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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattcagtcccgtttctttatgattacccgttccaatgtccataactttgacatagtgcattgtctttactatgccaatttggtgacagaactgaaattttattatgtatttcagGAACACTATTGATAGAGCCTAAACCACAGGAACCAACAAAACACCA

Basic information

species Zea mays
transcript GRMZM2G081682_T02
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081682_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os07g47290.3 (Oryza sativa), 3'ss of exon 11
gtaattcagtcccgtttctttatgattacccgttccaatgtccataactttgacatagtgcattgtctttactatgccaatttggtgacagaactgaaattttattatgtatttcagGAACACTATTGATAGAGCCTAAACCACAGGAACCAACAAAACACCA
                                     |    |||  |  ||  |||   |||| |      |||| ||   |||  | |  |||||| |||  || | | ||||||||||||| |||||||||||||||||||| ||||| |||||||||||
-----------------------------------gtactcacatgtcactgctatatcacatttttccatgtatgaca---tggatataatactgaattttgtttttatttttcagGAACACTCTTGATAGAGCCTAAACCACAAGAACCCACAAAACACCA
















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|31349785|gb|CD434142.1|CD434142
EST:     TAACTTTCTTCAAGCTGCTGTTGACTACAAGAAGAAGATTGGATTCAACG                         GAACACTATTGATAGAGCCTAAACCACAGGAACCAACAAAACACCA
genomic: TAACTTTCTTCAAGCTGCTGTTGACTACAAGAAGAAGATTGGATTCAACGgtaattcagt ... tgtatttcagGAACACTATTGATAGAGCCTAAACCACAGGAACCAACAAAACACCA
EST: gi|33092171|gb|CF052165.1|CF052165
EST:     TAACTTTCTTCAAGCTGCTGTTGACTACAAGAAGAAGATTGGATTCAACG                         GAACACTATTGATAGAGCCTAAACCACAGGAACCAACAAAACACCA
genomic: TAACTTTCTTCAAGCTGCTGTTGACTACAAGAAGAAGATTGGATTCAACGgtaattcagt ... tgtatttcagGAACACTATTGATAGAGCCTAAACCACAGGAACCAACAAAACACCA
EST: gi|5846747|gb|AI999830.1|AI999830
EST:     TAACTTTCTTCAAGCTGCTGTTGACTACAAGAAGAAGATTGGATTCAACG                         GAACACTATTGATAGAGCCTAAACCACAGGAACCAACAAAACACCA
genomic: TAACTTTCTTCAAGCTGCTGTTGACTACAAGAAGAAGATTGGATTCAACGgtaattcagt ... tgtatttcagGAACACTATTGATAGAGCCTAAACCACAGGAACCAACAAAACACCA
EST: gi|5296207|gb|AI782887.1|AI782887
EST:     TAACTTTCTTCAAGCTGCTGTTGACTACAAGAAGAAGATTGGATTCAACG                         GAACACTATTGATAGAGCCTAAACCACAGGAACCAACAAAACACCA
genomic: TAACTTTCTTCAAGCTGCTGTTGACTACAAGAAGAAGATTGGATTCAACGgtaattcagt ... tgtatttcagGAACACTATTGATAGAGCCTAAACCACAGGAACCAACAAAACACCA

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: 593

GCTAACTTTCTTCAAGCTGCTGTTGACTACAAGAAGAAGATTGGATTCAACGgtaattcagt ... tgtatttcagGAACACTATTGATAGAGCCTAAACCACAGGAACCAACAAAACACCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 643

GCTAACTTTCTTCAAGCTGCTGTTGACTACAAGAAGAAGATTGGATTCAACGgtaattcagt ... tgtatttcagGAACACTATTGATAGAGCCTAAACCACAGGAACCAACAAAACACCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 515

GCTAACTTTCTTCAAGCTGCTGTTGACTACAAGAAGAAGATTGGATTCAACGgtaattcagt ... tgtatttcagGAACACTATTGATAGAGCCTAAACCACAGGAACCAACAAAACACCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1004

GCTAACTTTCTTCAAGCTGCTGTTGACTACAAGAAGAAGATTGGATTCAACGgtaattcagt ... tgtatttcagGAACACTATTGATAGAGCCTAAACCACAGGAACCAACAAAACACCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtctttactatgccaatttggtgacagaactgaaattttattatgtatttcagGAACACTATTGATAGAGCCTAAACCACAGGAACCAACAAAACACCA
                             aactgaaattttatta  TA-rich tract