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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaagtgacctagcatattatgtagtttgtcgtggaccttttattagtaaaataaagcacacatatttattttttaaaatataacactcactgcagactatttcattgaccttttaccgtccttcattatctatgagttaatttgtgttgttatattgtatagATTGGGAAAGGTTCAAGAGGAGATGTTACTATATTGCCTACACTTGTTGTGAACAACCGGCAATATCGAG

Basic information

species Zea mays
transcript AC211785.2_FGT003
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC211785.2_FGT003 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os10g20630.1 (Oryza sativa), 3'ss of exon 3
gtgaagtgacctagcatattatgtagtttgtcgtggaccttttattagtaaaataaagcacacatatttattttttaaaatataacactcactgcagactatttcattgaccttttaccgtccttcattatctatgagtt-aatttgtgttgttatattgtatagATTGGGAAAGGTTCAAGAGGAGATGTTACTATATTGCCTACACTTGTTGTGAACAACCGGCAATATCGAG
||||| | |||| |  |  | ||| | || | ||      ||||| |||||| | ||| ||            | |||| ||  | | |       || | ||| |||  | ||| |     ||| | ||||| || |||  || || |||   || |||  |||||||||||||| ||||||||||||||||||||||||||||| |||||||||||||| |||||||| ||||
gtgaatttaccttg--tgatgtgttggttattgtta--tatttatcagtaaattgaagtac------------tgtaaactagtatattt------gaatgttt-attaccttttaataccgctttaatatctttgtgtttgatatgagttacaatgttgcgtagATTGGGAAAGGATCAAGAGGAGATGTTACTATATTGCCTACTCTTGTTGTGAACAATCGGCAATACCGAG

upper sequence: AC211785.2_FGT003 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA11G00370.1 (Glycine max), 3'ss of exon 3
gtgaagtgacctagcatattatgtagtttgtcgtggaccttttattagtaaaataaagcacacatatttattttttaaaatataacactcactgcagactatttcattgaccttttaccgtccttcattatctatgagttaatttgtgttgttatattgtatagATTGGGAAAGGTTCAAGAGGAGATGTTACTATATTGCCTACACTTGTTGTGAACAACCGGCAATATCGAG
                                                                                |||   |||   |     |||||  ||| |    || |     | || ||      || |  ||     | |||  ||   |||||||| || || ||  |||| |||||||| ||||||||||| |||||||| || || || ||||||||||
-------------------------------------------------------------------------------gtattgtactttataattgctatta-attcattcattgcatcagtgcagtaatatatagatgtttaacaatattagttttggtagATTGGAAAGGGATCGCGAGGTGATGTTACCATATTGCCTACTCTTGTTGTCAATAATCGACAATATCGAG

upper sequence: AC211785.2_FGT003 (Zea mays), 3'ss of exon 1
lower sequence: Vv03s0091g00740.t01 (Vitis vinifera), 3'ss of exon 3
gtgaagtgacctagcatattatgtagtttgtcgtggaccttttattagtaaaataaagcacacatatttattttttaaaatataacactcactgcagactatttcattgaccttttaccgtccttcattatctatgagttaatttgtgttgttatattgtatagATTGGGAAAGGTTCAAGAGGAGATGTTACTATATTGCCTACACTTGTTGTGAACAACCGGCAATATCGAG
|| |||   |    | |  ||| |  ||| |  |     ||  | |  |  |  ||  | |   | ||  || ||     | |  |  | | | |  | | | |    ||    |||      |||| |    |     |  ||         |  |  || || ||||||||||  ||||||| ||||| ||||||||||| || ||||||||||||||  | ||||||||||
gt-aagcatctcttcttcatatattttttatttta----ttgaagtgcttcagcaa--cccttttgttgtttgttgggcttctggctttta-tacgcattgtcttga-gattggttattccagttcaat---caaacactgtttgacaagaacacttcctacagGTTGGGAAAGGAACAAGAGGCGATGTCACTATATTGCCCACCCTTGTTGTGAACAATAGACAATATCGAG

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: 26 (upstream exon), 49 (downstream exon)
Score: 124

ATGGGAGACCCAAATGCTGATTCTGACCACCCGATACTTAAAATGGAACAAGATGCTCAGgtgaagtgac ... tattgtatagATTGGGAAAGGTTCAAGAGGAGATGTTACTATATTGCCTACACTTGTTGTGAACAACCGGCAATATCGAG


Block sizes: 26 (upstream exon), 49 (downstream exon)
Score: 98

ATGGGAGACCCAAATGCTGATTCTGACCACCCGATACTTAAAATGGAACAAGATGCTCAGgtgaagtgac ... tattgtatagATTGGGAAAGGTTCAAGAGGAGATGTTACTATATTGCCTACACTTGTTGTGAACAACCGGCAATATCGAG


Block sizes: 24 (upstream exon), 49 (downstream exon)
Score: 85

ATGGGAGACCCAAATGCTGATTCTGACCACCCGATACTTAAAATGGAACAAGATGCTCAGgtgaagtgac ... tattgtatagATTGGGAAAGGTTCAAGAGGAGATGTTACTATATTGCCTACACTTGTTGTGAACAACCGGCAATATCGAG


Block sizes: 26 (upstream exon), 49 (downstream exon)
Score: 105

ATGGGAGACCCAAATGCTGATTCTGACCACCCGATACTTAAAATGGAACAAGATGCTCAGgtgaagtgac ... tattgtatagATTGGGAAAGGTTCAAGAGGAGATGTTACTATATTGCCTACACTTGTTGTGAACAACCGGCAATATCGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accttttaccgtccttcattatctatgagttaatttgtgttgttatattgtatagATTGGGAAAGGTTCAAGAGGAGATGTTACTATATTGCCTACACTTGTTGTGAACAACCGGCAATATCGAG
                                       ttgttatattgtata  TA-rich tract