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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGCACATGCCCACACCTGAACAGTGGACCAATGTGTTCAACCCTGCATTTTCATATTATGCGTACTACTGCTATGCTAACTTATTCACCCTAAACAAGgtgatcatatcttcctccccttcctcaattttctccacgtttctcagagtggtaatgattctgttcaattttcag

Basic information

species Zea mays
transcript GRMZM2G416667_T03
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G416667_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os05g28180.3 (Oryza sativa), 5'ss of exon 5
AAAGCACATGCCCACACCTGAACAGTGGACCAATGTGTTCAACCCTGCATTTTCATATTATGCGTACTACTGCTATGCTAACTTATTCACCCTAAACAAGgtgatcatatcttcctccccttcctcaattttctccacgtttctcagagtggtaatgattctgttcaattttcag
|||||| ||||| ||||||||||| ||||||||||| |||||||| ||||||||||||||||| || ||||||||||||||||||| ||| || || |||||    | ||   ||||      || |||||||  ||  || ||  ||   ||||   |||||| ||||||    
AAAGCATATGCCTACACCTGAACAATGGACCAATGTCTTCAACCCAGCATTTTCATATTATGCATATTACTGCTATGCTAACTTATACACACTCAATAAGgtaggaaaattgccctcatacctct-aattttcctcattttgct-ggaaaagtaacacttctgtgcaatttag--

upper sequence: GRMZM2G416667_T01 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA01G29470.2 (Glycine max), 5'ss of exon 14
AAAGCACATGCCCACACCTGAACAGTGGACCAATGTGTTCAACCCTGCATTTTCATATTATGCGTACTACTGCTATGCTAACTTATTCACCCTAAACAAGgtgatcatatcttcctcc----ccttcctcaattttctccacgtt------------tctcagagtggtaatgattctgttcaattttcag---------
||| |||||||| |||||||| || ||||| ||||| ||||| || ||||||||||| ||||  || ||||| ||||| ||  | | |||| ||||||||||    |  | || ||||      |   |||||||| | |   ||            | |||    |  ||  |   | ||   |  | |          
AAAACACATGCCTACACCTGAGCAATGGACTAATGTTTTCAATCCGGCATTTTCATACTATGTCTATTACTGTTATGCAAATCTTTACACCTTAAACAAGgtatgtaactttttctccagaatatgtatcaattttttacggcttatctatttactctttcaagaagaaaacaagcttcttttttactgattatggaaag

upper sequence: GRMZM2G416667_T01 (Zea mays), 5'ss of exon 13
lower sequence: Vv08s0105g00570.t01 (Vitis vinifera), 5'ss of exon 13
AAAGCACATGCCCACACCTGAACAGTGGACCAATGTGTTCAACCCTGCATTTTCATATTATGCGTACTACTGCTATGCTAACTTATTCACCCTAAACAAGgtgatcatatct------------tcctccccttcctcaattttctc---cacgtttctcag-agtggtaatgattctgttcaattttcag---------
||| || ||||| || || |  |||||||||||||  ||||| |||||||||||||| ||||  |||||||| ||||||||| | |  ||  | ||||||||      ||              ||||||||| | |  |||||  |    | | |   ||| | || |  || ||   |||||  |   |         
AAAACATATGCCTACTCCAGCTCAGTGGACCAATGCTTTCAATCCTGCATTTTCATACTATGTCTACTACTGTTATGCTAACCTCTATACATTGAACAAGgttcgtgcatgcacttagaaaatatcctcccctacttttattttgccatatatgatcaccagtaatgcttttggtttgtttcaacatatggtttgatagt

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|18661413|gb|BM501264.1|BM501264
EST:     TTTCATATTATGCGTACTACTGCTATGCTAACTTATTCACCCTAAACAAG                         CTGCGTGAGTCAAAGGGAATGACCACTATCAAATTCCGTCCACATGCTGGA
genomic: TTTCATATTATGCGTACTACTGCTATGCTAACTTATTCACCCTAAACAAGgtgatcatat ... caattttcagCTGCGTGAGTCAAAGGGAATGACCACTATCAAATTCCGTCCACATGCTGGA
EST: gi|5871432|gb|AW017903.1|AW017903
EST:     TTTCATATTATGCGTACTACTGCTATGCTAACTTATTCACCCTAAACAAG                         CTGCGTGAGTCAAAGGGAATGACCACTATCAAATTCCGTCCACATGCTGGA
genomic: TTTCATATTATGCGTACTACTGCTATGCTAACTTATTCACCCTAAACAAGgtgatcatat ... caattttcagCTGCGTGAGTCAAAGGGAATGACCACTATCAAATTCCGTCCACATGCTGGA

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: 41 (upstream exon), 47 (downstream exon)
Score: 38

AAAGCACATGCCCACACCTGAACAGTGGACCAATGTGTTCAACCCTGCATTTTCATATTATGCGTACTACTGCTATGCTAACTTATTCACCCTAAACAAGgtgatcatat ... caattttcagCTGCGTGAGTCAAAGGGAATGACCACTATCAAATTCCGTCCACATGCTGGAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 37

AAAGCACATGCCCACACCTGAACAGTGGACCAATGTGTTCAACCCTGCATTTTCATATTATGCGTACTACTGCTATGCTAACTTATTCACCCTAAACAAGgtgatcatat ... caattttcagCTGCGTGAGTCAAAGGGAATGACCACTATCAAATTCCGTCCACATGCTGGAGAG


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 26

AAAGCACATGCCCACACCTGAACAGTGGACCAATGTGTTCAACCCTGCATTTTCATATTATGCGTACTACTGCTATGCTAACTTATTCACCCTAAACAAGgtgatcatat ... caattttcagCTGCGTGAGTCAAAGGGAATGACCACTATCAAATTCCGTCCACATGCTGGAGAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 39

AAAGCACATGCCCACACCTGAACAGTGGACCAATGTGTTCAACCCTGCATTTTCATATTATGCGTACTACTGCTATGCTAACTTATTCACCCTAAACAAGgtgatcatat ... caattttcagCTGCGTGAGTCAAAGGGAATGACCACTATCAAATTCCGTCCACATGCTGGAGAG