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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtacttctatattatagtttcaactatggcaatgactcagtttgcatgaatccattagacacactcctttctaattttcactccctatttacgtttaaacagtaaacatgtgaattgttgttgaattgtagTGTCCACTTGGTGGAGTTGCTTGGCACAGGTGAATACTTTGCCATGAAAGCTATGGATAAAAGTGTCATGCTTAACCGAAACAAG

Basic information

species Zea mays
transcript GRMZM2G001457_T02
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G001457_T02 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os11g01140.3 (Oryza sativa), 3'ss of exon 13
gtaagtacttctatattatagtttcaactatggcaatgactcagtttgcatgaatccattagacacactcctttctaattttcactccctatttacgtttaaacagtaaacatgtgaattgttgttg-aattgtagTGTCCACTTGGTGGAGTTGCTTGGCACAGGTGAATACTTTGCCATGAAAGCTATGGATAAAAGTGTCATGCTTAACCGAAACAAG
|||| |  ||  ||  | | |||  || |  |  ||  | | | ||        |  |||    | ||   |  || |||||      | |||   |||| ||||      ||||| ||| |  ||| ||||| ||||| |||||||| |||||| |    ||||| ||||||||||||||||||||||||||||||||  ||||||||||||| || |||
gtaaatcatttcatggtttggtt--aaattggataaacattgaattgttgcct-tttattgctaatacatttgactcatttta-----caattgttgtttcaaca------atgtgtattatgattggaattgaagTGTACACTTGGTAGAGTTGTTGAATACAGGAGAATACTTTGCCATGAAAGCTATGGATAAAAGCATCATGCTTAACCGCAATAAG

upper sequence: GRMZM2G001457_T02 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os12g01140.4 (Oryza sativa), 3'ss of exon 9
gtaagtacttctatattatagtttcaactatggcaatgactcagtttgcatgaatccattagacacactcctttctaattttcactccctatttacgtttaaacagtaaacatgtgaattgttgttg-aattgtagTGTCCACTTGGTGGAGTTGCTTGGCACAGGTGAATACTTTGCCATGAAAGCTATGGATAAAAGTGTCATGCTTAACCGAAACAAG
||||  | ||| ||  | | |||  || |  |  ||  | | | ||        |  |||    | ||   |  || |||||      | |||   |||| ||||      ||||| ||| |  ||| ||||| ||||| |||||||| |||||| |    ||||| ||||||||||||||||||||||||||||||||  ||||||||||||| || |||
gtaatcatttc-atggtttggtt--aaattggataaacattgaattgttgcct-tttattgctaatacatttgactcatttta-----caattgttgtttcaaca------atgtgtattatgattggaattgaagTGTACACTTGGTAGAGTTGTTGAATACAGGAGAATACTTTGCCATGAAAGCTATGGATAAAAGCATCATGCTTAACCGCAATAAG

upper sequence: GRMZM2G001457_T02 (Zea mays), 3'ss of exon 12
lower sequence: Vv06s0004g03700.t01 (Vitis vinifera), 3'ss of exon 13
gtaagtacttctatattatagtttcaactatggcaatgactcagtttgcatgaa-tccattagacacactcctttctaattttcactccctatttacgtttaaacagtaaacatgtgaattgttgttgaattgtagTGTCCACTTGGTGGAGTTGCTTGGCACAGGTGAATACTTTGCCATGAAAGCTATGGATAAAAGTGTCATGCTTAACCGAAACAAG
                             | ||  ||||   |||    ||    ||||||       ||    || || |||  ||   | ||       |||   || ||   |  |||| | |||    | ||||| ||  ||||||| ||   ||| || |||||||||||||||||||||||||||||||||| ||||||||| ||||| ||||||
--------------------------ctcaggggtatgatcaagtccttattctctccattttgttttcttagctcaaacttttgctgtgtcttgg-----aaaatttagactcattgattggt-ttg----gcagTGTGCATCTGGTGGAATTATGTGGAACTGGTGAATACTTTGCCATGAAAGCTATGGATAAAAATGTCATGCTCAACCGCAACAAG

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|32793099|gb|CD945335.1|CD945335
EST:     GATCTGGTGATACTGGCAG                         TGTCCACTTGGTGGAGTTGCTTGGCACAGGTGAATACTTTGCCATGAAAGC
genomic: GATCTGGTGATACTGGCAGgtaagtactt ... tgaattgtagTGTCCACTTGGTGGAGTTGCTTGGCACAGGTGAATACTTTGCCATGAAAGC




















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), 44 (downstream exon)
Score: 15

GTTCTTGAGAACGGTGAAAGCATTGATTTGAAACATTTCAGACCAGTAAGGCCTTTAGGATCTGGTGATACTGGCAGgtaagtactt ... tgaattgtagTGTCCACTTGGTGGAGTTGCTTGGCACAGGTGAATACTTTGCCATGAAAGCTATGGATAAAAGTGTCATGCTTAACCGAAACAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 175

GTTCTTGAGAACGGTGAAAGCATTGATTTGAAACATTTCAGACCAGTAAGGCCTTTAGGATCTGGTGATACTGGCAGgtaagtactt ... tgaattgtagTGTCCACTTGGTGGAGTTGCTTGGCACAGGTGAATACTTTGCCATGAAAGCTATGGATAAAAGTGTCATGCTTAACCGAAACAAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 42

GTTCTTGAGAACGGTGAAAGCATTGATTTGAAACATTTCAGACCAGTAAGGCCTTTAGGATCTGGTGATACTGGCAGgtaagtactt ... tgaattgtagTGTCCACTTGGTGGAGTTGCTTGGCACAGGTGAATACTTTGCCATGAAAGCTATGGATAAAAGTGTCATGCTTAACCGAAACAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 46

GTTCTTGAGAACGGTGAAAGCATTGATTTGAAACATTTCAGACCAGTAAGGCCTTTAGGATCTGGTGATACTGGCAGgtaagtactt ... tgaattgtagTGTCCACTTGGTGGAGTTGCTTGGCACAGGTGAATACTTTGCCATGAAAGCTATGGATAAAAGTGTCATGCTTAACCGAAACAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcactccctatttacgtttaaacagtaaacatgtgaattgttgttgaattgtagTGTCCACTTGGTGGAGTTGCTTGGCACAGGTGAATACTTTGCCATGAAAGCTATGGATAAAAGTGTCATGCTTAACCGAAACAAG
         tatttacgtttaaa  TA-rich tract