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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cccataatgtttctattttccccacttttctctcatctaatttttctctgctccatcaggctgatgacagtgttaaaagattcttgtatttatgatgcagAAATTTTTGGATAGTTCAAAGCTGAAAAGACACTTCCTGATTCATACAGGAGAGAGAGATTTTGTGTGTCCTCATGAAGGCTGTGGGAAG

Basic information

species Vitis vinifera
transcript Vv12s0035g00660.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0035g00660.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os02g34680.1 (Oryza sativa), 3'ss of exon 3
------cccataatgtttctattttccccacttttctctcatctaatttttctctgctccatcaggctgat--gacagtgttaaaagattcttgtattt-atgatgcagAAATTTTTGGATAGTTCAAAGCTGAAAAGACACTTCCTGATTCATACAGGAGAGAGAGATTTTGTGTGTCCTCATGAAGGCTGTGGGAAG
      ||  |||| |||||    | |       | |||     | | |  |  |||| | || || |  |  |  | |||||     || ||| || | |   ||||||||||||| || || || |||||||| || || || || ||||||||||||||||   | ||||| || ||||||||||||||||| |||
gtactgcctgtaatctttcttgcctgcgttggcctttctggatcactatggcattgctgcttctgggttgttcgctaatgttattttctttttgaatctgactttgcagAAATTTTTAGACAGCTCTAAGCTGAAGAGGCATTTTCTTATTCATACAGGAGAGAAGAACTTTGTCTGCCCTCATGAAGGCTGTGGAAAG

upper sequence: Vv12s0035g00660.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM5G885700_T02 (Zea mays), 3'ss of exon 3
cccataatgtttctattttccccacttttctctcatctaatttttctctgctccatcaggct--gatgacagt--gttaaaagattcttgtatttatga---------tgcagAAATTTTTGGATAGTTCAAAGCTGAAAAGACACTTCCTGATTCATACAGGAGAGAGAGATTTTGTGTGTCCTCATGAAGGCTGTGGGAAG
    || ||||| || || |    |   || |  |   |  ||   |||||     || | |   ||  ||||   || |   || ||| |  |  | |         |||||||||| || |||||||| ||| |||| ||||| || || |||||||||||||| |   |||||||||| || |||||||| |||||||||
---gtactgtttataattcctggtcacatcccagagtaatcttcagtctgcaaaggcatgtttctatttcagttgcttgattaatcctttttctgctaaatctgattttgcagAAATTCTTAGATAGTTCTAAGTTGAAGAGACATTTTCTTATTCATACAGGAGAAAAGAATTTTGTGTGCCCACATGAAGGTTGTGGGAAG

upper sequence: Vv12s0035g00660.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA08G13310.1 (Glycine max), 3'ss of exon 2
-cccataatgtttctattttccccacttttctctcatctaatttttctctgctccatcaggctgat--gacagtgttaaaagattcttgtatttatgatgcagAAATTTTTGGATAGTTCAAAGCTGAAAAGACACTTCCTGATTCATACAGGAGAGAGAGATTTTGTGTGTCCTCATGAAGGCTGTGGGAAG
    ||  |  | | || |  |    |    |  | |    |  ||  ||       ||||   ||    ||||| | ||||  | ||||  |||   ||||||||||| ||||||| |||||| |||||||||| || || ||||||||||| ||||| ||||||||||||||||||||||||||||| |||
atttatt-taatgccatgtatcaagatgcgatagcttgctgtggtttactctaatggcaggtctatttagcagtgctgaaagtattttgt--ttacattgcagAAATTTCTGGATAGCTCAAAGTTGAAAAGACATTTTCTCATTCATACAGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAG

upper sequence: Vv12s0035g00660.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA05G30150.1 (Glycine max), 3'ss of exon 3
-cccataatgtttctattttccccacttttctctcatcta-atttttctctgctccatcaggctgat--gacagtgttaaaagattcttgtatttatgatgcagAAATTTTTGGATAGTTCAAAGCTGAAAAGACACTTCCTGATTCATACAGGAGAGAGAGATTTTGTGTGTCCTCATGAAGGCTGTGGGAAG
       |||| || | || |   |  || || |   ||    ||| ||||  |    ||||   ||    ||||| | ||||  | ||||  | |   ||||||||||| ||||||| |||||| |||||||||| || || ||||||||||| ||||| ||||||||||||||||||||||||||||| |||
taatgctatgtatcaagttgcaatagcttgctgtggactgtggtttactctaat--ggcaggtctatttagcagtgctgaaagtattttgt--tcacattgcagAAATTTCTGGATAGCTCAAAGTTGAAAAGACATTTTCTCATTCATACAGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAG

upper sequence: Vv12s0035g00660.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT4G06634.3 (Arabidopsis thaliana), 3'ss of exon 3
cccataatgtttc-tattttccccacttttctctcatctaatttttctctgctccatcaggctgatgacagtgttaaaagattcttgtatttatgatgcagAAATTTTTGGATAGTTCAAAGCTGAAAAGACACTTCCTGATTCATACAGGAGAGAGAGATTTTGTGTGTCCTCATGAAGGCTGTGGGAAG
        ||||  || | ||| | ||||  | |    ||     || ||        |   ||| | ||   |       || |||| ||| ||   ||||||||| |||||||||||||| |||| ||||| |  || |||||||| ||||||||| ||| | | ||| || ||||||| ||||| |||
--------gtttaataatatcctctctttggtttggcttacacactcactttcatgatatattgaagccatctt------gtttttgttttt-tgtaacagAAATTTCTGGATAGTTCAAAGTTGAAGAGACATTATCTTATTCATACTGGAGAGAGAAATTATATATGTACTTATGAAGGATGTGGAAAG

upper sequence: Vv12s0035g00660.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S42_134V6.1 (Physcomitrella patens), 3'ss of exon 3
--cccataatgtttctattttccccacttttctctcatctaatttttctctgctccatcaggctgatgacagtgttaaaagattcttgtatttatgatgcagAAATTTTTGGATAGTTCAAAGCTGAAAAGACACTTCCTGATTCATACAGGAGAGAGAGATTTTGTGTGTCCTCATGAAGGCTGTGGGAAG
  |  ||    ||||||    | |    ||  |   || |   || |  |       ||    | || |   | | | || ||| |  | | || | | |||   ||  | || || ||||||||||||||||| || ||||||||||| || ||||   ||||||| |||||   |||||||||||| |||
tccttatctgttttctagacacgctttattattggaatatgtgttcttaccaagttctctttgtcatcaacttatgataacatt-tgatgtctacg-tacagCGTTTCGTCGACAGCTCAAAGCTGAAAAGACATTTTCTGATTCATACGGGGGAGAAGCATTTTGTTTGTCCATTTGAAGGCTGTGGCAAG

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|30125100|gb|CB910439.1|CB910439
EST:     ATATCCATGGCGAGAGACAATATGTTTGCCATTATGAGGGGTGTGGAAAG                         AAATTTTTGGATAGTTCAAAGCTGAAAAGACACTTCCTGATTCATACAGGA
genomic: ATATCCATGGCGAGAGACAATATGTTTGCCATTATGAGGGGTGTGGAAAGgtaatgtgtt ... tatgatgcagAAATTTTTGGATAGTTCAAAGCTGAAAAGACACTTCCTGATTCATACAGGA
EST: gi|110729446|gb|EE105404.1|EE105404
EST:     ATATCCATGGCGAGAGACAATATGTTTGCCATTATGAGGGGTGTGGAAAG                         AAATTTTTGGATAGTTCAAAGCTGAAAAGACACTTCCTGATTCATACAGGA
genomic: ATATCCATGGCGAGAGACAATATGTTTGCCATTATGAGGGGTGTGGAAAGgtaatgtgtt ... tatgatgcagAAATTTTTGGATAGTTCAAAGCTGAAAAGACACTTCCTGATTCATACAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctgctccatcaggctgatgacagtgttaaaagattcttgtatttatgatgcagAAATTTTTGGATAGTTCAAAGCTGAAAAGACACTTCCTGATTCATACAGGAGAGAGAGATTTTGTGTGTCCTCATGAAGGCTGTGGGAAG
             ggctgat  putative branch site (score: 4)
                           ttaaaagattcttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cccataatgtttctattttccccacttttctctcatctaatttttctctgctccatcaggctgatgacagtgttaaaagattcttgtatttatgatgcagAAATTTTTGGATAGTTCAAAGCTGAAAAGACACTTCCTGATTCATACAGGAGAGAGAGATTTTGTGTGTCCTCATGAAGGCTGTGGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
cccataa
- - - - - - - - - tccccac
- - - - - - - - - - - - - - -ctctcat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaagat