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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattgcttatggatcacattttgatttctcataagggaaagagatacatgctgtgatgtatggtttactaagcttatagatagaggtagtaagttcctgcagttcctagtttaagcaatcaaggactctttttgcagGTTGCTAAAGATCTGGTTTTTGAGAAAGCATATTGCCCATTGGGTGTTCTTCTCATTATTTTTGAGTCTCGTCCTGATGCATTGGTCCAG

Basic information

species Zea mays
transcript GRMZM2G028535_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G028535_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g62900.1 (Oryza sativa), 3'ss of exon 9
gtgattgcttatggatcacattttgatttctcataagggaaagagatacatgctgtgatgtat-ggtttactaagcttatagatagaggtagtaagttcctgcagttcctagtttaagcaatcaaggactctttttgcagGTTGCTAAAGATCTGGTTTTTGAGAAAGCATATTGCCCATTGGGTGTTCTTCTCATTATTTTTGAGTCTCGTCCTGATGCATTGGTCCAG
|||| ||| |||  | |  ||| | |  ||  |  | |  | | ||||  | ||   ||  ||   | |  ||||       ||  |  |  ||  ||| ||   ||     | ||| |||| |||||||  ||||| |||||||||||||||| |||||||||||| |||||||||||||||||||||| || |||||||||||||| ||||||||||| ||||| |||
gtgaatgcatat--accctattctaaaatccaaacacg--atgtgataagtactacaatcaatcaatgtgataagtactacaatcaa--tcatagcttcatgtgatt-----tgtaaccaatgaaggacttgttttgtagGTTGCTAAAGATCTTGTTTTTGAGAAAACATATTGCCCATTGGGTGTTCTCCTAATTATTTTTGAGTCCCGTCCTGATGCCTTGGTACAG
















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|24934245|gb|CA452463.1|CA452463
EST:     AAACTGCTGACATGGAGGACCCTATTTCCCATACATTGAAAAGAACAGAG                         GTTGCTAAAGATCTGGTTTTTGAGAAAGCATATTGCCCATTGGGTGTTCTT
genomic: AAACTGCTGACATGGAGGACCCTATTTCCCATACATTGAAAAGAACAGAGgtgattgctt ... ctttttgcagGTTGCTAAAGATCTGGTTTTTGAGAAAGCATATTGCCCATTGGGTGTTCTT
EST: gi|211307860|gb|FL092738.1|FL092738
EST:     CATTGAAAAGAACAGAG                         GTTGCTAAAGATCTGGTTTTTGAGAAAGCATATTGCCCATTGGGTGTTCTT
genomic: CATTGAAAAGAACAGAGgtgattgctt ... ctttttgcagGTTGCTAAAGATCTGGTTTTTGAGAAAGCATATTGCCCATTGGGTGTTCTT
EST: gi|6538931|gb|AW225070.1|AW225070
EST:     AACTGCTGACATGGAGGACCCTATTTCCCATACACTTGAAAAGAACAGAG                         GTTGCTAAAGATCTGGTTTTTGAGACAGCATATTGCCCATTGCGTGTTCTT
genomic: AACTGCTGACATGGAGGACCCTATTTCCCATACA-TTGAAAAGAACAGAGgtgattgctt ... ctttttgcagGTTGCTAAAGATCTGGTTTTTGAGAAAGCATATTGCCCATTGGGTGTTCTT
EST: gi|211307862|gb|FL092740.1|FL092740
EST:     CATTGAAAAGAACAGAG                         GTTGCTAAAGATCTGGTTTTTGAGAAAGCATATTGCCCATTGGGTGTTCTT
genomic: CATTGAAAAGAACAGAGgtgattgctt ... ctttttgcagGTTGCTAAAGATCTGGTTTTTGAGAAAGCATATTGCCCATTGGGTGTTCTT

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), 48 (downstream exon)
Score: 115

ATAACAAATCTTGCAAGATCCATTCGTAAAACTGCTGACATGGAGGACCCTATTTCCCATACATTGAAAAGAACAGAGgtgattgctt ... ctttttgcagGTTGCTAAAGATCTGGTTTTTGAGAAAGCATATTGCCCATTGGGTGTTCTTCTCATTATTTTTGAGTCTCGTCCTGATGCATTGGTCCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 22

ATAACAAATCTTGCAAGATCCATTCGTAAAACTGCTGACATGGAGGACCCTATTTCCCATACATTGAAAAGAACAGAGgtgattgctt ... ctttttgcagGTTGCTAAAGATCTGGTTTTTGAGAAAGCATATTGCCCATTGGGTGTTCTTCTCATTATTTTTGAGTCTCGTCCTGATGCATTGGTCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 9

ATAACAAATCTTGCAAGATCCATTCGTAAAACTGCTGACATGGAGGACCCTATTTCCCATACATTGAAAAGAACAGAGgtgattgctt ... ctttttgcagGTTGCTAAAGATCTGGTTTTTGAGAAAGCATATTGCCCATTGGGTGTTCTTCTCATTATTTTTGAGTCTCGTCCTGATGCATTGGTCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 495

ATAACAAATCTTGCAAGATCCATTCGTAAAACTGCTGACATGGAGGACCCTATTTCCCATACATTGAAAAGAACAGAGgtgattgctt ... ctttttgcagGTTGCTAAAGATCTGGTTTTTGAGAAAGCATATTGCCCATTGGGTGTTCTTCTCATTATTTTTGAGTCTCGTCCTGATGCATTGGTCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaggtagtaagttcctgcagttcctagtttaagcaatcaaggactctttttgcagGTTGCTAAAGATCTGGTTTTTGAGAAAGCATATTGCCCATTGGGTGTTCTTCTCATTATTTTTGAGTCTCGTCCTGATGCATTGGTCCAG
                                           ctctttttgc  CT-rich tract
                        tagtttaa  TA-rich tract