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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccgtctagatcctctctgtctaattgcatttgctttcttgagttgaacgattttagatacgatactccgtacgttacagCTGTCCAAGTTATATGAGGTCGTGCCTCCGATCCTCACTGAGCTGGGAAAG

Basic information

species Zea mays
transcript GRMZM2G063909_T02
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063909_T03 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 16
gtccgtctagatcctctctgtctaattgcatttgctttc-ttgagttgaacgattttagatacgatactccgtacgttacagCTGTCCAAGTTATATGAGGTCGTGCCTCCGATCCTCACTGAGCTGGGAAAG
||  ||||| || ||  |||  |   |   ||   |  |  ||  |  |  |  |||| || |||     | |   || ||| | |||||||| ||||| || |||||||| |||||||||||||| || |||
gttagtctaaattctagctgcatggctctcttcagtcccactgtctcaataggatttatat-cgacctatcctc--tttcagGTCTCCAAGTTGTATGAAGTTGTGCCTCCTATCCTCACTGAGCTTGGCAAG

upper sequence: GRMZM2G063909_T03 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 16
gtccgtctagatcctctctgtctaattgcatttgctttcttg-agttgaacgatttta----gatac--gatactccgtacgtta-cagCTGTCCAAGTTATATGAGGTCGTGCCTCCGATCCTCACTGAGCTGGGAAAG
||  ||||| |   | |||||| || |||||  ||| ||||| |||  ||| || | |    ||| |       ||  ||   |  ||| | |||||||| ||||| || |||||||| |||||||||||||| || |||
gttagtctaaaa--tgtctgtccaactgcatg-gctctcttgcagtccaactatctcattgggattcttatcgatctatatcctgtcagGTCTCCAAGTTGTATGAAGTTGTGCCTCCAATCCTCACTGAGCTTGGCAAG
















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|211314255|gb|FK994155.1|FK994155
EST:     AAAGGGAGTTTGCCCTGAAGTATTTGCCAGAGGATCCGCTTTTCCAACTG                         CTGTCCAAGTTATATGAGGTCGTGCCTCCGATCCTCACTGAGCTGGGAAAG
genomic: AAAGGGAGTTTGCCCTGAAGTATTTGCCAGAGGATCCGCTTTTCCAACTGgtccgtctag ... tacgttacagCTGTCCAAGTTATATGAGGTCGTGCCTCCGATCCTCACTGAGCTGGGAAAG
EST: gi|60357508|gb|DN224481.1|DN224481
EST:     AAAGGGAGTTTGCCCTGAAGTATTTGCCAGAGGATCCGCTTTTCCAACTG                         CTGTCCAAGTTATATGAGGTCGTGCCTCCGATCCTCACTGAGCTGGGAAAG
genomic: AAAGGGAGTTTGCCCTGAAGTATTTGCCAGAGGATCCGCTTTTCCAACTGgtccgtctag ... tacgttacagCTGTCCAAGTTATATGAGGTCGTGCCTCCGATCCTCACTGAGCTGGGAAAG
EST: gi|78076903|gb|DV505337.1|DV505337
EST:     AAAGGGAGTTTGCCCTGAAGTATTTGCCAGAGGATCCGCTTTTCCAACTG                         CTGTCCAAGTTATATGAGGTCGTGCCTCCGATCCTCACTGAGCTGGGAAAG
genomic: AAAGGGAGTTTGCCCTGAAGTATTTGCCAGAGGATCCGCTTTTCCAACTGgtccgtctag ... tacgttacagCTGTCCAAGTTATATGAGGTCGTGCCTCCGATCCTCACTGAGCTGGGAAAG
EST: gi|211458206|gb|FL358448.1|FL358448
EST:     AAAGGGAGTTTGCCCTGAAGTATTTGCCAGAGGATCCGCTTTTCCAACTG                         CTGTCCAAGTTATATGAGGTCGTGCCTCCGATCCTCACTGAGCTGGGAAAG
genomic: AAAGGGAGTTTGCCCTGAAGTATTTGCCAGAGGATCCGCTTTTCCAACTGgtccgtctag ... tacgttacagCTGTCCAAGTTATATGAGGTCGTGCCTCCGATCCTCACTGAGCTGGGAAAG
EST: gi|60345083|gb|DN212056.1|DN212056
EST:     AAAGGGAGTTTGCCCTGAAGTATTTGCCAGAGGATCCGCTTTTCCAACTG                         CTGTCCAAGTTATATGAGGTCGTGCCTCCGATCCTCACTGAGCTGGGAAAG
genomic: AAAGGGAGTTTGCCCTGAAGTATTTGCCAGAGGATCCGCTTTTCCAACTGgtccgtctag ... tacgttacagCTGTCCAAGTTATATGAGGTCGTGCCTCCGATCCTCACTGAGCTGGGAAAG
EST: gi|50331232|gb|CO526358.1|CO526358
EST:     AAAGGGAGTTTGCCCTGAAGTATTTGCCAGAGGATCCGCTTTTCCAACTG                         CTGTCCAAGTTATATGAGGTCGTGCCTCCGATCCTCACTGAGCTGGGAAAG
genomic: AAAGGGAGTTTGCCCTGAAGTATTTGCCAGAGGATCCGCTTTTCCAACTGgtccgtctag ... tacgttacagCTGTCCAAGTTATATGAGGTCGTGCCTCCGATCCTCACTGAGCTGGGAAAG
EST: gi|40334210|gb|CK368280.1|CK368280
EST:     AAAGGGAGTTTGCCCTGAAGTATTTGCCAGAGGATCCGCTTTTCCAACTG                         CTGTCCAAGTTATATGAGGTCGTGCCTCCGATCCTCACTGAGCTGGGAAAG
genomic: AAAGGGAGTTTGCCCTGAAGTATTTGCCAGAGGATCCGCTTTTCCAACTGgtccgtctag ... tacgttacagCTGTCCAAGTTATATGAGGTCGTGCCTCCGATCCTCACTGAGCTGGGAAAG
EST: gi|60400601|gb|DN233408.1|DN233408
EST:     AAAGGGAGTTTGCCCTGAAGTATTTGCCAGAGGATCCGCTTTTCCAACTG                         CTGTCCAAGTTATATGAGGTCGTGCCTCCGATCCTCACTGAGCTGGGAAAG
genomic: AAAGGGAGTTTGCCCTGAAGTATTTGCCAGAGGATCCGCTTTTCCAACTGgtccgtctag ... tacgttacagCTGTCCAAGTTATATGAGGTCGTGCCTCCGATCCTCACTGAGCTGGGAAAG
EST: gi|60354991|gb|DN221964.1|DN221964
EST:     AAAGGGAGTTTGCCCTGAAGTATTTGCCAGAGGATCCGCTTTTCCAACTG                         CTGTCCAAGTTATATGAGGTCGTGCCTCCGATCCTCACTGAGCTGGGAAAG
genomic: AAAGGGAGTTTGCCCTGAAGTATTTGCCAGAGGATCCGCTTTTCCAACTGgtccgtctag ... tacgttacagCTGTCCAAGTTATATGAGGTCGTGCCTCCGATCCTCACTGAGCTGGGAAAG

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: 48 (upstream exon), 47 (downstream exon)
Score: 206

TGGATTTGGTCATGGAGTTCTGCGTAGGACGGACCCACGGTATCTATGCCAAAGGGAGTTTGCCCTGAAGTATTTGCCAGAGGATCCGCTTTTCCAACTGgtccgtctag ... tacgttacagCTGTCCAAGTTATATGAGGTCGTGCCTCCGATCCTCACTGAGCTGGGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 265

TGGATTTGGTCATGGAGTTCTGCGTAGGACGGACCCACGGTATCTATGCCAAAGGGAGTTTGCCCTGAAGTATTTGCCAGAGGATCCGCTTTTCCAACTGgtccgtctag ... tacgttacagCTGTCCAAGTTATATGAGGTCGTGCCTCCGATCCTCACTGAGCTGGGAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 79

TGGATTTGGTCATGGAGTTCTGCGTAGGACGGACCCACGGTATCTATGCCAAAGGGAGTTTGCCCTGAAGTATTTGCCAGAGGATCCGCTTTTCCAACTGgtccgtctag ... tacgttacagCTGTCCAAGTTATATGAGGTCGTGCCTCCGATCCTCACTGAGCTGGGAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 79

TGGATTTGGTCATGGAGTTCTGCGTAGGACGGACCCACGGTATCTATGCCAAAGGGAGTTTGCCCTGAAGTATTTGCCAGAGGATCCGCTTTTCCAACTGgtccgtctag ... tacgttacagCTGTCCAAGTTATATGAGGTCGTGCCTCCGATCCTCACTGAGCTGGGAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcatttgctttcttgagttgaacgattttagatacgatactccgtacgttacagCTGTCCAAGTTATATGAGGTCGTGCCTCCGATCCTCACTGAGCTGGGAAAG
                         attttagata  TA-rich tract