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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgctcacgtttattaaaagagtgtttctctgtattatataatgtctccttttgttcacgaacttactattgagctaatgtgcacctgttgagctttctcaatatttggtgatgtcattttgtagGAATTGTCATTAGATTCGTCCCAGCATGTCCGCTCTGCCTTGGCTTCAGTTTTAATGGGAATGGCTCCCGTCTTAGGAAAG

Basic information

species Vitis vinifera
transcript Vv01s0011g03280.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 6
gtgctcacgtttattaaaagagtgtttctctgtattatataatgtctccttttgttcacgaacttactattgagctaatgtgcacctgttgagctttctcaata------tttggtgatgtcattttgtagGAATTGTCATTAGATTCGTCCCAGCATGTCCGCTCTGCCTTGGCTTCAGTTTTAATGGGAATGGCTCCCGTCTTAGGAAAG
                                           ||   |    | | |   |  || |||| | ||  | | |  ||| ||    ||| ||  |       |||   |   ||| | | |||||||||||| |||||| || |||||||| || || || |||||||||||| | ||||||||||| || ||||| ||||||
-------------------------------------------gtgggccaacgcttaaccaaatattattaa-ctggttttctgctgctgtttattcccagcaaactaacttgccaactgcatct-gcagGAATTGTCATCAGATTCATCTCAGCATGTTCGTTCAGCTTTGGCTTCAGTTATTATGGGAATGGCCCCGGTCTTGGGAAAG

upper sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 6
gtgctcacgtttattaaaagagtgtttctctgtattatataatgtctccttttgttcacgaacttactattgagctaatgtgcacctgttgagctttctcaatatttggtgatgtcattttgtagGAATTGTCATTAGATTCGTCCCAGCATGTCCGCTCTGCCTTGGCTTCAGTTTTAATGGGAATGGCTCCCGTCTTAGGAAAG
                            |  ||   |   |||   || |||||||  | |  ||  |  ||||  |||            | ||   |||     || | ||  |||||  ||||||||||||| |||||| ||||||||||| || || || || || |||||  | |||||||||||||| ||  | ||||||
---------------------------gtgggtgcaaagcaattattcgttttgtt-gctattttttttctgagtgaatt-----------aactagttca-----tgctaattgcattt-atagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTCATTATGGGAATGGCTCCTGTACTGGGAAAG

upper sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 6
gtgctcacgtttattaaaagagtgtttctctgtattatataatgtctccttttgttcacgaacttactattgagctaatgtgcacctgttgagctttctcaatatttggtgatgtcattttgtagGAATTGTCATTAGATTCGTCCCAGCATGTCCGCTCTGCCTTGGCTTCAGTTTTAATGGGAATGGCTCCCGTCTTAGGAAAG
                                       |   | |        ||   ||||  || |||  | |  | |    ||  |||| |   | ||    ||   |   ||| |   |||||||||||| |||||| ||||||||||| || || || || || |||||  | |||||||||||||| ||  | ||||||
--------------------------------------gtgggggcaaagca-attattgaac--accatttcgttgctatttttcttctgag-tgaattaactcatgccaagtgcatct-acagGAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAG

upper sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 6
gtgctcacgtttattaaaagagt------------gtttctctgtat-tatataatgtctccttttgttcacgaacttactattgagc-taatgtgcacctgttgagctttctcaatatttggtgatgtcattttgtagGAATTGTCATTAGATTCGTCCCAGCATGTCCGCTCTGCCTTGGCTTCAGTTTTAATGGGAATGGCTCCCGTCTTAGGAAAG
||   ||  |||   |||  | |            || |  |||  | |||| |  | ||  | ||| |   |      | ||| ||  |  |       | || |    | | | |  || |  |   | ||||| |||||||||||| |||||| || ||||||||||| ||||| |||||||||||  |||||||||||||||| || || ||||||
gtatacatctttggaaaagaaattataacacattagtattactgattatatacagaggcttttcttggttttggttggtcaattcagtatgctaaatttatatttacaggtttaagttctttgaaacaac-ttttgcagGAATTGTCATCAGATTCTTCTCAGCATGTCCGGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAG

upper sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 6
gtgctcacgtttattaaaagagt------------gtttctctgtat-tatataatgtctccttttgttcacgaacttactattgagcta-atgtgcacctgttgagctttctcaatatttggtgatgtcattttgtagGAATTGTCATTAGATTCGTCCCAGCATGTCCGCTCTGCCTTGGCTTCAGTTTTAATGGGAATGGCTCCCGTCTTAGGAAAG
||   ||  |||   |||  | |             | |  |||  | |||| |  | ||    ||| |   |   |  | ||| ||    ||       | || |    | | | |  || |  |   | ||||| |||||||||||| |||||| || ||||||||||| ||||| |||||||||||  |||||||||||||||| || || ||||||
gtatacatctttggaaaagaaattataacacattaatattactgattatatacagaggctttccttggttttggtttgtcaattcagtaggataaatttatatttacaggtttaagttctttgaaacaac-ttttgcagGAATTGTCATCAGATTCTTCACAGCATGTCCGGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAG

upper sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA02G10790.2 (Glycine max), 3'ss of exon 6
gtgctcacgtttattaaaagagtgtttctctgtattatataatgtctccttttgttcacgaacttactattgagctaatgtgcacc-tgttgagctttctcaatatttggtgatgtcattttgtagGAATTGTCATTAGATTCGTCCCAGCATGTCCGCTCTGCCTTGGCTTCAGTTTTAATGGGAATGGCTCCCGTCTTAGGAAAG
                                           || ||  |||| |   |  |||   ||| || || | || |   | || |        |||| || |  |  ||  |||| |||||||||||   ||||| |  |||||||| |||||||| |||||||| ||  |||||||||||||||| || |||||||||
-------------------------------------------gtgtctctttggttttggtcttgaaattcag-tattctgaattatatttacaggctaaaatactttgcaagatc--tttgcagGAATTGTCAACGGATTCTTTGCAGCATGTTCGCTCTGCTTTGGCTTCCGTGATAATGGGAATGGCTCCAGTGTTAGGAAAG

upper sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 6
gtgctcacgtttattaaaagagtgttt-ctctgtattatataatgtctccttttgttcacgaacttactattgagctaatgtgcacctgttgagctttctcaatatttggtgatgtcattttgtagGAATTGTCATTAGATTCGTCCCAGCATGTCCGCTCTGCCTTGGCTTCAGTTTTAATGGGAATGGCTCCCGTCTTAGGAAAG
  |  |||  |||  || || |||||   |   ||||||  || |             || ||  |||| | |         |    || | ||||| |  |  | |               ||||||||| |||| ||| || || ||||| ||| | ||||| ||||| |||||| |||||||||||||||| ||||| || |||
--gtacacacttaagaagagtgtgttgatttcatattatgcaaagg------------accaaaatactgtcg---------gtgtttgctaagcttacctataaatctaca---------cgtagGAATTATCATCAGACTCTTCTCAGCACGTCAGATCTGCATTGGCATCAGTTATAATGGGAATGGCTCCAGTCTTGGGTAAG

upper sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT3G25800.2 (Arabidopsis thaliana), 3'ss of exon 5
gtgctcacgtttattaaaagagtgtttctctgtattatataatgtctccttttgttcacgaacttactattgagctaatgtgcacctgttgagctttctcaatatttggtgatgtcatt--ttgtagGAATTGTCATTAGATTCGTCCCAGCATGTCCGCTCTGCCTTGGCTTCAGTTTTAATGGGAATGGCTCCCGTCTTAGGAAAG
                          |   ||  | | | ||| ||   | || | || |  | |   |   |   || ||  |  |||||    ||    ||  ||  |  |     |   |||||||  | |||| ||| || || ||||||||| | ||||| ||||| |||||| |||||||||||||||| ||||| || |||
-------------------------gtacatgcttaagagaat-tcaattgttttccaagttccttacagaaaatcaacgtatagttgttgcatattactgatgattcctcttaatgctacctgtagGAGCTATCATCAGACTCTTCTCAGCATGTCAGATCTGCATTGGCCTCAGTTATAATGGGAATGGCTCCAGTCTTGGGTAAG

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|71884601|gb|DT033656.1|DT033656
EST:     AGATCTTAAATCCAGAACTTGCAATTCATCATATTCTTCCCTGTGTAAAG                         GAATTGTCATTAGATTCGTCCCAGCATGTCCGCTCTGCCTTGGCTTCAGTT
genomic: AGATCTTAAATCCAGAACTTGCAATTCATCATATTCTTCCCTGTGTAAAGgtgctcacgt ... cattttgtagGAATTGTCATTAGATTCGTCCCAGCATGTCCGCTCTGCCTTGGCTTCAGTT
EST: gi|351038699|gb|FQ464565.1|FQ464565
EST:     AGATCTTAAATCCAGAACTTGCAATTCATCATATTCTTCCCTGTGTAAAG                         GAATTGTCATTAGATTCGTCCCAGCATGTCCGCTCTGCCTTGGCTTCAGTT
genomic: AGATCTTAAATCCAGAACTTGCAATTCATCATATTCTTCCCTGTGTAAAGgtgctcacgt ... cattttgtagGAATTGTCATTAGATTCGTCCCAGCATGTCCGCTCTGCCTTGGCTTCAGTT
EST: gi|71884162|gb|DT033217.1|DT033217
EST:     AGATCTTAAATCCAGAACTTGCAATTCATCATATTCTTCCCTGTGTAAAG                         GAATTGTCATTAGATTCGTCCCAGCATGTCCGCTCTGCCTTGGCTTCAGTT
genomic: AGATCTTAAATCCAGAACTTGCAATTCATCATATTCTTCCCTGTGTAAAGgtgctcacgt ... cattttgtagGAATTGTCATTAGATTCGTCCCAGCATGTCCGCTCTGCCTTGGCTTCAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagctaatgtgcacctgttgagctttctcaatatttggtgatgtcattttgtagGAATTGTCATTAGATTCGTCCCAGCATGTCCGCTCTGCCTTGGCTTCAGTTTTAATGGGAATGGCTCCCGTCTTAGGAAAG
  agctaat  putative branch site (score: 3)
                                            tcatttt  putative PPT
                            tcaatattt  TA-rich tract