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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctattaggcggtaacaaagcactaactataatgattgtatactttgataagatttgcttctacttgtggcattatcttctgtcatccgtctttgtacagCTACTACATTGACAAGCTGGCATCTTCTGGTCACTTTCTGTTCTCTTCATGTGGCTCTATGGATGAAATTGTTTGAACACAAACCATTTGATGCAAAAGC

Basic information

species Vitis vinifera
transcript Vv13s0067g02970.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0067g02970.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os01g60780.2 (Oryza sativa), 3'ss of exon 1
-gctattaggcggtaacaa--agcactaactataatgattgtatactttgataagatttgcttctacttgtggcattatcttctgtcatccgtctttgtacagCTACTACATTGACAAGCTGGCATCTTCTGGTCACTTTCTGTTCTCTTCATGTGGCTCTATGGATGAAATTGTTTGAACACAAACCATTTGATGCAAAAGC
    | ||     | || |  |  || | ||   |  | |   |  ||   |||| | |    | |  ||    | |  |  |  ||  |    ||  | ||||||||||  |||||||||||||||| ||||| || || ||||| ||||||||||||||   ||||||  | || ||  |||||   || ||  | ||  |
tatgagtacaatatgacgaacaataccacctgagaaaactaactgtttcc-taagctatataacca--tgcaaaaatcacagcactctcctaatttctttcagCTACTACGCTGACAAGCTGGCATCTCCTGGTGACATTTTGTTCCCTTCATGTGGCTCTTCAGATGAAGCTTTTCGAGAACAAAGATTTAGACCCCAAGAC

upper sequence: Vv13s0067g02970.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os01g07310.4 (Oryza sativa), 3'ss of exon 2
gctattaggcggtaacaaagcactaactataatgattgtatactttgataagatttgcttctacttgtggcatta-tcttctgtcatccgtctttgtacagCTACTACATTGACAAGCTGGCATCTTCTGGTCACTTTCTGTTCTCTTCATGTGGCTCTATGGATGAAATTGTTTGAACACAAACCATTTGATGCAAAAGC
| |  ||    ||   | |  ||||  ||   | |     || |     || |   |  | | ||      |||| ||  ||    || || ||| | |||| ||||| ||||||||||||||||| || || || || || |||||||| |||||  |||| |||||  | ||||| |||||||| ||||||||||   |
ggttctaaagtgtgtgacaatactaggtaacgtaaaaagttagtacataaatagacgtgtttcctgtccaaattactcaacttcggtctgtgttt-tgcagCCACTACTTTGACAAGCTGGCATCTCCTCGTTACATTTTGCTCTCTTCACGTGGCATTATGTATGAAGCTCTTTGAGCACAAACCTTTTGATGCAAGGAC

upper sequence: Vv13s0067g02970.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G116053_T01 (Zea mays), 3'ss of exon 2
-----gctattaggcggtaacaaagcactaacta--taatgattgtatactttgataagatttgcttctacttgtggcattatcttctgtcatccgtctttgtacagCTACTACATTGACAAGCTGGCATCTTCTGGTCACTTTCTGTTCTCTTCATGTGGCTCTATGGATGAAATTGTTTGAACACAAACCATTTGATGCAAAAGC
     |   | ||| |  |      |  |||  |  ||||||| | | |    |  | | ||| || | |   |||  | ||   | ||  || | | ||    |||| ||||| ||||||||||||||||| ||||| || ||||||||||| ||||||||  |||| |||||  ||||||| |||||||| || |||||||   |
caagtgtggtgaggtgacagtgcgtctataaacagataatgatagcaaagaa-ggcaggttttcctccaa---gtgttaataaaatgtggtattcatttt---gcagCCACTACTTTGACAAGCTGGCATCTCCTGGTTACATTCTGTTCTCTCCATGTGGCATTATGTATGAAGCTGTTTGAGCACAAACCTTTCGATGCAAGGAC

upper sequence: Vv13s0067g02970.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G081848_T05 (Zea mays), 3'ss of exon 2
-----gctattaggcggtaacaaagcactaactataatgattgtatactttgataagatttgcttctacttgtggcattatcttctgtcatccgtctttgtacagCTACTACATTGACAAGCTGGCATCTTCTGGTCACTTTCTGTTCTCTTCATGTGGCTCTATGGATGAAATTGTTTGAACACAAACCATTTGATGCAAAAGC
     |   | | | |  |      |  |||  |  || ||  ||  |   ||    |  |  | || | | ||  | ||   |||   || | | ||    |||| || || |||||||||||||||||||||||||| ||||| ||||| ||||| ||  |||| |||||| | ||||| |||||||| || |||||||   |
cacgtgtcctcaagtgacagtccgtctataaaca-gataatatta-gcaaagaaggcaggttttcctccatatgctaataaaatctcgtattcatttt---gcagCCACCACTTTGACAAGCTGGCATCTTCTGGTCACCTTCTGCTCTCTCCATGTAGCATTATGTATGAAACTCTTTGAGCACAAACCTTTCGATGCAAGGAC

upper sequence: Vv13s0067g02970.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G063511_T02 (Zea mays), 3'ss of exon 2
----gctattaggcggtaacaaagcactaactataatgattgtatactttgataagatttgcttctacttgtggcattatcttctgtcatccgtctttgtacagCTACTACATTGACAAGCTGGCATCTTCTGGTCACTTTCTGTTCTCTTCATGTGGCTCTATGGATGAAATTGTTTGAACACAAACCATTTGATGCAAAAGC
    ||   |      || |||          |  |||   || |  ||| | | |  ||  |      | |||   |    | ||| ||  |||||  | |||| ||||| ||||||||||||||||| ||||| || ||||| || |||||||||||  ||||||||||||| ||||| || || || |||||| ||| | |
acacgccccttattt-tatcaacatgtggtggagtatgcaagtctgatttaa-atgtcttcttatggactatggttgtgaaatatgt-atttgtcttc-tgcagCCACTACCTTGACAAGCTGGCATCTGCTGGTTACATTCTGCTCCCTTCATGTGGCATTATGGATGAAATTCTTTGAGCATAAGCCTTTTGATTCAAGAAC

upper sequence: Vv13s0067g02970.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G063253_T09 (Zea mays), 3'ss of exon 1
---gctattaggcggtaacaaagcactaactataatgattgtatactttgataagatttgcttctacttgtggcattatcttctgtcatccgtctttgtacagCTACTACATTGACAAGCTGGCATCTTCTGGTCACTTTCTGTTCTCTTCATGTGGCTCTATGGATGAAATTGTTTGAACACAAACCATTTGATGCAAAAGC
     || |||    ||    | ||  |  |||  |  |    ||  |   |  |||||   |  |||| |   ||            |  |||||| | |||| ||||| ||||| ||||||||||| ||||| || ||||| || |||||||| ||  |||||||||| || ||||| || || || |||||| ||| | |
cagagtactagatcttatattatcaacatgtatg-tagtgaagtatgtaagtctgatttaaatg-acttctaatatctgtgaaatatgtatgtcttt-tgcagCCACTACCTTGACGAGCTGGCATCTGCTGGTTACATTCTGCTCCCTTCATGTAGCATTATGGATGAAGTTCTTTGAGCATAAGCCTTTTGATTCAAGAAC

upper sequence: Vv13s0067g02970.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G063253_T08 (Zea mays), 3'ss of exon 1
gctattaggcggtaacaaagcactaactataatgattgtatactttgataagatttgcttctacttgtggcattatcttctgtcatccgtctttgtacagCTACTACATTGACAAGCTGGCATCTTCTGGTCACTTTCTGTTCTCTTCATGTGGCTCTATGGATGAAATTGTTTGAACACAAACCATTTGATGCAAAAGC
                   | |   | |  | |   |||| | | ||||   | |  |||||| |    |    || |       |  |||||| | |||| ||||| ||||| ||||||||||| ||||| || ||||| || |||||||| ||  |||||||||| || ||||| || || || |||||| ||| | |
-------------------gtatgtagtgaagta--tgta-agtctgatttaaatgacttctaatatctgtgaaatat------gtatgtcttt-tgcagCCACTACCTTGACGAGCTGGCATCTGCTGGTTACATTCTGCTCCCTTCATGTAGCATTATGGATGAAGTTCTTTGAGCATAAGCCTTTTGATTCAAGAAC

upper sequence: Vv13s0067g02970.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA06G14980.1 (Glycine max), 3'ss of exon 2
gctattaggcggtaacaa-agcactaactataatgattgtatactttgataagatttgcttctacttgtggcattatcttctgtcatccg-tctttgtacagCTACTACATTGACAAGCTGGCATCTTCTGGTCACTTTCTGTTCTCTTCATGTGGCTCTATGGATGAAATTGTTTGAACACAAACCATTTGATGCAAAAGC
  ||      | ||  |  ||| | |      ||  |     | ||  |  | | |  | |  | ||| ||  |||   | | || |    |     | ||||||| || |||||||| ||||||||||| || || || ||||| ||||||||||| |||  | ||| | | ||||| |||||||| |||||    |||||
--taacttttgttagaagtagctccatgctgcatcctaacccatttgaagtataatgtcctagagttgaggttttaatatgtatccttgaattcccatgcagCTACAACTTTGACAAGTTGGCATCTTCTTGTAACATTTTGTTCCCTTCATGTGGCACTAAAGTTGAGACTTTTTGAGCACAAACCTTTTGAGCAGAAAGC

upper sequence: Vv13s0067g02970.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA04G39920.4 (Glycine max), 3'ss of exon 2
--gctattaggcggtaacaaagcactaactataatgattgtatactttgataagatttgct-tctacttgtggcattatcttctgtcatccgtctttgtacagCTACTACATTGACAAGCTGGCATCTTCTGGTCACTTTCTGTTCTCTTCATGTGGCTCTATGGATGAAATTGTTTGAACACAAACCATTTGATGCAAAAGC
      | | ||  ||   ||     | || | ||  ||  ||  |    ||   | ||   | |||  ||      |  || ||   |  |    | | ||||||| || ||||| ||||||||||| || ||||| || ||||| ||||||||||| ||    |||| ||| ||||| |||||||| |||||    |||||
ttatgttcatgctatatgcaaatttgagctttcatctttacattttaatgtactgtctgagatttacaagtttttgaaatttgtgctttttga---tatgcagCTACAACTTTGACCAGCTGGCATCTGCTTGTCACGTTTTGTTCCCTTCATGTGGCGCTCAAAATGAGATTCTTTGAGCACAAACCTTTTGAGCAGAAAGC

upper sequence: Vv13s0067g02970.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA06G14970.2 (Glycine max), 3'ss of exon 2
--gctattaggcggtaacaaagcactaactataatgattgtatactttgataagatttgct-tctacttgtggcattatcttctgtcatccgtctttgtacagCTACTACATTGACAAGCTGGCATCTTCTGGTCACTTTCTGTTCTCTTCATGTGGCTCTATGGATGAAATTGTTTGAACACAAACCATTTGATGCAAAAGC
    |   | |   ||   ||     | || | ||| ||  ||  |    ||   | ||   | |||  ||      |  || ||   |  |    | | ||||||| || ||||| ||||||||||| || ||||| || ||||| ||||||||||| ||    |||| ||| ||||| |||||||| |||||    |||||
ttatttccatgatatatgcaaatttgagctttcatgtttacattttaatgtactgtctgagatttacaagtttttgaaatttgtgctttttga---tatgcagCTACAACTTTGACCAGCTGGCATCTGCTTGTCACATTTTGTTCCCTTCATGTGGCGCTCAAAATGAGATTCTTTGAGCACAAACCTTTTGAGCAGAAAGC

upper sequence: Vv13s0067g02970.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G06890.2 (Arabidopsis thaliana), 3'ss of exon 2
gctattaggcggtaacaaagcactaactataatgattgtatactttg--ataagatttgcttctacttgtggcattatcttctgtcatccgtctttgtacagCTACTACATTGACAAGCTGGCATCTTCTGGTCACTTTCTGTTCTCTTCATGTGGCTCTATGGATGAAATTGTTTGAACACAAACCATTTGATGCAAAAGC
 |  || |  |        ||  ||||     | ||   ||  | ||  ||     |  | |   ||    |   |  ||  ||| ||   | | |||||||| ||||| |||||||| ||||||||| ||||||| || ||||| |||||||||||  ||||||||||  |||| |||||||| || |||||| ||  |||
-cattttgatgtctgtgttgccataacagcttttatgtcatcttatgcaattttgatctcataagctatctgttcttactcttgttattt-tgtatgtacagCGACTACTTTGACAAGTTGGCATCTTTTGGTCACATTTTGTTCCCTTCATGTGGCATTATGGATGAAGATGTTCGAACACAAGCCTTTTGATCCACGAGC

upper sequence: Vv13s0067g02970.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT2G30460.1 (Arabidopsis thaliana), 3'ss of exon 3
gctattaggcggtaacaaagcactaactataatgattgtatactttgataagatttgcttctacttgtggcattatcttctgtcatccgtctttg----tacagCTACTACATTGACAAGCTGGCATCTTCTGGTCACTTTCTGTTCTCTTCATGTGGCTCTATGGATGAAATTGTTTGAACACAAACCATTTGATGCAAAAGC
     |   |  |     | | | |   || || |  || ||       ||  |     ||||  ||||   | ||| | | | |       |||    |||||| ||||| |||||||||||||||||| |||| || || ||||| |||||||||||  |||||||||| || ||||| ||||| || |||||| ||  |||
---tctttaccatgggtgaactccattcatgataacagtttatgcatggaatctcatagtctatctgtg-tgtaatcatttattactttatattgaacttacagCAACTACTTTGACAAGCTGGCATCTTTTGGTGACATTTTGTTCACTTCATGTGGCATTATGGATGAAGTTTTTTGAGCACAAGCCTTTTGATCCACGAGC

upper sequence: Vv13s0067g02970.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S123_22V6.1 (Physcomitrella patens), 3'ss of exon 2
gctattaggcggtaacaaagcactaactataatgattgtatactttgataagatttgcttctacttgtggcattatcttctgtcatccgtctttgt-----acagCTACTACATTGACAAGCTGGCATCTTCTGGTCACTTTCTGTTCTCTTCATGTGGCTCTATGGATGAAATTGTTTGAACACAAACCATTTGATGCAAAAGC
  | |||   | | |  | | |||    |   | ||  |||  ||  ||      || ||      | || ||| ||||    | || || || ||     |||||||| ||||||||||||||||||||   ||| || ||||| || ||||| || || | ||   ||||| | ||||| ||||| || || ||  ||    |
--ttttaaaagttgattacgtacttttcact-tcatcttat-tttgaattcttcgtgtttagggaagaggtatt-tctttgaccttctgtgttcgtttagtacagCTACCACATTGACAAGCTGGCATCTAGCGGTGACATTCTGCTCACTTCACGTTGCACGATCATTGAAACTATTTGAGCACAAGCCTTTCGACTCACGGAC

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|110370848|gb|EC934415.1|EC934415
EST:     GATTGTGATTTGCAATAAAGCTCTCATTAGCTCATTGGGTTTCACTTTTG                         CTACTACATTGACAAGCTGGCATCTTCTGGTCACTTTCTGTTCTCTTCATG
genomic: GATTGTGATTTGCAATAAAGCTCTCATTAGCTCATTGGGTTTCACTTTTGgtgagttgca ... ctttgtacagCTACTACATTGACAAGCTGGCATCTTCTGGTCACTTTCTGTTCTCTTCATG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgataagatttgcttctacttgtggcattatcttctgtcatccgtctttgtacagCTACTACATTGACAAGCTGGCATCTTCTGGTCACTTTCTGTTCTCTTCATGTGGCTCTATGGATGAAATTGTTTGAACACAAACCATTTGATGCAAAAGC
 ctttgat  putative branch site (score: 5)
                                        tccgtcttt  putative PPT
                          attatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctattaggcggtaacaaagcactaactataatgattgtatactttgataagatttgcttctacttgtggcattatcttctgtcatccgtctttgtacagCTACTACATTGACAAGCTGGCATCTTCTGGTCACTTTCTGTTCTCTTCATGTGGCTCTATGGATGAAATTGTTTGAACACAAACCATTTGATGCAAAAGC

- - - - - -gtaacaa
- - - - - - - - - - cactaac
- - - - - - - - - - - - - - - - - - - - - - - gataaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggcatta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgtcat