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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccattgctaatccatatgctttagtgagctcaggttaatagacttttcatagaagtgctgtaatgatgtgaatattcaccatttggttttgcttctggatgcagACACTCCATTCCATAAAAGGACATCGGGACTACTCATTTGCATCGGCTTGGAGCCCTGATGGGCGAACATTTGCTACTGGCAACCAAGACAAGACATGCC

Basic information

species Zea mays
transcript GRMZM2G048045_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G048045_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g48964.1 (Oryza sativa), 3'ss of exon 9
--------gtaccattgctaatc----catatgctttagtgagctcaggttaatagacttttcatagaag----tgctgtaatgatgtg-aatattcaccat--ttggtt---ttgcttctggatgcagACACTCCATTCCATAAAAGGACATCGGGACTACTCATTTGCATCGGCTTGGAGCCCTGATGGGCGAACATTTGCTACTGGCAACCAAGACAAGACATGCC
        | ||    || || |    ||||     |         | | |||   |  | | ||||||     ||    | ||| ||     || ||  ||   |||||   ||| |||    ||||||| || |||||| | ||||| ||    || ||||| |||||||| ||||||||||| |||||  ||||||||||||||||||||||||| ||||||||||
gtatgccagcacacacgcaaacctgggcataaaacgtcacatatatatgataaccaagctgtgatagaaaattatgtgacattgaagtatggcatgcatgataactggttactttgtttccctgtgcagACTCTTCATTCCTTGAAAGGTCACTTTGATTACTCGTTTGCATCAGCTTGGAGCCCAGATGGCAGAACATTTGCTACTGGCAACCAAGATAAGACATGCC

upper sequence: GRMZM2G048045_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA07G40060.1 (Glycine max), 3'ss of exon 9
gtaccattgctaatccatatgctttagtgagctcaggttaatagacttttcatagaagtgctgtaatgatgtgaat-attcaccatttgg-ttttgcttctggatgcagACACTCCATTCCATAAAAGGACATCGGGACTACTCATTTGCATCGGCTTGGAGCCCTGATGGGCGAACATTTGCTACTGGCAACCAAGACAAGACATGCC
                 | | || |  |||  |   ||||  |    || |||||  || ||||    | || ||| ||  |  ||||   ||||| ||||   || ||||  || |  |  ||   |||||   ||| |||||||||||||| || |||   |||||||| || |  ||||||||||| ||||||||||| |||||||
-------------gtggtgtactctgttga-tttgtgttacaaa---ttccatag--gtactgtttgcaggtaaattatgaataatttaaattttggttct--ttgtagACTGTCAAGCCTTTATGTGGACACTTGGATTACTCATTTGCATCTGCGTGGCATCCTGATGGCCGTATTTTTGCTACTGGGAACCAAGACAAAACATGCC
















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|71332421|gb|DR803166.1|DR803166
EST:     TTGTCGGTGATGATCCTGATGGTCTACTTATTGATGCCAACTCTGGAAAG                         ACACTCCATTCCATAAAAGGACATCGGGACTACTCATTTGCATCGGCTTGG
genomic: TTGTCGGTGATGATCCTGATGGTCTACTTATTGATGCCAACTCTGGAAAGgtaccattgc ... ctggatgcagACACTCCATTCCATAAAAGGACATCGGGACTACTCATTTGCATCGGCTTGG
EST: gi|9952998|gb|BE639581.1|BE639581
EST:     ATCCTGATGGTCTACTTATTGATGCCAACTCTGGAAAG                         ACACTCCATTCCATAAAAGGACATCGGGACTACTCATTTGCATCGGCTTGG
genomic: ATCCTGATGGTCTACTTATTGATGCCAACTCTGGAAAGgtaccattgc ... ctggatgcagACACTCCATTCCATAAAAGGACATCGGGACTACTCATTTGCATCGGCTTGG
EST: gi|211465756|gb|FL467272.1|FL467272
EST:     GTCTACTTATTGATGCCAACTCTGGAAAG                         ACACTCCATTCCATAAAAGGACATCGGGACTACTCATTTGCATCGGCTTGG
genomic: GTCTACTTATTGATGCCAACTCTGGAAAGgtaccattgc ... ctggatgcagACACTCCATTCCATAAAAGGACATCGGGACTACTCATTTGCATCGGCTTGG
EST: gi|32850691|gb|CD990372.1|CD990372
EST:     TTGTCGGTGATGATCCTGATGGTCTACTTATTGATGCCAACTCTGGAAAG                         ACACTCCATTCCATAAAAGGACATCGGGACTACTCATTTGCATCGGCTTGG
genomic: TTGTCGGTGATGATCCTGATGGTCTACTTATTGATGCCAACTCTGGAAAGgtaccattgc ... ctggatgcagACACTCCATTCCATAAAAGGACATCGGGACTACTCATTTGCATCGGCTTGG
EST: gi|89251785|gb|DY623571.1|DY623571
EST:     TTGTCGGTGATGATCCTGATGGTCTACTTATTGATGCCAACTCTGGAAAG                         ACACTCCATTCCATAAAAGGACATCGGGACTACTCATTTGCATCGGCTTGG
genomic: TTGTCGGTGATGATCCTGATGGTCTACTTATTGATGCCAACTCTGGAAAGgtaccattgc ... ctggatgcagACACTCCATTCCATAAAAGGACATCGGGACTACTCATTTGCATCGGCTTGG
EST: gi|60344231|gb|DN211204.1|DN211204
EST:     TTGTCGGTGATGATCCTGATGGTCTACTTATTGATGCCAACTCTGGAAAG                         ACACTCCATTCCATAAAAGGACATCGGGACTACTCATTTGCATCGGCTTGG
genomic: TTGTCGGTGATGATCCTGATGGTCTACTTATTGATGCCAACTCTGGAAAGgtaccattgc ... ctggatgcagACACTCCATTCCATAAAAGGACATCGGGACTACTCATTTGCATCGGCTTGG
EST: gi|113702002|gb|EE679506.1|EE679506
EST:     GATCCTGATGGTCTACTTATTGATGCCAACTCTGGAAAG                         ACACTCCATTCCATAAAAGGACATCGGGACTACTCATTTGCATCGGCTTGG
genomic: GATCCTGATGGTCTACTTATTGATGCCAACTCTGGAAAGgtaccattgc ... ctggatgcagACACTCCATTCCATAAAAGGACATCGGGACTACTCATTTGCATCGGCTTGG
EST: gi|71320209|gb|DR796859.1|DR796859
EST:     TTGTCGGTGATGATCCTGATGGTCTACTTATTGATGCCAACTCTGGAAAG                         ACACTCCATTCCATAAAAGGACATCGGGACTACTCATTTGCATCGGCTTGG
genomic: TTGTCGGTGATGATCCTGATGGTCTACTTATTGATGCCAACTCTGGAAAGgtaccattgc ... ctggatgcagACACTCCATTCCATAAAAGGACATCGGGACTACTCATTTGCATCGGCTTGG
EST: gi|211395425|gb|FL283715.1|FL283715
EST:     TTGTCGGTGATGATCCTGATGGTCTACTTATTGATGCCAACTCTGGAAAG                         ACACTCCATTCCATAAAAGGACATCGGGACTACTCATTTGCATCGGCTTGG
genomic: TTGTCGGTGATGATCCTGATGGTCTACTTATTGATGCCAACTCTGGAAAGgtaccattgc ... ctggatgcagACACTCCATTCCATAAAAGGACATCGGGACTACTCATTTGCATCGGCTTGG
EST: gi|32847209|gb|CD986890.1|CD986890
EST:     TTGTCGGTGATGATCCTGATGGTCTACTTATTGATGCCAACTCTGGAAAG                         ACACTCCATTCCATAAAAGGACATCGGGACTACTCATCTGCATCGGCTTGG
genomic: TTGTCGGTGATGATCCTGATGGTCTACTTATTGATGCCAACTCTGGAAAGgtaccattgc ... ctggatgcagACACTCCATTCCATAAAAGGACATCGGGACTACTCATTTGCATCGGCTTGG
EST: gi|83278454|gb|DV942462.1|DV942462
EST:     TTATTGATGCCAACTCTGGAAAG                         ACACTCCATTCCATAAAAGGACATCGGGACTACTCATTTGCATCGGCTTGG
genomic: TTATTGATGCCAACTCTGGAAAGgtaccattgc ... ctggatgcagACACTCCATTCCATAAAAGGACATCGGGACTACTCATTTGCATCGGCTTGG
EST: gi|71320210|gb|DR796860.1|DR796860
EST:     TTGTCGGTGATGATCCTGATGGTCTACTTATTGATGCCAACTCTGGGAAG                         ACACTCCATTCCATAAAAGGACATCGGGACTACTCATTTGCATCGGCTTGG
genomic: TTGTCGGTGATGATCCTGATGGTCTACTTATTGATGCCAACTCTGGAAAGgtaccattgc ... ctggatgcagACACTCCATTCCATAAAAGGACATCGGGACTACTCATTTGCATCGGCTTGG

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: 240

CATGCTTCTTTGAGTCCTGACAGAAAGGTCGTTGTTATTGTCGGTGATGATCCTGATGGTCTACTTATTGATGCCAACTCTGGAAAGgtaccattgc ... ctggatgcagACACTCCATTCCATAAAAGGACATCGGGACTACTCATTTGCATCGGCTTGGAGCCCTGATGGGCGAACATTTGCTACTGGCAACCAAGACAAGACATGCC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 206

CATGCTTCTTTGAGTCCTGACAGAAAGGTCGTTGTTATTGTCGGTGATGATCCTGATGGTCTACTTATTGATGCCAACTCTGGAAAGgtaccattgc ... ctggatgcagACACTCCATTCCATAAAAGGACATCGGGACTACTCATTTGCATCGGCTTGGAGCCCTGATGGGCGAACATTTGCTACTGGCAACCAAGACAAGACATGCC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 301

CATGCTTCTTTGAGTCCTGACAGAAAGGTCGTTGTTATTGTCGGTGATGATCCTGATGGTCTACTTATTGATGCCAACTCTGGAAAGgtaccattgc ... ctggatgcagACACTCCATTCCATAAAAGGACATCGGGACTACTCATTTGCATCGGCTTGGAGCCCTGATGGGCGAACATTTGCTACTGGCAACCAAGACAAGACATGCC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 318

CATGCTTCTTTGAGTCCTGACAGAAAGGTCGTTGTTATTGTCGGTGATGATCCTGATGGTCTACTTATTGATGCCAACTCTGGAAAGgtaccattgc ... ctggatgcagACACTCCATTCCATAAAAGGACATCGGGACTACTCATTTGCATCGGCTTGGAGCCCTGATGGGCGAACATTTGCTACTGGCAACCAAGACAAGACATGCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagaagtgctgtaatgatgtgaatattcaccatttggttttgcttctggatgcagACACTCCATTCCATAAAAGGACATCGGGACTACTCATTTGCATCGGCTTGGAGCCCTGATGGGCGAACATTTGCTACTGGCAACCAAGACAAGACATGCC
                                     ttttgcttct  CT-rich tract
                   tgaatatt  TA-rich tract