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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaggtttttctctcttcccttgcaactttatgatctatttcagtttattttgcatctttattttctgttaatttattctcctgtgtaaggtccctgttatggaagtctactactaaattctataatgttttctgtttagGGTTCCGTCGACATTCTTCAGAAATATCCTGTACCAGAGTGTGATATTTGGTTTATCAAATTCTCCTGTGATTTCCATTATAATGCAGCGGCTATAG

Basic information

species Vitis vinifera
transcript Vv19s0014g05210.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0014g05210.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os08g04270.1 (Oryza sativa), 3'ss of exon 10
--gttaggtttt--tctctcttcccttgcaactttatgatctatttcagtt-tattttg-------catcttta---ttttctgttaatttattctcctgtgtaaggtccctgttatggaagtctactactaaattcta--taatgttttctgtt------tagGGTTCCGTCGACATTCTTCAGAAATATCCTGTACCAGAGTGTGATATTTGGTTTATCAAATTCTCCTGTGATTTCCATTATAATGCAGCGGCTATAG
  ||||   ||     |||||     | ||    | | ||  |||| | || | || ||       |||||  |   |||||||| |  ||| | |  | |  |   ||||| ||    | |||| |  || || |  |  || | |||| | ||      ||||||  | | || ||||||||||| |||||||| ||||| |||||||| ||||||||||||||||| || ||||| || |  |||  |  ||| ||||
gtgttataattcaacttctctagaactacagacct-taattcattttacttgtcttctgatctgatcatctcaacagttttctgtcatgttactttagttttcactatccct-ttccatacgtctccctctcaagtaaaattactttttttttttcaaatgtagGGTAGCATTGATATTCTTCAGAAGTATCCTGTGCCAGAATGTGATATCTGGTTTATCAAATTCTCATGCGATTTTCACTTCAATCAATTGGCAATAG

upper sequence: Vv19s0014g05210.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G148924_T03 (Zea mays), 3'ss of exon 9
---gttaggtttttctctcttccc-ttgcaactttatgatctatttcagtttattttgcatctttattttctgttaatttattctcctgtgt-aaggtccctgtta-------tggaagtctactactaaattctataatgttttctgtt------tagGGTTCCGTCGACATTCTTCAGAAATATCCTGTACCAGAGTGTGATATTTGGTTTATCAAATTCTCCTGTGATTTCCATTATAATGCAGCGGCTATAG
    ||  ||||  || ||      ||| |    ||| ||  ||  ||  |  ||  |||   || |   || ||     || ||    | | ||||| |  | |        |  |  | | | ||| || |  |||   |||||||||      |||||   | |||| || |||||||| |||||||| ||||| ||||| ||||||||||||||||| || |||||||| || |  |||     ||| ||||
gtaattcagtttaactttcccagaattgtattcctattata-atgccatatatttacgcacagttgtaaactatttccagatccttagatttcaaggtactggctgccaatattaaatatgttccactgaagta-atatgattttctgttgcctcatagGGAAGCATCGATATCCTTCAGAAGTATCCTGTCCCAGAATGTGACATTTGGTTTATCAAATTTTCATGTGATTTTCACTTCAATCAGTTGGCGATAG

upper sequence: Vv19s0014g05210.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA02G17110.1 (Glycine max), 3'ss of exon 9
gttaggtttttctctcttcccttgcaactttatgatctatttcagtttattttgcatctttattttctgttaatttattctcctgtgtaaggtccctgttatggaagtctactactaaattctataatgttttctgtttagGGTTCCGTCGACATTCTTCAGAAATATCCTGTACCAGAGTGTGATATTTGGTTTATCAAATTCTCCTGTGATTTCCATTATAATGCAGCGGCTATAG
                                            |||  || |  ||| |||| || | |||||| ||| |    |||        |        | ||  || |    || | |  | ||   ||||||||||   || ||||| ||||||||||| ||||| || ||||||||||| ||||| ||||| || || |||||||||||||  ||   ||| ||  |||
--------------------------------------------gttagttata-atcattatcttttcttaatt-attttttaatgtgtaactttt--------aatcagcttcagttttttttttttttggatgtttagGGTGTAGTTGACATCCTTCAGAAATACCCTGTTCCCGAGTGTGATATCTGGTTCATCAAGTTTTCTTGTGATTTCCATTTCAACATAGCCGCAGTAG

upper sequence: Vv19s0014g05210.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA10G02690.3 (Glycine max), 3'ss of exon 8
gttaggtttttctctcttcccttgcaactttatgatctatttcagtttattttgcatctttattttctgttaatt-tattctcctgtgtaaggtccctgttatggaagtctactactaaattctataatgttttctgtttagGGTTCCGTCGACATTCTTCAGAAATATCCTGTACCAGAGTGTGATATTTGGTTTATCAAATTCTCCTGTGATTTCCATTATAATGCAGCGGCTATAG
                                            |||| || |  ||| | || || | |||||| |||| |  || ||||  |     |||   |  |  | |  |   || |  |        ||||||||||   || ||||| ||||||||||| ||||| || ||||||||||| ||||| ||||| || || |||||||||||||  ||   ||| ||  | |
--------------------------------------------gtttgttata-atcatgatcttttcttaattatattttaatgggtaacat-----ttaatcagattcagtttt---ttttgga--------tgtttagGGTGTAGTTGACATCCTTCAGAAATACCCTGTTCCTGAGTGTGATATCTGGTTCATCAAGTTTTCTTGTGATTTCCATTTCAACTTAGCCGCAGTGG

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|110378718|gb|EC943862.1|EC943862
EST:     ATGAAATTGTGTTATGGGAACCCAAAACCAAGGAACAGTCTCCTGGCGAG                         GGTTCCGTCGACATTCTTCAGAAATATCCTGTACCAGAGTGTGATATTTGG
genomic: ATGAAATTGTGTTATGGGAACCCAAAACCAAGGAACAGTCTCCTGGCGAGgttaggtttt ... ttctgtttagGGTTCCGTCGACATTCTTCAGAAATATCCTGTACCAGAGTGTGATATTTGG
EST: gi|351033874|gb|FQ447912.1|FQ447912
EST:     ATGAAATTGTGTTATGGGAACCCAAAACCAAGGAACAGTCTCCTGGCGAG                         GGTTCCGTCGACATTCTTCAGAAATATCCTGTACCAGAGTGTGATATTT
genomic: ATGAAATTGTGTTATGGGAACCCAAAACCAAGGAACAGTCTCCTGGCGAGgttaggtttt ... ttctgtttagGGTTCCGTCGACATTCTTCAGAAATATCCTGTACCAGAGTGTGATATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaaggtccctgttatggaagtctactactaaattctataatgttttctgtttagGGTTCCGTCGACATTCTTCAGAAATATCCTGTACCAGAGTGTGATATTTGGTTTATCAAATTCTCCTGTGATTTCCATTATAATGCAGCGGCTATAG
                          tactaaa  putative branch site (score: 1)
                                           ttttctgttt  putative PPT
                          tactaaattctataat  TA-rich tract