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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaatgtgcgtaagcttaatagtaacaagggtgttgaagttttcttatttttgtgtgtgtctcttcccttgcagATCCCAATCAAGTGGCCAAAAAGCAGAGATGAAGTATGGAAAGCAAACATACCTCATACTCACCTTGCACATGAGAAATCTGACCAGAATTGGATGGTTG

Basic information

species Vitis vinifera
transcript Vv05s0049g01180.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0049g01180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os10g33720.1 (Oryza sativa), 3'ss of exon 3
---------------------------gtgagaatgtgcgtaagcttaatagtaacaagggtgttgaagttttcttatttttgtgtgtgtctcttcccttgcagATCCCAATCAAGTGGCCAAAAAGCAGAGATGAAGTATGGAAAGCAAACATACCTCATACTCACCTTGCACATGAGAAATCTGACCAGAATTGGATGGTTG
                              | |||||    |||    |  ||   |    |  |  |   |  ||    |  |     |   |  | |||||| | || || || |||||||||||  | |||   || ||||||||||| || || || |||||||||||||||||||| || ||||||||||||||| |||
tctgttccgtccaatctatgcctttcaaaaaaaatgttttcaagtgctaatgtcctatccttactaca-cctcattggactcataaaaat---tgactttgcagGTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATTCCGCACACTCACCTTGCACATGAGAAGTCAGACCAGAATTGGATGATTG

upper sequence: Vv05s0049g01180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G575696_T01 (Zea mays), 3'ss of exon 1
----------------gtgagaatgtgcgta-agcttaatagtaacaagggt--gttgaagtttt-cttatttttgt---gtgtgtctcttcccttgcagATCCCAATCAAGTGGCCAAAAAGCAGAGATGAAGTATGGAAAGCAAACATACCTCATACTCACCTTGCACATGAGAAATCTGACCAGAATTGGATGGTTG
                |  ||| ||  | |  |   ||| | ||     | |   ||| |   || || |  | | |    |     | ||   || ||| |||| || || |||||||||||  | |||| |||||||||||||||||| || || |||||||||||| | ||||| || |||||||| ||||||||||
taataacacgtgccctgacagactgaccttccaatctaaaattagttctgtttgattgcatccttgctgagctgtatccgatccacatttttttttccagGTCCCCATAAAATGGCCAAAAAGTCGTGATGTAGTATGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG

upper sequence: Vv05s0049g01180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G107629_T03 (Zea mays), 3'ss of exon 4
--------------gtgagaatgtgcgtaagcttaatagtaacaagggtgttgaa--gttttcttattt--ttgtgtgtgtctc-----ttcccttgcagATCCCAATCAAGTGGCCAAAAAGCAGAGATGAAGTATGGAAAGCAAACATACCTCATACTCACCTTGCACATGAGAAATCTGACCAGAATTGGATGGTTG
               ||| |   ||      ||   |   |  |    ||||  |  |  | |||  |    ||| |  | | |     ||   || ||| |||| || || |||||||||||  | |||| |||||||||||||||||| || || |||||||||||| | ||||| || |||||||| ||||||||||
taataacacgtgccctgacagactgaccttcctatctgaaattagttctgtttgattgcatccttgctgagctgtatccgacccacaattttttttccagGTCCCTATAAAATGGCCAAAAAGTCGTGATGTAGTATGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG

upper sequence: Vv05s0049g01180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G067764_T02 (Zea mays), 3'ss of exon 3
----------------------gtgagaatgtgcgtaagcttaat-agtaacaagggtgttgaagttttcttatttttgtgtgtgtctcttcccttgcagATCCCAATCAAGTGGCCAAAAAGCAGAGATGAAGTATGGAAAGCAAACATACCTCATACTCACCTTGCACATGAGAAATCTGACCAGAATTGGATGGTTG
                         |  || | |  |     ||| |||       |  | ||   || || | || | |  |   | ||    || ||| | || || || |||||||||||  | |||| ||| |||||||||||||| || || |||||||||||| | ||||| || |||||||| ||||||||||
ggtttaacacgtccactgaccttccactatatactcatctgaaattagttctgtttgaatggatccttgctgagttgtatcagatccactattttttcagGTTCCTATAAAATGGCCAAAAAGTCGTGATGTAGTGTGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG

upper sequence: Vv05s0049g01180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA10G32470.1 (Glycine max), 3'ss of exon 3
-----------gtgagaatgtgcgtaagcttaatagta---------acaagggtgttgaagttttcttatttttgtgtgtgtctcttcccttgcagATCCCAATCAAGTGGCCAAAAAGCAGAGATGAAGTATGGAAAGCAAACATACCTCATACTCACCTTGCACATGAGAAATCTGACCAGAATTGGATGGTTG
            | ||| | |  || | ||| |    |         |||   || ||    |  ||  |  ||||| ||| ||| |    |||||| |||| || ||||||||| ||||||||||||| |||||||||||||| || || ||||||||||||||||| ||||||||||||||||||||||||||||
gtgaaaatttgctaagagtatatgtgatcttcaacacaccctctgatacatatgtattattttagtccaacatttgt-tgtttctataatgttgcagGTCCCTATTAAGTGGCCACAAAGCAGAGATGAGGTATGGAAAGCAAATATCCCACATACTCACCTTGCACACGAGAAATCTGACCAGAATTGGATGGTTG

upper sequence: Vv05s0049g01180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA20G35120.4 (Glycine max), 3'ss of exon 3
gtgagaatgtgcgtaagcttaatagtaacaagggtgt----tgaagttttcttatttttgtgtgtgtctcttcccttgcagATCCCAATCAAGTGGCCAAAAAGCAGAGATGAAGTATGGAAAGCAAACATACCTCATACTCACCTTGCACATGAGAAATCTGACCAGAATTGGATGGTTG
|||| ||| |||  |   |  ||   | |     | |    |    |  |  | |  |||| ||| | | |    |||||| | || || ||||||||| ||||||||||||| || ||||||||||| || || ||||||||||||||||| ||||| ||||||||||||||||||  ||
gtgaaaatttgctaagagtatatgtgatcttcaatatactctctgatactgatgtaattgt-tgtttatataatgttgcagGTTCCTATTAAGTGGCCACAAAGCAGAGATGAGGTGTGGAAAGCAAATATCCCACATACTCACCTTGCACACGAGAAGTCTGACCAGAATTGGATGACTG

upper sequence: Vv05s0049g01180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA10G00880.2 (Glycine max), 3'ss of exon 3
------------------------------------gtgagaatgtgc--gtaagcttaatagtaacaagggtgttgaagttttcttatttttgtgtgtgtctcttcccttgcagATCCCAATCAAGTGGCCAAAAAGCAGAGATGAAGTATGGAAAGCAAACATACCTCATACTCACCTTGCACATGAGAAATCTGACCAGAATTGGATGGTTG
                                     | |  || | |  || |    | | ||| || |    |    || |  | |||| ||| |    || |    |||||| |||| || ||||||||| | ||||||||||| || ||||||||||| || || || || ||||||||||||||||| ||||||||||| |||||| |||
gtaaagaatatgccgagactagatgcgatcttaaacatcaacatatcctcgttaatacatttgtatcatgttcatcagtgtctaataatttctgttt----ctatggtgttgcagGTCCCTATTAAGTGGCCACAGAGCAGAGATGAGGTGTGGAAAGCAAATATTCCACACACACACCTTGCACATGAGAAGTCTGACCAGAACTGGATGATTG

upper sequence: Vv05s0049g01180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA02G00550.1 (Glycine max), 3'ss of exon 2
------------------------gtgagaatgtgcgtaagctta---atagtaacaagggtgttgaagttttcttatttt-------tgtgtgtgtctcttcccttgcagATCCCAATCAAGTGGCCAAAAAGCAGAGATGAAGTATGGAAAGCAAACATACCTCATACTCACCTTGCACATGAGAAATCTGACCAGAATTGGATGGTTG
                        ||||   |   | | | | ||     | ||| |    |||  || |||    ||  |       |   ||| ||| |    || |||||||| || ||||||||| | ||||||||||| || ||||||| ||| || || || |||||||||||||| ||||| ||||||||||| |||||| |||
gtaaagaatatgccgagactcgatgtgatcttcaacttcaacatatcctcattaatacatttgtataattttgtcaatgctaaaacaattgttgtttctatggtgtttcagATCCCTATTAAGTGGCCACAGAGCAGAGATGAGGTGTGGAAAGTAAATATTCCACACACTCACCTTGCACACGAGAAGTCTGACCAGAACTGGATGATTG

upper sequence: Vv05s0049g01180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT4G14360.2 (Arabidopsis thaliana), 3'ss of exon 3
----gtgagaatgtgcgtaagcttaatagtaacaagggtgttgaagttttcttatttttgtgtgtgtctcttcccttgcagATCCCAATCAAGTGGCCAAAAAGCAGAGATGAAGTATGGAAAGCAAACATACCTCATACTCACCTTGCACATGAGAAATCTGACCAGAATTGGATGGTTG
     |    || ||    |   |  ||   | | |  |  | | | |  | ||  | | |     ||   |   ||  || | || || || ||||||||||||||||||||||| |||||||  ||||||||||||||||| |||||||||||||| |||||||| || ||||||||||
gtgtctatcgatatgttatacagttttatcgatatgattagttacgatgacataactgttttctcttccaatatgttttagGTTCCGATTAAATGGCCAAAAAGCAGAGATGAAGTGTGGAAAGTGAACATACCTCATACTCATCTTGCACATGAGAAGTCTGACCAAAACTGGATGGTTG

upper sequence: Vv05s0049g01180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G04430.1 (Arabidopsis thaliana), 3'ss of exon 3
------------------------gtgagaatgtgcgtaagcttaatagtaacaagggtgttgaagttttcttatttttgtgtgtgtctcttcccttgcagATCCCAATCAAGTGGCCAAAAAGCAGAGATGAAGTATGGAAAGCAAACATACCTCATACTCACCTTGCACATGAGAAATCTGACCAGAATTGGATGGTTG
                        |     || || |   | ||  | || |||  | | ||||  || | || || ||   ||| |   ||  | |  || | || || |||||||| || || ||||||||||| |||||||||||||||||||| |||||||||||| | ||||| ||||| ||||| ||||||||||
gtgctatatttgctttcttgttttgctttgatttgtgattggttcctggttacattg-tcttgatattgttttgttctt---tgtattgatttgcgtttagGTTCCTATTAAGTGGCCTAAGAGTAGAGATGAAGTGTGGAAAGCAAACATACCTCACACTCACCTTGCAAAAGAGAAGTCTGATCAGAACTGGATGGTTG

upper sequence: Vv05s0049g01180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT3G23300.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgagaatgtgcgtaagcttaatag---taacaagggtgttgaagttttcttatttttgtgtgtgtctcttcccttgcagATCCCAATCAAGTGGCCAAAAAGCAGAGATGAAGTATGGAAAGCAAACATACCTCATACTCACCTTGCACATGAGAAATCTGACCAGAATTGGATGGTTG
||| |    | |   |||||  | |   | |  || || ||||  | || | |  ||| | | | | |       |  |||| |||||||||||||| ||||||||||| ||||| |||||||  ||||| |||||||||||| | || |||||||| |||||||| || ||||||||||
gtgtgttatttctctagctttgttgatatgatcagtgtcttgacatattttgaagtttttttctatgtgaatgtgtctagATTCCAATCAAGTGGCCGAAAAGCAGAGACGAAGTTTGGAAAGTGAACATTCCTCATACTCACTTAGCGCATGAGAAGTCTGACCAAAACTGGATGGTTG

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|110384343|gb|EC948773.1|EC948773
EST:     TTCCTGAGAGGCGGTACAATTGCTTGATTCCTCCACCAGCAGGGTACAAG                         ATCCCAATCAAGTGGCCAAAAAGCAGAGATGAAGTATGGAAAGCAAACATA
genomic: TTCCTGAGAGGCGGTACAATTGCTTGATTCCTCCACCAGCAGGGTACAAGgtgagaatgt ... tcccttgcagATCCCAATCAAGTGGCCAAAAAGCAGAGATGAAGTATGGAAAGCAAACATA
EST: gi|161710886|gb|FC058577.1|FC058577
EST:     ACCAGCAGGGTACAAG                         ATCCCAATCAAGTGGCCAAAAAGTAGAGATGAAGTATGGAAAGCAAACATA
genomic: ACCAGCAGGGTACAAGgtgagaatgt ... tcccttgcagATCCCAATCAAGTGGCCAAAAAGCAGAGATGAAGTATGGAAAGCAAACATA
EST: gi|110724467|gb|EE100319.1|EE100319
EST:     TTCCTGAGAGGCGGTACAATTGCTTGATTCCTCCACCAGCAGGGTACAAG                         ATCCCAATCAAGTGGCCAAAAAGTAGAGATGAAGTATGGAAAGCAAACATA
genomic: TTCCTGAGAGGCGGTACAATTGCTTGATTCCTCCACCAGCAGGGTACAAGgtgagaatgt ... tcccttgcagATCCCAATCAAGTGGCCAAAAAGCAGAGATGAAGTATGGAAAGCAAACATA
EST: gi|110357412|gb|EC920933.1|EC920933
EST:     TTCCTGAGAGGCGGTACAATTGCTTGATTCCTCCACCAGCAGGGTACAAG                         ATCCCAATCAAGTGGCCAAAAAGCAGAGATGAAGTATGGAAAGCAAACATA
genomic: TTCCTGAGAGGCGGTACAATTGCTTGATTCCTCCACCAGCAGGGTACAAGgtgagaatgt ... tcccttgcagATCCCAATCAAGTGGCCAAAAAGCAGAGATGAAGTATGGAAAGCAAACATA
EST: gi|110722017|gb|EE097877.1|EE097877
EST:     TCCTGAGAGGCGGTACAATTGCTTGATTCCTCCACCAGCNAGG-TACAAG                         ATCCCAATCAAGTGGCCAAAAAGTAGAGATGAAGTATGGAAAGCAAACATA
genomic: TCCTGAGAGGCGGTACAATTGCTTGATTCCTCCACCAGC-AGGGTACAAGgtgagaatgt ... tcccttgcagATCCCAATCAAGTGGCCAAAAAGCAGAGATGAAGTATGGAAAGCAAACATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtaacaagggtgttgaagttttcttatttttgtgtgtgtctcttcccttgcagATCCCAATCAAGTGGCCAAAAAGCAGAGATGAAGTATGGAAAGCAAACATACCTCATACTCACCTTGCACATGAGAAATCTGACCAGAATTGGATGGTTG
                                    tgtgtctcttccctt  CT-rich tract
                 aagttttcttattttt  TA-rich tract