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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgacaattctctttctccctcgaatctccatcttctttctcaaatgggtcctttctctgaaactgttttaaactcccagGGACCTTAAGCCTCACAATCTCTTGATGGACCGCAAGACAATGATGCTGAAAATAGCAGATCTTGGACTGGCTAGGGCGTTTACTCTTCCTATTAAGAAG

Basic information

species Vitis vinifera
transcript Vv18s0122g00550.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0122g00550.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA09G08250.2 (Glycine max), 3'ss of exon 2
-----------------gtgacaattctctttc---tccctcgaatctccatcttctttctcaaatgggtcctttctctgaaactgttttaaactccc-----------agGGACCTTAAGCCTCACAATCTCTTGATGGACCGCAAGACAATGATGCTGAAAATAGCAGATCTTGGACTGGCTAGGGCGTTTACTCTTCCTATTAAGAAG
                        ||| |||||   ||||||     |  || |   |    |  |  || | |  | |||||   ||| ||  |              |||||| | |||||||||||||| ||||||||||| || ||||||||||| ||||| || ||||||||||| ||| |||| |||||| | || |||||||| 
gtagtacttaacccttaacccttgttccctttcatttccctcactcatgtatgtaactatgtatgtatgtacatattatgaaataatttgaatttttatttatttattaagGGACTTGAAGCCTCACAATCTGTTGATGGACCGGAAAACAATGATGCTTAAAATTGCTGATCTTGGACTCGCTCGGGCATTTACTGTGCCAATTAAGAAA

upper sequence: Vv18s0122g00550.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA07G07640.1 (Glycine max), 3'ss of exon 3
---gtgacaattctctttctccctcgaatctccatcttctttctcaaatgggtcctttctctgaaactgttttaaactccca-gGGACCTTAAGCCTCACAATCTCTTGATGGACCGCAAGACAATGATGCTGAAAATAGCAGATCTTGGACTGGCTAGGGCGTTTACTCTTCCTATTAAGAAG
    |   ||||  |  |   ||     || |  || | |  |||| | | ||    |   ||||  | |  | |  |   | ||||| | || ||||||||||| ||||||||||| || ||||||||||| ||||| || ||||||||||| ||| |||| |||||| | || |||||||| 
gtactagtaattaacccttaacccttgttccctttcatttccctcacacgtgtataat---tgaatttttacttatttattaagGGACTTGAAACCTCACAATCTGTTGATGGACCGAAAAACAATGATGCTTAAAATTGCTGATCTTGGACTCGCTCGGGCATTTACTGTGCCAATTAAGAAA

upper sequence: Vv18s0122g00550.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA14G39760.1 (Glycine max), 3'ss of exon 2
gtgacaattctctttctccctcgaatctccatcttctttctcaaatgggtcctttctctgaaactg---ttttaaact---cccagGGACCTTAAGCCTCACAATCTCTTGATGGACCGCAAGACAATGATGCTGAAAATAGCAGATCTTGGACTGGCTAGGGCGTTTACTCTTCCTATTAAGAAG
       |      |   ||   | || |  || | | ||||| |     | |     |  |||||    ||||| ||      |||||| | |||||||||||||||||||||||||| || || |||||||| ||||| || ||||||||||| ||| | || |||||  | || |||||||| 
------gtatgtagttaaccctaattccctttcatttctctcacaccatccttccgatttgaactggatctttaatctttatttagGGACTTGAAGCCTCACAATCTCTTGATGGACCGAAAAACCATGATGCTTAAAATTGCTGATCTTGGACTCGCTCGAGCATTTACCGTGCCAATTAAGAAA

upper sequence: Vv18s0122g00550.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA17G38210.1 (Glycine max), 3'ss of exon 1
gtgacaattctctttctccctcgaatctccatcttctttctcaaatgggtcctttctctgaaact----gttttaaactcccagGGACCTTAAGCCTCACAATCTCTTGATGGACCGCAAGACAATGATGCTGAAAATAGCAGATCTTGGACTGGCTAGGGCGTTTACTCTTCCTATTAAGAAG
      | |||  ||| |  ||   ||||   |  ||   || |||     |  |   |||| ||     | || |      |||||| | || ||||||||||||||||||||||  || || |||||||| ||||| || ||||||||||| ||| | || |||||| | || |||||||| 
---ggtactctagttccctttcatttctctcacacctccttcgaata---tcaattgatgaatctttcaatctttattattaaGGGACTTGAAACCTCACAATCTCTTGATGGACCCAAAAACCATGATGCTTAAAATTGCTGATCTTGGACTCGCTCGAGCATTTACTGTGCCGATTAAGAA-

upper sequence: Vv18s0122g00550.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G20930.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgacaattctctttctccctcga-atctccatctt---------ctttctcaaatgggtcctttctctgaaactgttttaaactcc---cagGGACCTTAAGCCTCACAATCTCTTGATGGACCGCAAGACAATGATGCTGAAAATAGCAGATCTTGGACTGGCTAGGGCGTTTACTCTTCCTATTAAGAAG
|| | |||  ||||| |      | | ||    |||         | || | | |  | ||  |  ||  |   ||| ||    ||    |||||| ||||||||||||||||||||||||||||| |||||||||| ||| |||||||||||||||||| | || || || || ||||| || || || |||
gtaaaaatcgtctttgttttggaagaactatgacttgagataacccattttgacacagatctctaatcctac-ttgtcttggtttcattacagGGATCTTAAGCCTCACAATCTCTTGATGGACCGGAAGACAATGACGCTCAAAATAGCAGATCTTGGATTAGCCAGAGCCTTCACTCTCCCAATGAAAAAG

upper sequence: Vv18s0122g00550.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G76540.1 (Arabidopsis thaliana), 3'ss of exon 3
gtga-caattctctttctccctcgaatctccatcttctt-----------tctcaaat----------------gggtcctttctctgaa-actgttttaaactcc----cagGGACCTTAAGCCTCACAATCTCTTGATGGACCGCAAGACAATGATGCTGAAAATAGCAGATCTTGGACTGGCTAGGGCGTTTACTCTTCCTATTAAGAAG
||||    ||||||  ||  | |   | | || |||||            | | | ||                |  | |||  ||| |  | |  |      | |    ||| || || ||||||||||||||||||||||| | ||||||||||| ||| |||||||||||||||||  | || || || || ||||| || || ||||||
gtgaattgttctctggctttcccttgttttcaacttctaagtgagaatgattttagataataacttggaagagagatttcttcttcttactatttctccttgtttcaaaacagAGATCTCAAGCCTCACAATCTCTTGATGGATCCCAAGACAATGAGGCTCAAAATAGCAGATCTTGGTTTAGCCAGAGCCTTCACTCTGCCAATGAAGAAG

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|34542681|gb|CF510913.1|CF510913
EST:     CAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGGGTATTGCACAG                         GGACCTTAAGCCTCACAATCTCTTAATGGACCGCAAGACAATGATGCTGAA
genomic: CAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGGGTATTGCACAGgtgacaattc ... aaactcccagGGACCTTAAGCCTCACAATCTCTTGATGGACCGCAAGACAATGATGCTGAA
EST: gi|351046614|gb|FQ453230.1|FQ453230
EST:     CAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGGGTATTGCACAG                         GGACCTTAAGCCTCACAATCTCTTAATGGACCGCAAGACAATGATGCTGAA
genomic: CAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGGGTATTGCACAGgtgacaattc ... aaactcccagGGACCTTAAGCCTCACAATCTCTTGATGGACCGCAAGACAATGATGCTGAA
EST: gi|351055531|gb|FQ442327.1|FQ442327
EST:     CAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGGGTATTGCACAG                         GGACCTTAAGCCTCACAATCTCTTAATGGACCGCAAGACAATGATGCTGAA
genomic: CAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGGGTATTGCACAGgtgacaattc ... aaactcccagGGACCTTAAGCCTCACAATCTCTTGATGGACCGCAAGACAATGATGCTGAA
EST: gi|351056035|gb|FQ453496.1|FQ453496
EST:     CAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGGGTATTGCACAG                         GGACCTTAAGCCTCACAATCTCTTAATGGACCGCAAGACAATGATGCTGAA
genomic: CAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGGGTATTGCACAGgtgacaattc ... aaactcccagGGACCTTAAGCCTCACAATCTCTTGATGGACCGCAAGACAATGATGCTGAA
EST: gi|110376059|gb|EC941099.1|EC941099
EST:     CAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGGGTATTGCACAG                         GGACCTTAAGCCTCACAATCTCTTAATGGACCGCAAGACAATGATGCTGAA
genomic: CAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGGGTATTGCACAGgtgacaattc ... aaactcccagGGACCTTAAGCCTCACAATCTCTTGATGGACCGCAAGACAATGATGCTGAA
EST: gi|110426132|gb|EC992529.1|EC992529
EST:     CAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGGGTATTGCACAG                         GGACCTTAAGCCTCACAATCTCTTAATGGACCGCAAGACAATGATGCTGAA
genomic: CAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGGGTATTGCACAGgtgacaattc ... aaactcccagGGACCTTAAGCCTCACAATCTCTTGATGGACCGCAAGACAATGATGCTGAA
EST: gi|351039035|gb|FQ457710.1|FQ457710
EST:     CAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGGGTATTGCACAG                         GGACCTTAAGCCTCACAATCTCTTAATGGACCGCAAGACAATGATGCTGAA
genomic: CAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGGGTATTGCACAGgtgacaattc ... aaactcccagGGACCTTAAGCCTCACAATCTCTTGATGGACCGCAAGACAATGATGCTGAA
EST: gi|349827747|gb|FQ422615.1|FQ422615
EST:     CAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGGGTATTGCACAG                         GGACCTTAAGCCTCACAATCTCTTAATGGACCGCAAGACAATGATGCTGAA
genomic: CAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGGGTATTGCACAGgtgacaattc ... aaactcccagGGACCTTAAGCCTCACAATCTCTTGATGGACCGCAAGACAATGATGCTGAA
EST: gi|33404794|gb|CF210421.1|CF210421
EST:     CAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGGGTATTGCACAG                         GGACCTTAAGCCTCACAATCTCTTAATGGACCGCAAGACAATGATGCTGAA
genomic: CAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGGGTATTGCACAGgtgacaattc ... aaactcccagGGACCTTAAGCCTCACAATCTCTTGATGGACCGCAAGACAATGATGCTGAA
EST: gi|352795715|gb|FQ480303.1|FQ480303
EST:     CAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGGGTATTGCACAG                         GGACCTTAAGCCTCACAATCTCTTAATGGACCGCAAGACAATGATGCTGAA
genomic: CAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGGGTATTGCACAGgtgacaattc ... aaactcccagGGACCTTAAGCCTCACAATCTCTTGATGGACCGCAAGACAATGATGCTGAA
EST: gi|34542594|gb|CF510826.1|CF510826
EST:     CAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGGGTATTGCACAG                         GGACCTTAAGCCTCACAATCTCTTAATGGACCGCAAGACAATGATGCTGAA
genomic: CAATTATGCAAAGGTGTTGCTTTCTGCCATGGTCATGGGGTATTGCACAGgtgacaattc ... aaactcccagGGACCTTAAGCCTCACAATCTCTTGATGGACCGCAAGACAATGATGCTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctccatcttctttctcaaatgggtcctttctctgaaactgttttaaactcccagGGACCTTAAGCCTCACAATCTCTTGATGGACCGCAAGACAATGATGCTGAAAATAGCAGATCTTGGACTGGCTAGGGCGTTTACTCTTCCTATTAAGAAG
                                                ctccc  CT-rich tract
                                       tgttttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgacaattctctttctccctcgaatctccatcttctttctcaaatgggtcctttctctgaaactgttttaaactcccagGGACCTTAAGCCTCACAATCTCTTGATGGACCGCAAGACAATGATGCTGAAAATAGCAGATCTTGGACTGGCTAGGGCGTTTACTCTTCCTATTAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG