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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagtcaacatcatgaatgtttgttagcaacttgtttgattacattaattagtagttcaagttgtgtgatattttctatgtttatgattgcagTATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATATGGTCAGACTGGTTCTGGAAAGACATTCACAATTTATGGTTCTGATGGTA

Basic information

species Vitis vinifera
transcript Vv04s0044g02020.t01
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: LOC_Os04g57140.2 (Oryza sativa), 3'ss of exon 18
gcaag-tcaacatcatgaatgtttgttagca-acttgt-ttgattacattaattagtagttcaagttgtgtgatattttctatgtttatgattgcagTATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATATGGTCAGACTGGTTCTGGAAAGACATTCACAATTTATGGTTCTGATGGTA
|  |  |     | |  | |  || ||| || || |||  | |||| |||| ||   | |  |     |||| |  |    |  ||| |||| ||||||| | ||||||||||| || |||||||||||||| || |||||||| ||||| || |||||||||||||| || || ||||||||||| |||||    |
gtgaccttttttttaacacttctttttaacatacatgtgctcattagattatttgcaattggactccatgtgtttatcatgaattttgtgat-gcagTATCTAGTTCAATCGGCCGTTGATGGATATAATGTTTGTATATTTGCTTATGGGCAAACTGGTTCTGGAAAAACTTTTACAATTTATGGATCTGAAAACA

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GRMZM2G423861_T02 (Zea mays), 3'ss of exon 17
---------gcaagtcaacatcatgaatgtt-----tgttagcaacttg--tttgattacattaattagtagttcaag---ttgtgtgatattttctatgtttatgattgcagTATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATATGGTCAGACTGGTTCTGGAAAGACATTCACAATTTATGGTTCTGATGGTA
          ||| |    ||| |   ||||       | || ||  |   ||| ||| |    | |  |   | | |   |  | |||| | ||  || | | |||| ||||||  |||| ||||| ||||| ||||||||||| || |||||||||||||||||||| ||||||||||||||||| ||||| ||||||||||| |||   |
gtgaatatttcaaat-gctatcttttgtgttgatgccatcagtaatataaattttatttctaggactgttcactgagggtttcatatgatgtgttgaatttatgtgat-gcagTACCTGGTACAATCAGCTGTTGATGGATATAACGTTTGCATATTTGCATATGGTCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGATAACA

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GRMZM2G070273_T01 (Zea mays), 3'ss of exon 17
----------------------------------------gcaagtcaacatc---atgaatgtttgttagca--acttgtttgattacattaattagtagttcaagttgtgtgatattttctatgtttatg-attgcagTATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATATGGTCAGACTGGTTCTGGAAAGACATTCACAATTTATGGTTCTGATGGTA
                                        | ||  |||  |     |  | | ||||| ||   |  || |   ||  ||| ||    | ||   |||   |   || |  |   ||||||   |||||||| |||| ||||| ||||| |||||||||||||| || |||||||| ||||| || ||||||||||||||||| ||||| ||||||||||| ||    |
gtgaatatttcaaatgctatcttttgtgttgatgccgtcggtaatacaaattttatttctaagattgttggcttcatatgatctgttgaatttatgttcattttgggtttcatatgatctgttgaatttatgtgatgcagTATCTGGTACAATCAGCTGTTGATGGATATAATGTCTGTATATTTGCGTATGGCCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGAAAACA

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA16G21340.1 (Glycine max), 3'ss of exon 22
gcaagtcaacatcatgaatgtttgttagcaacttgtttgattacattaattagtagttcaagttgtgtgatattttctatgtttatgattgcagTATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATATGGTCAGACTGGTTCTGGAAAGACATTCACAATTTATGGTTCTGATGGTA
||||||||   | |    | ||| ||     ||| |   |  | ||  || | |    |   ||     || | |  | | |||   || |||||||||||| ||||| ||||||||||| |||||||| ||||||||||| |||||||| ||||| |||||||||||||| ||||| ||||| || ||    |
gcaagtca---taaattgtatttatttcttgcttatggaaacatat--ataacttacactcattac-caatttctcgtgtatttgcaat-gcagTATTTGGTGCAATCTGCTGTAGATGGTTATAATGTTTGCATATTTGCTTATGGTCAAACTGGATCTGGAAAGACATTTACAATCTATGGATCGGACATCA

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA09G32740.1 (Glycine max), 3'ss of exon 19
------------gcaagtcaacatcatgaatgtttgttagcaacttgttt--gattacattaattagtagttcaagttgtgtgatattttctatgtttatgattgcagTATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATATGGTCAGACTGGTTCTGGAAAGACATTCACAATTTATGGTTCTGATGGTA
             |||    |  ||||  ||   | ||     |||||||  |   ||||  || | |    |   || |   || | |  |   |||   || |||||||||||| || || ||||||||||| |||||||| ||||||||||| |||||||| ||||| |||||||||||||| ||||| ||||| |||||    |
gtatttgaggatacaaaggcaagtcatttat-catatttatttcttgtttatgggaacatatataacttacactcattat-caatttctcgtggatttgcaat-gcagTATTTGGTGCAGTCTGCTGTAGATGGTTATAATGTTTGCATATTTGCCTATGGTCAAACTGGCTCTGGAAAGACATTTACAATCTATGGATCTGACAACA

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA01G35950.1 (Glycine max), 3'ss of exon 19
-----------gcaagtca-acatcatgaatgtttgtt------agca-acttgtttgattacattaattagtagttcaagttgt--gtgatattttctatgt-----ttatgattgcagTATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATATGGTCAGACTGGTTCTGGAAAGACATTCACAATTTATGGTTCTGATGGTA-------
            ||| | | | |||||   | |||| |      |||| |    ||  | |  ||| | || |  ||  | |  |     || ||||   | |     ||   | ||||||| || || ||||| ||||| ||||| |||||||| ||||||||||| |||||||| ||||||||||||||||| || ||||| |||||   |||    |       
gtcttagtataacaaattatagatcatagttttttgctttagatagcatatacattgaaatggatttaatattttttatactcattaccaatgtttttcttttggaaatttgcaatgcagtacttagTGCAATCTGCTGTGGATGGTTATAATGTTTGCATATTTGCTTATGGTCAAACTGGTTCTGGAAAGACTTTTACAATCTATGGAGTTGAAAACAATCCTGG

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA11G09480.1 (Glycine max), 3'ss of exon 19
---------------gcaagtcaac-atcatgaatgtttgtt---agcaacttgt----ttgattacattaattagtagttcaagttgtgtgatattttctatgtttatgat--------tgcagTATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATATGGTCAGACTGGTTCTGGAAAGACATTCACAATTTATGGTTCTGATGGTA
                ||| | ||  ||| |   | |||| |      ||  |||    |  | || ||| | || |  |  |   |   |  || | | | | |||  ||         ||||||| || || ||||| ||||||||||| |||||||| ||||||||||| || ||||| ||||||||||| ||||| || ||||| |||||  ||||    |
gcaagtcttagtataacaaattaaagatcctagttttttgctttagataatatgtacattgaaatagatttaatatttttctatactcattactaatgtttttcttttggacatttgcaatgcagTACTTAGTGCAATCTGCTGTAGATGGTTATAATGTTTGCATATTTGCTTACGGTCAAACTGGTTCTGGGAAGACTTTTACAATCTATGGAGCTGAAAACA

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: AT5G65930.3 (Arabidopsis thaliana), 3'ss of exon 16
gcaagtcaacatcatgaatgtttgttagcaacttgtttgattacattaattagtagttcaagttgtgtgatattttctatgtttatgattgcagTATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATATGGTCAGACTGGTTCTGGAAAGACATTCACAATTTATGGTTCTGATGGTA
          || ||  || | |    |       ||   || |||   ||  || ||     ||  |  ||   ||  | ||  |  |  ||||||||||| || |||||||||||||| ||||| || ||||| |||||||||||||| |||||||||||||| || ||||| || |||||   |||  | |
--------gtattattgatatgtaactgtgttcatttacctttcatcctttgttattttcttgtggttactaacatc-gttttccttttaacagTATTTGGTACAGTCGGCTGTAGATGGGTATAACGTTTGCATCTTTGCATATGGTCAAACTGGTTCTGGAAAAACTTTCACTATATATGGGCATGAGAGCA

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: EFJ06058 (Selaginella moellendorffii), 3'ss of exon 18
gcaagtcaacatcatgaatgtttgttagcaacttgtttgattacattaattagtagttcaagttgtgtgatattttctatgtt-tatgattgcagTATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATATGGTCAGACTGGTTCTGGAAAGACATTCACAATTTATGGTTCTGATGGTA
                                            | | ||   |  || | ||| | |  |   |   ||||| ||| ||  ||||||||||| |||||||| || || ||||| || |||||||| || || |||||||| ||||| || || || ||||| ||||| |||||| | ||   ||
------------------------------------------gtaatgatgtctctttgacgttattttgttactaacatgttctatcatc-cagTATTTGGTGCAATCGGCAGTCGACGGATACAACGTGTGCATTTTCGCTTATGGTCAAACTGGGTCCGGCAAAACATTTACAATATATGGTCCGGAAAATA

upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: EFJ30174 (Selaginella moellendorffii), 3'ss of exon 18
gcaagtcaacatcatgaatgtttgttagcaacttgtttgattacattaattagtagttcaagttgtgtgatattttctatgtttatgattgcagTATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATATGGTCAGACTGGTTCTGGAAAGACATTCACAATTTATGGTTCTGATGGTA
                                            | | ||   || || | ||| | |  |   |   |||||      | ||||||||||| |||||||| || || ||||| || |||||||| || || |||||||| ||||| || || || ||||| ||||| |||||| | ||   ||
------------------------------------------gtaatgatgtctatttgacgttattttgttactaacatgttctgtcatccagTATTTGGTGCAATCGGCAGTCGACGGATACAACGTGTGCATTTTCGCTTATGGTCAAACTGGGTCCGGCAAAACATTTACAATATATGGTCCGGAAAATA

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|351015272|gb|FQ445556.1|FQ445556
EST:     ATGTGTTTGGTGGTAGTGCCACTCAAGAAGATGTGTTTGAGGATACAAGG                         TATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATAT
genomic: ATGTGTTTGGTGGTAGTGCCACTCAAGAAGATGTGTTTGAGGATACAAGGgcaagtcaac ... atgattgcagTATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATAT
EST: gi|351043062|gb|FQ443904.1|FQ443904
EST:     ATGTGTTTGGTGGTAGTGCCACTCAAGAAGATGTGTTTGAGGATACAAGG                         TATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATAT
genomic: ATGTGTTTGGTGGTAGTGCCACTCAAGAAGATGTGTTTGAGGATACAAGGgcaagtcaac ... atgattgcagTATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATAT
EST: gi|351026499|gb|FQ428511.1|FQ428511
EST:     ATGTGTTTGGTGGTAGTGCCACTCAAGAAGATGTGTTTGAGGATACAAGG                         TATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATAT
genomic: ATGTGTTTGGTGGTAGTGCCACTCAAGAAGATGTGTTTGAGGATACAAGGgcaagtcaac ... atgattgcagTATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attacattaattagtagttcaagttgtgtgatattttctatgtttatgattgcagTATTTGGTTCAATCGGCTGTAGATGGATATAATGTGTGCATATTTGCATATGGTCAGACTGGTTCTGGAAAGACATTCACAATTTATGGTTCTGATGGTA
    cattaat  putative branch site (score: 3)
                              atattttctatgttta  TA-rich tract