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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcattctattaatacttgattagtgatacgtatctagcacttgcatattgtcctttggccataacttattcttgtgattattgtcataatgctctccagATTGCATTGGTTCAGCATTCAATATCAAAGGGGCAATGCAATGTCCTAATTGTCGGAAAATTGAAAAAGGTCAATGGCTTTATGCAAATGGTTGTCGTAC

Basic information

species Vitis vinifera
transcript Vv14s0060g02280.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0060g02280.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os05g06270.1 (Oryza sativa), 3'ss of exon 1
atcattctattaatacttgattagtgatacgtatctagcacttgcatatt----gtcctttggccataacttattcttgtgattattgtcataatgctctccagATTGCATTGGTTCAGCATTCAATATCAAAGGGGCAATGCAATGTCCTAATTGTCGGAAAATTGAAAAAGGTCAATGGCTTTATGCAAATGGTTGTCGTAC
  | || ||    |  |       ||||    |  | | | ||    |||    ||  |||     ||    |   || |||| |||||   | || | ||||||||||||||| |||||||| |||  |||||| |  |||||||| || || || || ||||||||||| ||  | ||||| |||||||||||||  ||  |
--ctttttacatttgttaagcgtatgatcttcaagtggaagttttgaatttctagtattttcatt-tattacaacattttgatgattgtggcattgtt-tccagATTGCATTGGATCAGCATTTAATGCCAAAGGCGTTATGCAATGCCCCAACTGCCGCAAAATTGAAAAGGGGAACTGGCTCTATGCAAATGGTTCCCGACC

upper sequence: Vv14s0060g02280.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os08g42640.1 (Oryza sativa), 3'ss of exon 1
atcattctattaatacttgattagtgatacgtatcta-gcacttgcatat-tgtcctttggccataacttattcttgtgattattgtcataatgctctcc----agATTGCATTGGTTCAGCATTCAATATCAAAGGGGCAATGCAATGTCCTAATTGTCGGAAAATTGAAAAAGGTCAATGGCTTTATGCAAATGGTTGTCGTAC
  |||    | |   | | ||  ||| ||| | |  | |||  |  | |  |   |||||||     | |   |  ||| |||   | | | |  |  ||    ||| |||||||| || ||||| |||   |||||||| |||||||| |||||||||||||| ||||| ||||| |  |||||||| |||| |||    | | |
--catgtattcatagcctcatctgtg-tacatcttcatgcatgtataaaaataaactttggc---gcccttcacaggtggttaaactaacattttttccctgttagACTGCATTGGATCGGCATTTAATGCAAAAGGGGCCATGCAATGCCCTAATTGTCGGAAGATTGAGAAAGGCCGCTGGCTTTACGCAAGTGGGCACCATCC

upper sequence: Vv14s0060g02280.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G153250_T01 (Zea mays), 3'ss of exon 1
--atcattctattaatacttgattag-tgatacgtatctagcacttgcatattgtcctttggccataacttattcttgtgattattgtcataatgctctccagATTGCATTGGTTCAGCATTCAATATCAAAGGGGCAATGCAATGTCCTAATTGTCGGAAAATTGAAAAAGGTCAATGGCTTTATGCAAATGGTTGTCGTAC
  |  | |||| |     | || ||  |   |   |   ||  ||   | ||| || ||     ||||  | ||  | || | | | | | | |  ||||||||||||||||| |||||||| |||  ||||||||  |||||||| || || || || ||||| || |||||  | ||||||||||||||||||| |||  |
ttaataatctactttgtgtggactaactaggatcaaagcagtgctctga-attatctttgcttgataatct-ttgatatgctaagtat-acatttttctccagATTGCATTGGATCAGCATTTAATGCCAAAGGGGTTATGCAATGCCCCAACTGCCGCAAAATCGAGAAAGGGAATTGGCTTTATGCAAATGGTTCTCGATC

upper sequence: Vv14s0060g02280.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G011473_T01 (Zea mays), 3'ss of exon 1
atcattctattaatacttgattagtgatacgtatctagcacttgcatattgtcctttgg--ccata-acttattcttgtgattattgtcataatgctctccagATTGCATTGGTTCAGCATTCAATATCAAAGGGGCAATGCAATGTCCTAATTGTCGGAAAATTGAAAAAGGTCAATGGCTTTATGCAAATGGTTGTCGTAC
 ||  ||   | |  ||||  |  | || || ||   |  | || | | |    | ||   || ||  |  |||  ||   | ||    ||  || |  |||||||| ||||| || |||||||||   ||||| || |||||||| ||||| |||||||| ||||| |||||||  |||||||||||||  ||   |||  |
-tctgtcccctcacccttgtgtgtttatgcg-ataatgtgcatgaaaaatacattatgataccttacgcagattgctgaactaatcaagattttgttg-ccagATTGTATTGGGTCTGCATTCAATGCAAAAGGAGCGATGCAATGCCCTAACTGTCGGAAGATTGAGAAAGGTCGCTGGCTTTATGCAAGCGGACATCGCGC

upper sequence: Vv14s0060g02280.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G053027_T01 (Zea mays), 3'ss of exon 1
---atcattctattaatacttgattagtgatacgtatctagcacttgcatattgtcctttggccataacttattcttgtgattattgtcataatgctctccagATTGCATTGGTTCAGCATTCAATATCAAAGGGGCAATGCAATGTCCTAATTGTCGGAAAATTGAAAAAGGTCAATGGCTTTATGCAAATGGTTGTCGTAC
    ||     |   ||    | |||     | || |  |  |     | ||| |  | |  |   | |  |||  ||   | |     ||  | ||  |||||||| ||||| || |||||||||   ||||| || |||||||| ||||| |||||||| ||||| |||||||  ||||||||||||| |||  |||   |
tctgtcccctcacccatgtgcgtttatgtgaatgtttgcatgaaaaatacattatgatat--cttaagcagattgctgaactaagcaaaatttt-cttgccagATTGTATTGGGTCTGCATTCAATGCAAAAGGAGCGATGCAATGCCCTAACTGTCGGAAGATTGAGAAAGGTCGCTGGCTTTATGCAAGTGGACGTCACCC

upper sequence: Vv14s0060g02280.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA10G29230.1 (Glycine max), 3'ss of exon 1
----atcattctattaatacttgattag--tgatacgtatctagcacttgcatattgtcctttggccataacttattcttgtgattattgtcataatgctctccagATTGCATTGGTTCAGCATTCAATATCAAAGGGGCAATGCAATGTCCTAATTGTCGGAAAATTGAAAAAGGTCAATGGCTTTATGCAAATGGTTGTCGTAC
     | ||   || |||   ||  ||   ||||   |   | | |     |||| |    || ||  |  ||||| ||| | |||| | | | |||  |    |||||||||||||||||||||||| || ||||| |||||||| || |||||||||||||| ||||| |||||||||||||| ||||| |||||||||||  |
aatagtgatgtcatgaatttctgcatacactgatttcttgttggtaacaatatatggaatattagcatt--cttatgcttattattact-ttacaatattt---agATTGCATTGGTTCAGCATTCAACATAAAAGGAGCAATGCAGTGCCCTAATTGTCGGAAGATTGAGAAAGGTCAATGGCTATATGCTAATGGTTGTCGCTC

upper sequence: Vv14s0060g02280.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA20G38050.2 (Glycine max), 3'ss of exon 1
atcattctattaatacttgattagtgatacgtatctagcacttgcatattgtcctttggccataa-cttattcttgtgattattgtca--taatgctctccagATTGCATTGGTTCAGCATTCAATATCAAAGGGGCAATGCAATGTCCTAATTGTCGGAAAATTGAAAAAGGTCAATGGCTTTATGCAAATGGTTGTCGTAC
   ||   || |||  |||  ||    |   |   ||       ||   | | |  | |  |||  ||||| ||| || ||||| | |  | |   | |  ||||||||||||||| |||||||| || ||||| |||||||| || || ||||||||||| ||||| |||||||||||||| ||||| |||||||||||  |
--gatgtcatgaatttttgcata-cactgatttcttattgacaacaatatatgcaatagtaatattcttatgcttatgcttattattactttacattatttagATTGCATTGGTTCGGCATTCAACATAAAAGGAGCAATGCAGTGCCCCAATTGTCGGAAGATTGAGAAAGGTCAATGGCTATATGCTAATGGTTGTCGGTC

upper sequence: Vv14s0060g02280.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA03G39490.1 (Glycine max), 3'ss of exon 1
atcattctattaatacttgattagtgatacgtatctag---cacttgcatattgtcctttggccataac-ttattcttgtgattattgtcataatgctctccagATTGCATTGGTTCAGCATTCAATATCAAAGGGGCAATGCAATGTCCTAATTGTCGGAAAATTGAAAAAGGTCAATGGCTTTATGCAAATGGTTGTCGTAC
    || || |   |     ||  | ||| ||   |||   ||  |||||    || |   | ||||    ||| ||| | |||||  || | ||  | | ||||||||||||| ||||| |||||||| || ||||||||||| || || |||||||| || |||||||||||||| ||||||||||| |||||||| ||  |
-atgttttactggaatcaattttataataagttgatagctgcatctgcatggcatcgt---gtcatattgctatccttcttattatattctttatattgttcagATTGCATTGGCTCAGCCTTCAATATAAAGGGGGCAATGCAGTGCCCCAATTGTCGTAAGATTGAAAAAGGTCAGTGGCTTTATGCTAATGGTTGCCGATC

upper sequence: Vv14s0060g02280.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA19G42100.1 (Glycine max), 3'ss of exon 1
atcattctattaatacttgattagtgatacgtatctag---cacttgcatattgtcctttggccataac-ttattcttgtgattattgtcataatgctctccagATTGCATTGGTTCAGCATTCAATATCAAAGGGGCAATGCAATGTCCTAATTGTCGGAAAATTGAAAAAGGTCAATGGCTTTATGCAAATGGTTGTCGTAC
    || || |   |     ||  | ||| |    |||   ||  |||||    || |   | ||||    ||| ||| | ||||| ||| | ||  | | ||||||||||||| ||||| |||||||| || ||||||||||| || || |||||||| ||  ||||||||||||| ||||||||||| |||||||||||  |
-atgttttacttgaatcaattttataataagctgatagctgcatctgcatggcatcat---gtcatattgctatgcttcttattatagtctttatattgttcagATTGCATTGGCTCAGCCTTCAATATAAAGGGGGCAATGCAGTGCCCCAATTGTCGTAAGGTTGAAAAAGGTCAGTGGCTTTATGCTAATGGTTGTCGATC

upper sequence: Vv14s0060g02280.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT3G05545.1 (Arabidopsis thaliana), 3'ss of exon 1
atcattctattaatacttg--attagtgatacgtatctagcacttgcatattgtcctttggccataac---ttattcttgtgattattgtcataatgctctccagATTGCATTGGTTCAGCATTCAATATCAAAGGGGCAATGCAATGTCCTAATTGTCGGAAAATTGAAAAAGGTCAATGGCTTTATGCAAATGGTTGTCGTAC
   ||| |  | | | | |  |||| | ||     |  |    | |  | || |  ||| | || | |    ||   |      | || || |  || | |  |||||| |||||||| || ||||||   || || |  |||||||| || || ||||||||| | |||||||| || |||||||||||||| ||||||||| |
---attttcctcagattagggattattcattatgcttcatggttggtttcttatgtttttgacaaagccatctaacttcacatctgttttctt--tgtttttaagATTGTATTGGTTCGGCTTTCAATGCAAAGGGAGTGATGCAATGCCCCAACTGTCGGAAAGTAGAAAAAGGCCAGTGGCTTTATGCAAACGGTTGTCGTTC

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|294966052|gb|GW837419.1|GW837419
EST:     TGGGGATCGGGCCTGGGCCAAGCTTCAATGCGGACATCAATTTCATCTAG                         ATTGCATTGGTTCAGCATTCAATATCAAAGGGGCAATGCAATGTCCTAATT
genomic: TGGGGATCGGGCCTGGGCCAAGCTTCAATGCGGACATCAATTTCATCTAGgtgagtgaaa ... tgctctccagATTGCATTGGTTCAGCATTCAATATCAAAGGGGCAATGCAATGTCCTAATT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atattgtcctttggccataacttattcttgtgattattgtcataatgctctccagATTGCATTGGTTCAGCATTCAATATCAAAGGGGCAATGCAATGTCCTAATTGTCGGAAAATTGAAAAAGGTCAATGGCTTTATGCAAATGGTTGTCGTAC
              ccataac  putative branch site (score: 3)
                                             tgctctcc  putative PPT
                                attattgtcataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcattctattaatacttgattagtgatacgtatctagcacttgcatattgtcctttggccataacttattcttgtgattattgtcataatgctctccagATTGCATTGGTTCAGCATTCAATATCAAAGGGGCAATGCAATGTCCTAATTGTCGGAAAATTGAAAAAGGTCAATGGCTTTATGCAAATGGTTGTCGTAC

- - - - - - - - - - - - - - - - - - - cacttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccataac