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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggattgaaattttgataaaacattaatttcttctgtttggtttttttttttctttcctaaatttctctacttcaaaattcaactcctaaatctaatcacctcatttgcagGTCTTCATTGTTCTATCTTGCCTGATATCTGTTTCTGTAAACTTCAGTACATTTCTAGTTATTGGGAAGACATCTCCTGTAACATACCAGGTCCTGGGAC

Basic information

species Vitis vinifera
transcript Vv06s0004g07960.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g07960.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G063253_T08 (Zea mays), 3'ss of exon 5
gtgaggattgaaattttgataaaacattaatttcttctgtttggtttttttttttctttcctaaatttctctacttcaaaattcaactcctaaatctaatcacctcatttgcagGTCTTCATTGTTCTATCTTGCCTGATATCTGTTTCTGTAAACTTCAGTACATTTCTAGTTATTGGGAAGACATCTCCTGTAACATACCAGGTCCTGGGAC
                         | || |      | ||||||    || |  |       | |||| | |  |   ||||   ||| ||            ||   ||||| | ||||| || || || ||| ||||||||||||| || |||||||| || || || || || || |||||||||||||| || ||||| |||||||| |
----------------------gtgagtagtaaaacatctttggtgcacttatcccaac----agtttcaccatattctaatttttctctta----------tttcgcatgcagTTTTTCATCGTCCTGTCATGCTTGATATCTGTTTCAGTGAACTTCAGCACTTTCCTTGTGATCGGAAAGACATCTCCTGTTACTTACCAAGTCCTGGGCC

upper sequence: Vv06s0004g07960.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G063511_T02 (Zea mays), 3'ss of exon 6
gtgaggattgaaattttgataaaacattaatttcttctgtttggtttttttttttctttcctaaatttctctacttcaaaattcaactcctaaatctaatc--acctcatttgcagGTCTTCATTGTTCTATCTTGCCTGATATCTGTTTCTGTAAACTTCAGTACATTTCTAGTTATTGGGAAGACATCTCCTGTAACATACCAGGTCCTGGGAC
                                        |||       | |||  | |  | ||  ||  | ||   |  |||    |||| | |  ||  |  |  | ||||| | ||||||||  | || ||||||||||| || || || |||||||| || ||||| || ||||| ||||| |||||||| || ||||| |||||||| |
-----------------------------------gtgagttgcaaaacatctttggtgcacatatccctacagtttcca--tcacactctaagttttctcttattttgtgtgcagTTTTTCATTGTGTTGTCATGCCTGATATCGGTCTCAGTGAACTTCAGCACTTTTCTTGTGATTGGAAAGACGTCTCCTGTTACTTACCAAGTCCTGGGCC

upper sequence: Vv06s0004g07960.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G116053_T01 (Zea mays), 3'ss of exon 6
gtgaggattgaaattttgataaaacattaatttcttctgtttggtttttttttttctttcctaaatttctctacttcaaaattcaactcctaaatctaatcacctcatttgcagGTCTTCATTGTTCTATCTTGCCTGATATCTGTTTCTGTAAACTTCAGTACATTTCTAGTTATTGGGAAGACATCTCCTGTAACATACCAGGTCCTGGGAC
                     || |||||       || |  ||  |||   ||   |  | | ||  ||| |  | |  ||    || |   || |  |  ||||   ||||| | ||||| || || || |||||||| || || || || |||||||| || ||||| || || |||||||| ||||||||||| ||||| ||||| || |
-------------------gtaagcattagaccaggctttggggagtttgcgttaactgtcgatatcgctccatctgatcatgggtctgc---atttg-ttgcctc---tgcagTTTTTCATCGTGCTGTCGTGCCTGATTTCAGTCTCGGTGAACTTCAGCACTTTTCTCGTGATCGGGAAGACGTCTCCTGTAACCTACCAAGTCCTTGGCC

upper sequence: Vv06s0004g07960.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT1G06890.2 (Arabidopsis thaliana), 3'ss of exon 6
gtgaggattgaaattttgataaaacattaatttcttctgtttggtttttttttttctttcctaaatttctctacttcaaaattcaactcctaaatctaatcacctcatttgcagGTCTTCATTGTTCTATCTTGCCTGATATCTGTTTCTGTAAACTTCAGTACATTTCTAGTTATTGGGAAGACATCTCCTGTAACATACCAGGTCCTGGGAC
|||||  |  |  |   |   |  |    |    |  |   || | || ||  |||  |    |   |   || |    | |    || ||   |  |          |||||| ||||||| || || |||||||| ||||| || |||||||||||||| |||||||| || ||||| || ||||||||||| ||||| ||||| || ||||
gtgagactcaatttcccggggattctaccaaacttattaactgatcttcttgcttccatgtcgatcctgcatattaacgagt---gcttctttgttga----------ttgcagTTCTTCATCGTCCTGTCTTGCCTCATATCAGTCTCTGTAAACTTCAGCACATTTCTTGTCATTGGAAAAACATCTCCTGTCACATATCAGGTTCTAGGAC

upper sequence: Vv06s0004g07960.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT2G30460.1 (Arabidopsis thaliana), 3'ss of exon 7
gtgaggattgaaattttgataaaacattaatttcttctgtttggtttttttttttctttcctaaatttctctacttcaaaattcaactcctaaatctaatcacctcatttgcagGTCTTCATTGTTCTATCTTGCCTGATATCTGTTTCTGTAAACTTCAGTACATTTCTAGTTATTGGGAAGACATCTCCTGTAACATACCAGGTCCTGGGAC
                ||| ||   |  ||| | |   |  |||| ||  || ||  |||   |       || ||  |||  || ||  |             |    ||||| ||||||| ||  | || ||||| ||||||||||| ||||||||||| || ||||| || ||||| |||||||||||||| || || ||||| || ||||
---------------gtgagaatgaagcaatatatgtggaatggtcttcattattgcttctaca-------tatttacaaacacaccttgt-------------ttgaatgcagTTCTTCATCGTCTTGTCCTGCCTCATATCTGTTTCAGTAAACTTCAGCACGTTTCTCGTCATTGGAAAGACATCTCCTGTCACTTATCAGGTTCTAGGAC

upper sequence: Vv06s0004g07960.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: PP1S311_78V6.1 (Physcomitrella patens), 3'ss of exon 5
gtgaggattgaaattttgataaaacattaatttcttctgtttggtttttttttttctttcctaaatttctctacttcaaaattcaactcctaaatctaatcacc--tcatttgcagGTCTTCATTGTTCTATCTTGCCTGATATCTGTTTCTGTAAACTTCAGTACATTTCTAGTTATTGGGAAGACATCTCCTGTAACATACCAGGTCCTGGGAC
             |     |||   ||    |    |  ||||| ||||| |  | |||  | |  || |   | |      |   || || | | |         |   |  ||| ||||||| || || || || || |||||||| || || |||||||| || |||||||||||||||||||||||  | || || || || || || ||||
-------------taagagtaacggatcg--tgacaccatttgggtttttctgct-tttgatgagcttattatccttgtctcttgtcttctcattgtggcttttgttgggtgccagTTCTTCATCGTGCTTTCGTGTCTCATATCTGTATCAGTTAACTTCAGCACGTTTCTAGTTATTGGGAAGACATCAGCGGTGACTTATCAAGTGCTTGGAC

upper sequence: Vv06s0004g07960.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: PP1S123_22V6.2 (Physcomitrella patens), 3'ss of exon 5
gtgaggattgaaattttgataaaac--attaatttcttctgtttggtttttttttttctttcctaaatttctctacttcaaaattcaactcctaaatctaatcacctcatttgc-agGTCTTCATTGTTCTATCTTGCCTGATATCTGTTTCTGTAAACTTCAGTACATTTCTAGTTATTGGGAAGACATCTCCTGTAACATACCAGGTCCTGGGAC
            || | | |||     | |||| || | |||  |    ||     || ||  |||| |||  | |       || |  | || |   |       |    ||| || ||||| | || || || || ||||||||||| || || |||||||| || ||| |||||||||| ||||||||| | || || || || || || || |
---------atcatctgggtaatgttgactaatctcctatgtcag----ttcgggatcattgataaacttccatgcgct----tttacgtgctcaccgtggcttgttgggatgccagTTCTTCGTCGTGCTTTCATGTCTGATATCTGTATCAGTCAACTTCAGCACGTTTTTAGTTATTGGAAAGACATCTGCGGTGACTTATCAAGTGCTTGGGC

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|46918108|gb|CN547437.1|CN547437
EST:     TTCTGACTAAGCAAAATGTTTTTGCTTTCAAATATACATCTGAAGTGCTG                         GTCTTCATTGTTCTGTCTTGCCTGATATCTGTTTCTGTAAACTTCAGTACA
genomic: TTCTGACTAAGCAAAATGTTTTTGCTTTCAAATATACATCTGAAGTGCTGgtgaggattg ... tcatttgcagGTCTTCATTGTTCTATCTTGCCTGATATCTGTTTCTGTAAACTTCAGTACA
EST: gi|110699675|gb|EE076891.1|EE076891
EST:     TTCTGACTAAGCAAAATGTTTTTGCTTTCAA-TATACATCTGAAGTGCTG                         GTCTTCATTGGTCTGTCTTGGCTGATATCTGTTTCTGTAAACTTCAGT
genomic: TTCTGACTAAGCAAAATGTTTTTGCTTTCAAATATACATCTGAAGTGCTGgtgaggattg ... tcatttgcagGTCTTCATTGTTCTATCTTGCCTGATATCTGTTTCTGTAAACTTCAGT
EST: gi|110700329|gb|EE078245.1|EE078245
EST:     TTCTGACTAAGCAAAATGTTTTTGCTTTCAAATATACATCTGAAGTGCTG                         GTCTTCATTGTTCTGTCTTGCCTGATATCTGTTTCTGTAAACTTCAGTACA
genomic: TTCTGACTAAGCAAAATGTTTTTGCTTTCAAATATACATCTGAAGTGCTGgtgaggattg ... tcatttgcagGTCTTCATTGTTCTATCTTGCCTGATATCTGTTTCTGTAAACTTCAGTACA
EST: gi|33404567|gb|CF210194.1|CF210194
EST:     TTCTGACTAAGCAAAATGTTTTTGCTTTCAAATATACATCTGAAGTGCTG                         GTCTTCATTGTTCTATCTTGCCTGATATCTGTTTCTGTAAACTTCAGTACA
genomic: TTCTGACTAAGCAAAATGTTTTTGCTTTCAAATATACATCTGAAGTGCTGgtgaggattg ... tcatttgcagGTCTTCATTGTTCTATCTTGCCTGATATCTGTTTCTGTAAACTTCAGTACA
EST: gi|110699527|gb|EE076603.1|EE076603
EST:     TTCTGACTAAGCAAAATGTTTTTGCTTTCAA-TATACATCTGAAGTGCTG                         GGCCTCATTGTTCTGTCCTGCCTGATATCTGTTTCTGAAAACTTCAGTACA
genomic: TTCTGACTAAGCAAAATGTTTTTGCTTTCAAATATACATCTGAAGTGCTGgtgaggattg ... tcatttgcagGTCTTCATTGTTCTATCTTGCCTGATATCTGTTTCTGTAAACTTCAGTACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctaaatttctctacttcaaaattcaactcctaaatctaatcacctcatttgcagGTCTTCATTGTTCTATCTTGCCTGATATCTGTTTCTGTAAACTTCAGTACATTTCTAGTTATTGGGAAGACATCTCCTGTAACATACCAGGTCCTGGGAC
                                           cctcattt  CT-rich tract
                               taaatctaat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaggattgaaattttgataaaacattaatttcttctgtttggtttttttttttctttcctaaatttctctacttcaaaattcaactcctaaatctaatcacctcatttgcagGTCTTCATTGTTCTATCTTGCCTGATATCTGTTTCTGTAAACTTCAGTACATTTCTAGTTATTGGGAAGACATCTCCTGTAACATACCAGGTCCTGGGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA