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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttttgtaccttcatgcaactaatttttatctttaacaagttatattgattaaaatcaatttatttccaatctcagGATGTTGTAACAGAAAATGAATTTGAGAAAAGGCTTCTAGCTGATGTTATTCCACCATCTGACATTGGGGTCACATTTGATGATATTGGGGCCCTGGAAA

Basic information

species Vitis vinifera
transcript Vv17s0000g01550.t01
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g01550.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 20
-gtaatttttgtaccttcatgc----aactaatttttatctttaacaagtt--------atattgattaaaa-tcaattta--tttccaatctcagGATGTTGTAACAGAAAATGAATTTGAGAAAAGGCTTCTAGCTGATGTTATTCCACCATCTGACATTGGGGTCACATTTGATGATATTGGGGCCCTGGAAA
  || | |   |  | ||||      |||  ||| | ||  | |   ||||        | | || || |   | || |||  ||| |  ||| |||||||||| ||||| || |||||||||||||||||||| || |||||||| |||||   ||||||||| ||||| |||||||||||||| ||| ||||||
gttactctccatctcatcatattgcaaacatattatcatactcacacagttggaatctcacagtgctttactcttaaattactttttccttcttagGATGTTGTCACAGAGAACGAATTTGAGAAAAGGCTTCTGGCAGATGTTATACCACCTAATGACATTGGAGTCACCTTTGATGATATTGGAGCCTTGGAAA

upper sequence: Vv17s0000g01550.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 5
gtaatttttgtaccttcatgcaactaatttttatc-tttaacaagtta--tattgattaaa--atcaatttatttccaatctcagGATGTTGTAACAGAAAATGAATTTGAGAAAAGGCTTCTAGCTGATGTTATTCCACCATCTGACATTGGGGTCACATTTGATGATATTGGGGCCCTGGAAA
|||   | |   |  |  ||  |  | || |  |  ||   |||||||  |  ||| ||    ||  ||  ||      |||||||||||||| ||||| ||||| ||||||||||||||| | || |||||||| || |||  ||||||||| || || |||||||||||||| ||| |||| |
gtacactctcc-caatattgtcatgagttctggtgattcctcaagttagttgctgaatactctatgtataaatcctttttctcagGATGTTGTCACAGAGAATGAGTTTGAGAAAAGGCTTTTGGCAGATGTTATACCTCCAAATGACATTGGAGTTACCTTTGATGATATTGGAGCCTTGGAGA

upper sequence: Vv17s0000g01550.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 11
gtaatttttgtaccttcatgcaactaatttttatc-tttaacaagttatattgattaaaatcaattta----tttccaatctcagGATGTTGTAACAGAAAATGAATTTGAGAAAAGGCTTCTAGCTGATGTTATTCCACCATCTGACATTGGGGTCACATTTGATGATATTGGGGCCCTGGAAA
|||   |      | |  |||      ||||  |  ||   | |||||| |     | | || | |||    |      |||||||||||||| ||||| ||||||||||||||||||||| | |  |||||||| |||||   ||||||||| || || |||||||||||||| ||| |||| |
gtacaatcccctacatattgccgtgctttttggtgattcctcgagttatttactgaacactctacttacaagtcctttttctcagGATGTTGTCACAGAGAATGAATTTGAGAAAAGGCTTTTGGTGGATGTTATACCACCTAATGACATTGGAGTTACCTTTGATGATATTGGAGCCTTGGAGA

upper sequence: Vv17s0000g01550.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA17G13850.1 (Glycine max), 3'ss of exon 18
------------gtaatttttgtaccttcatg-caactaatttttatctttaacaagttatattga---------ttaaaatcaatttatttccaatc-----------tcagGATGTTGTAACAGAAAATGAATTTGAGAAAAGGCTTCTAGCTGATGTTATTCCACCATCTGACATTGGGGTCACATTTGATGATATTGGGGCCCTGGAAA
            |   ||||  ||| | | || |     |  |||   | | | |||||||  ||          | | || || | |||||  ||||           |||||||||||| ||||||||||||||||| || |||||| | |||||||||||||||||   ||||||||  || || |||||||||||||| || || ||||
gtgattgtttgtgcccttttgctacttacgtgtcgttccagctttgcttattagaagttattctgtcaggagagttcataaacactgtattttaaatcgttttgcttgctcagGATGTTGTGACAGAAAATGAATTTGAAAAGAGGCTTTTGGCTGATGTTATTCCACCTAGTGACATTGATGTTACTTTTGATGATATTGGAGCTCTTGAAA

upper sequence: Vv17s0000g01550.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 3
--------------------------------------------------------------------------------gtaatttttgtaccttcatgcaactaatttttatctttaacaagttatattgattaaaatcaattta--tttccaatctcagGATGTTGTAACAGAAAATGAATTTGAGAAAAGGCTTCTAGCTGATGTTATTCCACCATCTGACATTGGGGTCACATTTGATGATATTGGGGCCCTGGAAA
                                                                                || ||| |  |       |  ||   |||| | || | ||     | |  ||| | |   |  ||    |||   |  ||||||||||||||||||||| || ||||| || |||||| | |||||||||||||||||   ||||||||| || || |||||||||||||| || || ||||
gtgattgttatggacttttgctgctttgattgtgagagatagtgacatccagtagtttgttcccaacttactgcttggaagttattctgttgatagagtttaatcgatttatttcatgaatgttgtgttctgaattatccctcttatgttttttgaaatcagGATGTTGTAACAGAAAACGAGTTTGAAAAGAGGCTTTTGGCTGATGTTATTCCACCTAATGACATTGGTGTTACTTTTGATGATATTGGAGCTCTTGAAA

upper sequence: Vv17s0000g01550.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA05G03270.1 (Glycine max), 3'ss of exon 16
------------gtaatttttgtaccttcatgcaacta-atttttatctttaacaagttatattga---------ttaaaatcaatttatttccaatc-----------tcagGATGTTGTAACAGAAAATGAATTTGAGAAAAGGCTTCTAGCTGATGTTATTCCACCATCTGACATTGGGGTCACATTTGATGATATTGGGGCCCTGGAAA
            |   ||||  ||| | ||||  | |  |  |||   | | |||||||||  ||          | | || || | ||||   ||||           |||||||||||| ||||||||||||||||| || |||||| | |||||||||||||||||   |||||| |  || || |||||||||||||| || || ||||
gtgattgtttgtgcccttttgctacttacatgtgattccagctttgcttattacaagttattctgtcgggagagttcataaacactgtattctaaatcattttgcttgctcagGATGTTGTGACAGAAAATGAATTTGAAAAGAGGCTTTTGGCTGATGTTATTCCACCTAGTGACATCGATGTTACTTTTGATGATATTGGAGCTCTTGAAA

upper sequence: Vv17s0000g01550.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA06G17940.1 (Glycine max), 3'ss of exon 20
-------------------------------------------------------------------------------------gtaatttttgtaccttcatgcaactaatttttatctttaacaagttatattgattaaaatcaattt--atttccaatctcagGATGTTGTAACAGAAAATGAATTTGAGAAAAGGCTTCTAGCTGATGTTATTCCACCATCTGACATTGGGGTCACATTTGATGATATTGGGGCCCTGGAAA
                                                                                     || ||| |  |       |  ||  ||||||| ||   ||     | | |||| | |   |  ||    |||   |  ||||||||||||||||||||| || ||||| || |||||| | |||||||||||||||||    |||||||| || || || ||||||||||| || || ||||
gtgattgttatggagttttgctactttgattgtgggagatagtgacatgacatccagtagtttgttccgaacttactgcttggaagttattctgttgatagagtttaatcaatttttttcacgaatgctgtgttttgaattatccctcttatgttttttgaaatcagGATGTTGTAACAGAAAACGAGTTTGAAAAGAGGCTTTTGGCTGATGTTATTCCACCTAACGACATTGGTGTTACTTTCGATGATATTGGAGCTCTTGAAA

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|37186767|gb|CF606120.1|CF606120
EST:     TTCAGGCTATTCAGAATGAGTCTAAGAGCTTGAAGAAGTCACTCAAG                         GATGTTGTAACAGAAAATGAATTTGAGAAAAGGCTTCTAGCTGATGTTATT
genomic: TTCAGGCTATTCAGAATGAGTCTAAGAGCTTGAAGAAGTCACTCAAGgtaatttttg ... ccaatctcagGATGTTGTAACAGAAAATGAATTTGAGAAAAGGCTTCTAGCTGATGTTATT
EST: gi|30255057|gb|CB971504.1|CB971504
EST:     TTCTTCAGGCTATTCAGAATGAGTCTAAGAGCTTGAAGAAGTCACTCAAG                         GATGTTGTAACAGAAAATGAATTTGAGAAAAGGCTTCTAGCTGATGTTATT
genomic: TTCTTCAGGCTATTCAGAATGAGTCTAAGAGCTTGAAGAAGTCACTCAAGgtaatttttg ... ccaatctcagGATGTTGTAACAGAAAATGAATTTGAGAAAAGGCTTCTAGCTGATGTTATT
EST: gi|110720420|gb|EE096327.1|EE096327
EST:     TTCTTCAGGCTATTCAGAATGAGTCTAAGAGCTTGAAGAAGTCACTCAAG                         GATGTTGTAACAGAAAATGAATTTGAGAAAAGGCTTCTAGCTGATGTTATT
genomic: TTCTTCAGGCTATTCAGAATGAGTCTAAGAGCTTGAAGAAGTCACTCAAGgtaatttttg ... ccaatctcagGATGTTGTAACAGAAAATGAATTTGAGAAAAGGCTTCTAGCTGATGTTATT
EST: gi|110711745|gb|EE088578.1|EE088578
EST:     TTCTTCAGGCTATTCAGAATGAGTCTAAGAGCTTGAAGAAGTCACTCAAG                         GATGTTGTAACAGAAAATGAATTTGAGAAAAGGCTTCTAGCTGATGTTATT
genomic: TTCTTCAGGCTATTCAGAATGAGTCTAAGAGCTTGAAGAAGTCACTCAAGgtaatttttg ... ccaatctcagGATGTTGTAACAGAAAATGAATTTGAGAAAAGGCTTCTAGCTGATGTTATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttttatctttaacaagttatattgattaaaatcaatttatttccaatctcagGATGTTGTAACAGAAAATGAATTTGAGAAAAGGCTTCTAGCTGATGTTATTCCACCATCTGACATTGGGGTCACATTTGATGATATTGGGGCCCTGGAAA
                                      tttatttcc  CT-rich tract
     ttatctttaacaagtt  TA-rich tract