCTGTTCTTATGCTTATCGGTTATGTTATTATCGGCGGTGAAG
                                         gtttaat  putative branch site (score: 415)
                                     acatgtttaatatt  TA-rich tract