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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAACAAGTAGGCCCGCTCACTACCATGTCCTCTGGGATGAGAACAATTTCACAGCAGACGAAATGCAAACACTGACAAACAACCTTTGCTACACgtaacgcacttctttgtatattttatatttgtcctttgcacatttaaattttttttgagaattttcttagcttgttatacatgttattgatgcag

Basic information

species Zea mays
transcript AC189879.3_FGT003
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC189879.3_FGT003 (Zea mays), 5'ss of exon 19
lower sequence: LOC_Os06g39640.1 (Oryza sativa), 5'ss of exon 20
GGAACAAGTAGGCCCGCTCACTACCATGTCCTCTGGGATGAGAACAATTTCACAGCAGACGAAATGCAAACACTGACAAACAACCTTTGCTACACgtaacgcacttctttgtatattttatatttgtcctttgcacatttaaattttttttg-agaattttcttagcttgttatacatgttattgatgcag
|||||||||||||| ||||||||||| ||||| |||||||||||||||||||| |||||||||||||| ||| |||||||||||||||||||||||||  ||| | ||   | | | |||  ||| ||||||||||  | |  || | | |  |||| ||   |  |||| || |    ||  ||||||||
GGAACAAGTAGGCCAGCTCACTACCACGTCCTTTGGGATGAGAACAATTTCACTGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACACgtacggcattactgaatct-tgttaagtttatcctttgcactctgagcttctctctatagaaattgtctgacttggtacat---ttgctgatgcag

upper sequence: AC189879.3_FGT003 (Zea mays), 5'ss of exon 19
lower sequence: GLYMA17G12850.1 (Glycine max), 5'ss of exon 20
GGAACAAGTAGGCCCGCTCACTACCATGTCCTCTGGGATGAGAACAATTTCACAGCAGACGAAATGCAAACACTGACAAACAACCTTTGCTACACgtaacgcacttcttt-gtat-attttatatttgtcctttgcacatttaaattttttttgagaattttcttagcttgttatacatgttattgatgcag
|| |||||||| || ||||| || ||||| || ||||| |||||||||||||| || || || || ||| | ||||| |||||| | ||||||||||||   || ||| |   || || ||| |||||    |||| |  |||   || |  ||| |      | | ||  ||||     || | |      
GGTACAAGTAGACCAGCTCATTATCATGTTCTGTGGGACGAGAACAATTTCACTGCTGATGAGATCCAATCTCTGACCAACAACTTGTGCTACACgtaaaaaacctctctcacatcatcttaaatttg----ttgctccattattcttgtgatgaaa------taacctcattattttgattgtag------

upper sequence: AC189879.3_FGT003 (Zea mays), 5'ss of exon 19
lower sequence: GLYMA06G23920.1 (Glycine max), 5'ss of exon 20
GGAACAAGTAGGCCCGCTCACTACCATGTCCTCTGGGATGAGAACAATTTCACAGCAGACGAAATGCAAACACTGACAAACAACCTTTGCTACACgtaacgcacttctttgtatattttatatttgtcctttgcacatttaaattttttttgagaattttcttagcttgttatacatgttattgatgcag
|| |||||||| || || ||||| || ||||||||||| |||||||||||||| ||||| || || ||  | || || |||||  | ||||||||||||   | |||| |  ||   | || ||     |||    |||     | ||||| |||  |  | || | |     |||| ||   | |||||
GGTACAAGTAGACCAGCACACTATCACGTCCTCTGGGACGAGAACAATTTCACTGCAGATGAGATTCAGTCTCTAACCAACAATTTGTGCTACACgtaaacgatttctct--attcctcatcttgaattttt---tattctctctatttttaaga--tgacataaccttcctaacattttg--gttgcag

upper sequence: AC189879.3_FGT003 (Zea mays), 5'ss of exon 19
lower sequence: Vv05s0020g04190.t01 (Vitis vinifera), 5'ss of exon 18
GGAACAAGTAGGCCCGCTCACTACCATGTCCTCTGGGATGAGAACAATTTCACAGCAGACGAAATGCAAACACTGACAAACAACCTTTGCTACACgta------acgcacttctttg-tatatttta-------tatttgtcctttgca---------catttaaattttt-tttgagaattttcttagcttgttatacatgttattgatgcag-------------
                           ||  | |||||||||||||||||||||||||| | ||| ||| |  |||| ||||| ||||||||||| ||        ||||    | | | | | ||        | ||| |||||   |         ||| |  || |   ||  ||||||   ||      ||  | |  || | |    |              
---------------------------GTTTTATGGGATGAGAACAATTTCACAGCAGATGGAATTCAATCCTTGACGAACAATCTTTGCTACACATATGCAAGGTGCACACGATCGGTGTCTGTTGgtaagcctgtttttccttcctaatgaagtttcatatgcatctgcattcaagaattaaattgttcccttgaaaactttttcggaaaaaaatgtcaaagatt

upper sequence: AC189879.3_FGT003 (Zea mays), 5'ss of exon 19
lower sequence: Vv11s0016g04620.t01 (Vitis vinifera), 5'ss of exon 20
GGAACAAGTAGGCCCGCTCACTACCATGTCCTCTGGGATGAGAACAATTTCACAGCAGACGAAATGCAAACACTGACAAACAACCTTTGCTACACgtaacgcacttctttgtatattttatatttgtcctttgcacatttaaattttttttgagaattttcttagcttgttatacatgttattgatgcag
|| || ||  | |||||||| || ||||| ||||||||||||||||| || |||||||| || || ||| |  |||| |||||||| || |||||||||  | | ||       |||   |   |   |||| || | |||    ||||   |  ||||  |  | |||  |     |||   |      
GGGACCAGCCGACCCGCTCATTATCATGTTCTCTGGGATGAGAACAACTTTACAGCAGATGAGATCCAATCTTTGACGAACAACCTCTGTTACACgtaagacgcatc-------attcccttgcttctctttccagagttattaattttaccatgatttaatctggttgacaacttggttgcag------

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|166622653|gb|EG304138.1|EG304138
EST:     CTTTGCTACAC                         TTATGCCCGGTGCACACGCTCGGTTTCTGTTG
genomic: CTTTGCTACACgtaacgcact ... attgatgcagTTATGCCCGGTGCACACGCTCGGTTTCTGTTG
EST: gi|19351412|gb|BM895959.1|BM895959
EST:     AATTTCACAGCAGACGAAATGCAAACACTGACAAACAACCTTTGCTACAC                         TTATGCCCGGTGCACACGCTCGGTTTCTGTTG
genomic: AATTTCACAGCAGACGAAATGCAAACACTGACAAACAACCTTTGCTACACgtaacgcact ... attgatgcagTTATGCCCGGTGCACACGCTCGGTTTCTGTTG

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), 32 (downstream exon)
Score: 599

GGAACAAGTAGGCCCGCTCACTACCATGTCCTCTGGGATGAGAACAATTTCACAGCAGACGAAATGCAAACACTGACAAACAACCTTTGCTACACgtaacgcact ... attgatgcagTTATGCCCGGTGCACACGCTCGGTTTCTGTTG


Block sizes: 48 (upstream exon), 32 (downstream exon)
Score: 89

GGAACAAGTAGGCCCGCTCACTACCATGTCCTCTGGGATGAGAACAATTTCACAGCAGACGAAATGCAAACACTGACAAACAACCTTTGCTACACgtaacgcact ... attgatgcagTTATGCCCGGTGCACACGCTCGGTTTCTGTTG


Block sizes: 49 (upstream exon), 32 (downstream exon)
Score: 61

GGAACAAGTAGGCCCGCTCACTACCATGTCCTCTGGGATGAGAACAATTTCACAGCAGACGAAATGCAAACACTGACAAACAACCTTTGCTACACgtaacgcact ... attgatgcagTTATGCCCGGTGCACACGCTCGGTTTCTGTTG


Block sizes: 46 (upstream exon), 32 (downstream exon)
Score: 98

GGAACAAGTAGGCCCGCTCACTACCATGTCCTCTGGGATGAGAACAATTTCACAGCAGACGAAATGCAAACACTGACAAACAACCTTTGCTACACgtaacgcact ... attgatgcagTTATGCCCGGTGCACACGCTCGGTTTCTGTTG