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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattcggtgtttcatgttttaagtgtattccggtttgtttggaccaatggagtattgtgtttgttaatgatttcctttggcattttggttgaagGTTGTTGACTGTCGTATATGTGGTGATCCTAATTCCGTTCTCCGATTTGCCTTCGTTGAATTTACTGATGAGG

Basic information

species Vitis vinifera
transcript Vv16s0098g01040.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 3
gtaattcggtgtttcatgttttaagtgtattccggtttgtttggaccaatggagtattgtgtttgttaatgatttcctttggcattttggttgaagGTTGTTGACTGTCGTATATGTGGTGATCCTAATTCCGTTCTCCGATTTGCCTTCGTTGAATTTACTGATGAGG
          ||    | || |   |  |  |  | || | ||    ||| | | ||  |  |  || |   ||| ||||           |||||||||| ||||||||||| ||||| ||||| ||||| ||||| || ||||| ||| | || || ||||||||||
----------gtacatttttctggctccacacttgctt-tctgtgataattgtgcataataatc-ttgaaatttttcttt----------ctgaagGTTGTGGACTGTCGTATGTGTGGGGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGG

upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA04G40750.1 (Glycine max), 3'ss of exon 4
gtaattcggtgtttcatgttttaagtgtattccggtttgtttggaccaatggagtattgtgtttgttaatgatttcctttggcattttggttgaagGTTGTTGACTGTCGTATATGTGGTGATCCTAATTCCGTTCTCCGATTTGCCTTCGTTGAATTTACTGATGAGG
|||     | ||| |   || |   ||   |  | ||| ||   |   ||||   || |||||  | |||     | ||     | |||| |  |||||||||| || ||| ||||||| |||||||| ||  |||| ||||||||||||||||| || || ||||| |
gtagaaatg-gttacgatttgtttatgacatgtgctttcttcataattatggttgatcgtgttactaaattgacacgttgt---tcttggctatagGTTGTTGATTGCCGTGTATGTGGAGATCCTAACTCTATTCTTCGATTTGCCTTCGTTGAGTTCACAGATGAAG

upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA06G14030.1 (Glycine max), 3'ss of exon 5
gtaattcggtgtttcatgttttaagtgtattccggtttgtttggaccaatggagtattgtgtttgttaatga-tttcctttggcattttggttgaagGTTGTTGACTGTCGTATATGTGGTGATCCTAATTCCGTTCTCCGATTTGCCTTCGTTGAATTTACTGATGAGG
        ||     ||| ||   ||||  ||   ||| ||   |  ||| |   |  |||||  | | ||| | | ||      |  ||  |  |||||||||| || ||| | ||||| |||||||||||  ||||||| ||||||||| |||| ||||| || || |
--------gtagaa-atggttacggtgtgctcgcttttcttcttaataattgttgaccgtgttattgattgaatctactccactttcctgactatagGTTGTTGATTGCCGTGTTTGTGGGGATCCTAATTCTATTCTCCGGTTTGCCTTCATTGAGTTTACAGACGAAG

upper sequence: Vv16s0098g01040.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA06G14050.1 (Glycine max), 3'ss of exon 5
gtaattcggtgtttcatgttttaagtgtattccggtttgtttggaccaatggagtattgtgtt-tgttaatgatttcctttggcattttggttgaagGTTGTTGACTGTCGTATATGTGGTGATCCTAATTCCGTTCTCCGATTTGCCTTCGTTGAATTTACTGATGAGG
|||     |  |   || | || |   ||    | ||| ||   |   |||| | |||||||| ||  | |||   | | |    | |||| |  |||||||||| || ||| ||||||| |||||||| ||  |||| |||||||||||| |||| || || ||||| |
gtagaaacgattactatttgtttatgatacgt-gctttcttcttaattatggtggattgtgttatgaaattgacaccttgt----tcttggctatagGTTGTTGATTGCCGTGTATGTGGAGATCCTAACTCTATTCTTCGATTTGCCTTCATTGAGTTCACAGATGATG

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|110731191|gb|EE109131.1|EE109131
EST:     GTCACTGAGGAAAATCTTGCTGCCTCTTTT-ATCAATTGTGGGCAG                         GTTGTTGACCGTCGTATAGGTGGTGATCCTAATTCCGTTCTCCGATTTG
genomic: GTCACTGAGGAAGATCTTGCTGC-TCTTTTTATCAATTGTGGCCAGgtaattcggt ... ttggttgaagGTTGTTGACTGTCGTATATGTGGTGATCCTAATTCCGTTCTCCGATTTG
EST: gi|110385680|gb|EC950225.1|EC950225
EST:     AGCAGGTCACTGAGGAAGATCTTGCTGCTCTTTTTATCAATTGTGGCCAG                         GTTGTTGACTGTCGTATATGTGGTGATCCTAATTCCGTTCTCCGATTTGCC
genomic: AGCAGGTCACTGAGGAAGATCTTGCTGCTCTTTTTATCAATTGTGGCCAGgtaattcggt ... ttggttgaagGTTGTTGACTGTCGTATATGTGGTGATCCTAATTCCGTTCTCCGATTTGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggaccaatggagtattgtgtttgttaatgatttcctttggcattttggttgaagGTTGTTGACTGTCGTATATGTGGTGATCCTAATTCCGTTCTCCGATTTGCCTTCGTTGAATTTACTGATGAGG
                      tgttaat  putative branch site (score: 3)
                    tttgttaatgattt  TA-rich tract