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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgtagcttgtagagtgcatcagcatctgaaggctaccaacataaattcacattggatgttgataacatgtgattaataatttctatccattccttgtagGAATACAGTTTCAAAGGTATATCCAGCTATGTACATAGGAAATATTACTGAACTTGCATTTGATGATATTACACCTGAAGACCCTGATTTTTCATCCATT

Basic information

species Vitis vinifera
transcript Vv16s0050g00600.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0050g00600.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os03g64400.4 (Oryza sativa), 3'ss of exon 4
ctgtagcttgtagagtgcatcagcatctgaaggctaccaacataaattcacattggatgttgataacatgtgattaataatttctatccattcct---tgtagGAATACAGTTTCAAAGGTATATCCAGCTATGTACATAGGAAATATTACTGAACTTGCATTTGATGATATTACACCTGAAGACCCTGATTTTTCATCCATT
|    | | | |      ||      || |    |   ||  |   ||||| || |   || ||  |||  || |||    || | |  ||| |    | |||||| ||    || || || |||||||| ||||| || |  ||| | ||||||||||| ||||||||||| |||||||||||   ||||||| |||  || 
caaaggatggaatttcatatttttgccttataattttgaatttgg-ttcac-ttagtaattcattccata-gactaagttcttgtttggatttccaactatagGAACACTTCCTCCAAAGTGTATCCAGCAATGTATATTGAGAATGTGACTGAACTTGCCTTTGATGATATCACACCTGAAGATTTTGATTTTCCATTTATA

upper sequence: Vv16s0050g00600.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G140874_T01 (Zea mays), 3'ss of exon 1
-------------------------------------------------------------------------------ctgtagcttgtagagtgcatca-gcatctgaaggc---------taccaacataaattcacattggatgtt---gataac-atgtgattaa-----taatttctatccattccttgtagGAATACAGTTTCAAAGGTATATCCAGCTATGTACATAGGAAATATTACTGAACTTGCATTTGATGATATTACACCTGAAGACCCTGATTTTTCATCCATT
                                                                                |||    | |    | | |||  | | | | | |         | |   || |  ||||  || | | |    | | |  ||    ||||     | |||    |   |||| |  ||||| ||  | ||||| || |||| ||| ||||| || |  ||| | ||||||||||||||||| ||| | ||||||||||| ||||||||| ||| ||| 
gtgcatatctattattcctttgtatcagtagacctcccaagtgtttgttgcaaatatgcagtatggtcccatttctcttttgtcatatttcatattcttcatacgtttaaggtcattgcctcttgctgtcaaattttcagttttgctctcttaggtgattattctgttaaccaccttattctcgtggtttccatacagGAACACTTTCTCAAAAGTGTATCTAGCAATGTATATTGATAATGTCACTGAACTTGCATTTGACGATGTCACACCTGAAGATCCTGATTTTCCATTCATA

upper sequence: Vv16s0050g00600.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G077222_T01 (Zea mays), 3'ss of exon 4
------------------------------------------------------------------------------------------------ctgtagcttgtagagtgcatcagcatctgaaggctaccaacataaattcac---attggatgttgataacatgtgattaataatttctatccattccttgtagGAATACAGTTTCAAAGGTATATCCAGCTATGTACATAGGAAATATTACTGAACTTGCATTTGATGATATTACACCTGAAGACCCTGATTTTTCATCCATT
                                                                                                ||  |     |  ||  |||  || |||    | ||       |  ||  |    || | || | ||    |      | | |||    |   |||| |  ||||| ||  | ||||| || |||||||| ||||| || |  ||| | ||||||||||||||||| ||| | ||||||||||| ||||||||| ||| ||| 
gtgcatatctattattcctttgtatcagtagacctcccaagtgtttgttgcaaatatgcagtatggtcccatttctcttttgtcctatttcatattcttcatacgtttaaggtcatt-gcctcttgctgttaaattttcagttttgctctcttaggtgattattctgttaaccaacttattctcgtggtttccatacagGAACACTTTCTCAAAAGTGTATCCAGCAATGTATATTGATAATGTCACTGAACTTGCATTTGACGATGTCACACCTGAAGATCCTGATTTTCCATTCATA

upper sequence: Vv16s0050g00600.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA20G29970.1 (Glycine max), 3'ss of exon 3
--------ctgtagcttgtagagtgcatcagcatctgaaggctaccaacataaa----ttca--cattggatgttg--ataacatgtgat--taataatttctatccatt---ccttgtagGAATACAGTTTCAAAGGTATATCCAGCTATGTACATAGGAAATATTACTGAACTTGCATTTGATGATATTACACCTGAAGACCCTGATTTTTCATCCATT
         | |  ||| |       || |  || ||||        | |||||    || |   ||| | | ||    ||| |||||    ||    |  || ||   |   | || |||||| ||| | |||||||||||||| || | ||||||||  ||| ||||||  | ||||||||||||||| || ||||| |||||||||||||| | || |
gtagttggttatttcttcttcctctgattactatgtgaaataacaagatataaaaaagtttagctatttgctattattgtaatatgtggcgatatctgtgcctttctgattacctttttagGAAAACAATCTCAAAGGTATATCCTGCCACGTACATAGACAATGTTACTGGGCATGCATTTGATGATATCACCCCTGAGGACCCTGATTTTTCTTGCACT

upper sequence: Vv16s0050g00600.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA09G25200.1 (Glycine max), 3'ss of exon 8
ctgtagcttgtagagtgcatcagcatctgaaggctaccaacataaatt-cacattggatgttgataacatgtgattaataatttctatccattccttgtagGAATACAGTTTCAAAGGTATATCCAGCTATGTACATAGGAAATATTACTGAACTTGCATTTGATGATATTACACCTGAAGACCCTGATTTTTCATCCATT
       | |||   |   ||  ||| ||     || ||| ||   || || ||   || ||  |  ||| |   |   | |||||    | |  ||  ||||  ||||||||||| || ||||| || ||||||||||  ||| ||||||| ||||||||||||||| | |  || || |||||||||||||| ||||||
------gtagtaatttatttctacatatgtgaa-taacaaaatgtgttacatatgtaatatt--tggcat-tacatgtgactttctggtaacttgtt--agGAGCACAGTTTCAAAAGTGTATCCTGCCATGTACATAGACAATGTTACTGAGCTTGCATTTGATGATGTCATCCCCGAGGACCCTGATTTTTCTTCCATT

upper sequence: Vv16s0050g00600.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA10G37850.1 (Glycine max), 3'ss of exon 7
--------ctgtagcttgtagagtgcatcagcatctgaaggctaccaacata-aattcacattggatgttg---------ataacatgtgat--taataatttctatccatt---ccttgtagGAATACAGTTTCAAAGGTATATCCAGCTATGTACATAGGAAATATTACTGAACTTGCATTTGATGATATTACACCTGAAGACCCTGATTTTTCATCCATT
         | |  ||| |      ||  |  || ||||   || ||| ||| ||   |  |||| | ||           ||| ||||| |  ||    |  || ||   |   | || |||||| ||  | |||||||||||||| || |||| | |||  | | ||||||| ||||||||||||||||| || ||||| |||||||||||||| | ||||
gtagttgtttatttcttctttctatcactattatgtgaaa--taacaatatataaaaaaggttggctattttctattattgtaatatgtggtgatatgtgtgcctttctgattacctttttagGAAAACTATCTCAAAGGTATATCCTGCCATGTTCGTAGACAGTGTTACTGAGCTTGCATTTGATGATATCACCCCTGAGGACCCTGATTTTTCTTTCATT

upper sequence: Vv16s0050g00600.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA16G30160.1 (Glycine max), 3'ss of exon 4
ctgtagcttgtagagtgcatcagcatctgaaggctaccaacataaattcacattggatgttgataacatgtgattaataatttctatccatt--ccttgtagGAATACAGTTTCAAAGGTATATCCAGCTATGTACATAGGAAATATTACTGAACTTGCATTTGATGATATTACACCTGAAGACCCTGATTTTTCATCCATT
       | |||   ||  ||  | |        |   || |  ||      ||  ||||  |  |  ||  ||||    |  || ||   |  | |  |||||  ||||||||||| || ||||| || ||||| ||||  |||  |||||| ||||||||||||||| | || || || |||||||||||||| ||||||
------gtagtaatttgtttctaccttctgcatatgtgaataacaaaatgtgttacatgtgtaatatttggcattacgtgtgcctttctggtaacttgttagGAGCACAGTTTCAAAAGTGTATCCTGCCATGTATATAGACAATGCTACTGAGCTTGCATTTGATGATGTCACTCCCGAGGACCCTGATTTTTCTTCCATT

upper sequence: Vv16s0050g00600.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G52410.1 (Arabidopsis thaliana), 3'ss of exon 5
ctgtagcttgtagagtgcatcagcatctgaaggctaccaacataaattcacattggatgttgataacatgtgat-taataatttctatccattccttgtagGAATACAGTTTCAAAGGTATATCCAGCTATGTACATAGGAAATATTACTGAACTTGCATTTGATGATATTACACCTGAAGACCCTGATTTTTCATCCATT
         ||| | |     |  ||||     ||||      ||  |        || |   |  | |   |  | | ||| |||   ||||  || ||||||  |||  ||||| |||||||| || ||||| |||| |||| ||||||||||||||||||||||||||||||||||||| ||||||||| ||| ||||
---------gta-actatcaaaaaatctctttcctactcttgaaacattgtgaaatatttcactgccttacaacgtgaaaatatct--tcattggttatagGAACTCAGCATCAAAAGTATATCCTGCCATGTATATAGAAAATGTTACTGAACTTGCATTTGATGATATTACACCTGAAGATCCTGATTTTCCATTCATT

upper sequence: Vv16s0050g00600.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G23890.1 (Arabidopsis thaliana), 3'ss of exon 4
ctgtagcttgtagagtgcatcagcatctgaag-gctaccaacataa-----attcacattggatgttgataa-catgtgattaataatttctatccattccttgtagGAATACAGTTTCAAAGGTATATCCAGCTATGTACATAGGAAATATTACTGAACTTGCATTTGATGATATTACACCTGAAGACCCTGATTTTTCATCCATT
 | ||  ||   || |   | ||  | |   | |    ||| |||       |    ||| ||   ||| |  ||||   |||    | |   |  | || ||| || || |||   ||||| || ||||| |||||||| || |  ||| ||||||| ||||| |||||||||||||| || ||||||||||||||||| ||||||
gtatactttcatgattttgttagtgtttctggtggggtcaaaatatccttcgtatgtattagaaagtgaaattcatgcatttatgtgtgttctttaactctttgcagAAACACAACCTCAAAAGTGTATCCTGCTATGTATATTGAGAATGTTACTGAGCTTGCTTTTGATGATATTACTCCCGAAGACCCTGATTTTTCTTCCATT

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|161710954|gb|FC058613.1|FC058613
EST:     CGTCGTGAGTTTGCTCGTTGGTTGGTTTCTGCAAGTAGTGTTCTTTCAAG                         GAATACAGTTTCAAAGGTATATCCAGCTATGTACATAGGAAATATTACTGA
genomic: CGTCGTGAGTTTGCTCGTTGGTTGGTTTCTGCAAGTAGTGTTCTTTCAAGgtataccatc ... ttccttgtagGAATACAGTTTCAAAGGTATATCCAGCTATGTACATAGGAAATATTACTGA
EST: gi|161719035|gb|FC067655.1|FC067655
EST:     CGTCGTGAGTTTGCTCGTTGGTTGGTTTCTGCAAGTAGTGTTCTTTCAAG                         GAATACAGTTTCAAAGGTATATCCAGCTATGTACATAGGAAATATTACTGA
genomic: CGTCGTGAGTTTGCTCGTTGGTTGGTTTCTGCAAGTAGTGTTCTTTCAAGgtataccatc ... ttccttgtagGAATACAGTTTCAAAGGTATATCCAGCTATGTACATAGGAAATATTACTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcacattggatgttgataacatgtgattaataatttctatccattccttgtagGAATACAGTTTCAAAGGTATATCCAGCTATGTACATAGGAAATATTACTGAACTTGCATTTGATGATATTACACCTGAAGACCCTGATTTTTCATCCATT
                                   tttctatccattcctt  CT-rich tract
                 ataacatgtgattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgtagcttgtagagtgcatcagcatctgaaggctaccaacataaattcacattggatgttgataacatgtgattaataatttctatccattccttgtagGAATACAGTTTCAAAGGTATATCCAGCTATGTACATAGGAAATATTACTGAACTTGCATTTGATGATATTACACCTGAAGACCCTGATTTTTCATCCATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
-tgtagct
- - - - - - - - -catcagc
- - - - - - - - - - - - - ctgaagg
- - - - - - - - - - - - - - - - - -accaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - -tggatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtga