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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtactttgatctctttcgcaatgcttctggtggagtatctgaagagaacatcggttatatccattactaactctttatgttttatgtccggactgcagGGATTTGATAACCTTAGGAGTCAGAGTGTTGCCCCACCACAATGGACGATGCGTAACATTGATGACAG

Basic information

species Zea mays
transcript GRMZM2G099056_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G099056_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g42750.1 (Oryza sativa), 3'ss of exon 3
gtatgtactttgatctct--ttcgcaatgcttctggtggagtatctgaagagaacatcggttatatccattactaactctttatgttttatgtccggactgcagGGATTTGATAACCTTAGGAGTCAGAGTGTTGCCCCACCACAATGGACGATGCGTAACATTGATGACAG
|||  |||||||||| ||  || ||| ||  | |  || | ||  | |  | | |    |   |||||  | ||||||  ||  ||| |  | | ||| ||||||| |||||||||||||| ||||||||||||||||| ||||||||||| ||||| ||||||||||||||
gtacttactttgatccctcatttgcattgtctttc-tgtaatagttaataaaagctaatggcttatcctcttctaacttgtt--gttatggg-ctggattgcagGGGTTTGATAACCTTAGAAGTCAGAGTGTTGCCCCTCCACAATGGACAATGCGCAACATTGATGACAG

upper sequence: GRMZM2G099056_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA17G36540.1 (Glycine max), 3'ss of exon 3
-----------------------------------------------------------------------gtatgtactttgat---ctctttcgcaatgcttctggtggagtatctgaagagaacatcggttatatccattactaactctttatgttttatgtccggactgcagGGATTTGATAACCTTAGGAGTCAGAGTGTTGCCCCACCACAATGGACGATGCGTAACATTGATGACAG
                                                                         | | | | |||    | |  |  || | | | |  |||||| | |     ||   ||      |||  || ||   |     || |  ||||      |||||||||||||||||||||| || |||||||| || || || |||||||| ||||| || || ||||||||
gtaaagttccatgatggaagagatctttattttcttctagttctagaagacattttctcagtttttggcatagaagcaatatgagaagcaccctaccattccattttttggagtttgttttttga-tgtcttcccaatcatttgcttgttgggc-tgatgcatgtgtatcttgcagGGATTTGATAACCTTAGAAGCCAGAGTGTGGCTCCTCCTCAATGGACCATGCGCAATATCGATGACAG

upper sequence: GRMZM2G099056_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA09G18840.1 (Glycine max), 3'ss of exon 3
------------------------------------------------------------------------gtatgtactttgatctctttcgcaatgcttctggtggagtatctgaagagaacatcggttatatccattactaactcttta---tgttttatgtccggactgcagGGATTTGATAACCTTAGGAGTCAGAGTGTTGCCCCACCACAATGGACGATGCGTAACATTGATGACAG
                                                                         ||||         ||      |  || ||  |      | | |          |  ||  |  | || | |  ||  ||    || |  |||       |||||||||||||||||||||| || |||||||| || || || |||||||| ||||| || |||||||| ||
gtaaagttccatgatagaagagatctttatgttctagttctagacatgttctcagtttctggcactgaagcaatatgcgaagcatcctaccgttccctgttttggagttttttttttttttttttgtatgtcttcccaatcatttgcttgttgggctgatgcatgcgtatcttgcagGGATTTGATAACCTTAGAAGCCAGAGTGTGGCTCCTCCTCAATGGACCATGCGCAATATTGATGATAG

upper sequence: GRMZM2G099056_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 3
---gtatgtactttgatctctttcgcaatgcttctggtggagtatctgaagagaacatcggttatatccattactaactctttatgttttatgtccggactgcagGGATTTGATAACCTTAGGAGTCAGAGTGTTGCCCCACCACAATGGACGATGCGTAACATTGATGACAG
     ||| | ||  || | |   |    |  |||        || ||  |      ||  | |||| | ||  || |  ||  ||||   ||   |   |  ||||||||||||| || || || |||||||| || ||||| || ||||| ||||| || |||||||||||
gcaaaatgaa-ttcaatttttcctgttgaggctctaaacttagatttgtggtt--tctccatcatattcttt--taccctttgctgttgattgaatgtcatatagGGATTTGATAATCTCAGAAGCCAGAGTGTCGCTCCACCTCAGTGGACAATGCGCAATATTGATGACAG

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|20301121|gb|BQ164064.1|BQ164064
EST:     CAAAGGTTGAGGTTATTTCCAATGATCCCAGTGGTTGTACATTTGTTCTG                         GGATTTGATAACCTTAGGAGTCAGAGTGTTGCCCCGCCACAATGGACAATG
genomic: CAAAGGTTGAGGTTATTTCCAATGATCCCAGTGGTTGTACATTTGTTCTGgtatgtactt ... cggactgcagGGATTTGATAACCTTAGGAGTCAGAGTGTTGCCCCACCACAATGGACGATG
EST: gi|20299920|gb|BQ162863.1|BQ162863
EST:     CAATGATCCCAGTGGTTGTACATTTGTTCTG                         GGATTTGATANCCTTAGGAGTCAGAGTGTTGCCCCGCCACAATGGACAATG
genomic: CAATGATCCCAGTGGTTGTACATTTGTTCTGgtatgtactt ... cggactgcagGGATTTGATAACCTTAGGAGTCAGAGTGTTGCCCCACCACAATGGACGATG
EST: gi|20301101|gb|BQ164044.1|BQ164044
EST:     CAAAGGTTGAGGTTATTTCCAATGATCCCAGTGGTTGTACATTTGTTCTG                         GGATTTGATAACCTTAGGAGTCAGAGTGTTGCCCCGCCACAATGGACAATG
genomic: CAAAGGTTGAGGTTATTTCCAATGATCCCAGTGGTTGTACATTTGTTCTGgtatgtactt ... cggactgcagGGATTTGATAACCTTAGGAGTCAGAGTGTTGCCCCACCACAATGGACGATG

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: 153

CCAGCCAAACTTTACAAGCTGAAACATCTAACAAAGGTTGAGGTTATTTCCAATGATCCCAGTGGTTGTACATTTGTTCTGgtatgtactt ... cggactgcagGGATTTGATAACCTTAGGAGTCAGAGTGTTGCCCCACCACAATGGACGATGCGTAACATTGATGACAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 74

CCAGCCAAACTTTACAAGCTGAAACATCTAACAAAGGTTGAGGTTATTTCCAATGATCCCAGTGGTTGTACATTTGTTCTGgtatgtactt ... cggactgcagGGATTTGATAACCTTAGGAGTCAGAGTGTTGCCCCACCACAATGGACGATGCGTAACATTGATGACAG


Block sizes: 37 (upstream exon), 47 (downstream exon)
Score: 55

CCAGCCAAACTTTACAAGCTGAAACATCTAACAAAGGTTGAGGTTATTTCCAATGATCCCAGTGGTTGTACATTTGTTCTGgtatgtactt ... cggactgcagGGATTTGATAACCTTAGGAGTCAGAGTGTTGCCCCACCACAATGGACGATGCGTAACATTGATGACAG


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 82

CCAGCCAAACTTTACAAGCTGAAACATCTAACAAAGGTTGAGGTTATTTCCAATGATCCCAGTGGTTGTACATTTGTTCTGgtatgtactt ... cggactgcagGGATTTGATAACCTTAGGAGTCAGAGTGTTGCCCCACCACAATGGACGATGCGTAACATTGATGACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagaacatcggttatatccattactaactctttatgttttatgtccggactgcagGGATTTGATAACCTTAGGAGTCAGAGTGTTGCCCCACCACAATGGACGATGCGTAACATTGATGACAG
                     tactaac  putative branch site (score: 82)
                            tctttatgttttat  TA-rich tract