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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgcatcttttcttcatcaagggatgcatatccaagaagaacaatctatgcatgtggtatggcgatgtatgaactgaaccagtttgtttcttgcttgcagACTTATGGTTTTGAAAATCAGCTCAAAGTTTGAACTGCGGCGATTTTGCCGTACAACTGGAGCTGTTGCAGTT

Basic information

species Vitis vinifera
transcript Vv08s0007g07460.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g07460.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G083095_T03 (Zea mays), 3'ss of exon 6
---------------------------------------------------------------------------ttgcatcttttcttcat-caagggatgcatatc-caagaagaacaatctatgcatg--------tggtatgg----cgatgt-----atgaactgaaccagtttgtttcttgcttgcagACTTATGGTTTTGAAAATCAGCTCAAAGTTTGAACTGCGGCGATTTTGCCGTACAACTGGAGCTGTTGCAGTT
                                                                           ||| |  |||  || |  | || ||    |||   | |    | | | | | ||          | ||||||    |||  |     ||   |   ||    |  | |  || |||||| || |||||| ||||||||||||| |||||||||||| |  |||| |||||||| ||||| ||||||||| ||
gtgagtttttttgcttttcgtatgtgttctgaactgaataggttatctgaattttctgtgcagtattgctcattgttgaaaatttcttttagactagagagagttattgtatgtgttatattttctccaaaattaaggattgtatggtcatcgacctttttgatagccattacttactgatgttatgtttgcagGCTGATGGTTCTGAAAATCAGCTCGAAGTTTGAACTGAGAAGATTCTGCCGTACTACTGGGGCTGTTGCAATT

upper sequence: Vv08s0007g07460.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G381744_T01 (Zea mays), 3'ss of exon 6
----ttgcatcttttcttcatcaagggatgcatatccaagaagaacaatctatgcatgtggtatggcgatgtatgaactgaaccagtttgtttcttgcttgcagACTTATGGTTTTGAAAATCAGCTCAAAGTTTGAACTGCGGCGATTTTGCCGTACAACTGGAGCTGTTGCAGTT
    ||| || | |  |  ||      ||  ||     |    |  | | |||   ||| | |   |  ||| |   ||  ||   ||  | |  || |||||| || |||||| ||||||||||||| |||||||||||  |  | || |||||||| ||||| ||||||||| ||
attattgtatgtatgttatattctccaat--attggggactgtatgagtgtataggtgttg-acctctttgt-tagcctttacttattgatgttctgtttgcagGCTGATGGTTCTGAAAATCAGCTCGAAGTTTGAACTAAGAAGGTTCTGCCGTACTACTGGGGCTGTTGCAATT

upper sequence: Vv08s0007g07460.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA16G26920.1 (Glycine max), 3'ss of exon 6
-----------------------ttgcatcttttcttcatcaagggatgcatatccaagaagaacaatcta---tgcatgtggtatggcgatgtatgaactgaaccagtttgtttcttgcttgcagACTTATGGTTTTGAAAATCAGCTCAAAGTTTGAACTGCGGCGATTTTGCCGTACAACTGGAGCTGTTGCAGTT
                       |||    ||||  |  ||    | |    |   || | ||||| | ||   | || |||  |        | | ||||  |  |      | | ||||||||| ||||||||| ||||||||||||||||||||||||| || ||||||||||| ||||||||  |||||||  | 
gtatgtgaagtctttattcatgtttggtggttttaattgtctcttgctattaaattaatatgaacattataacttacaagtg-cacattagattgttaacttcaaaa------tccctgcttgcagGCTTATGGTTCTGAAAATCAGCTCAAAGTTTGAACTACGTCGATTTTGCCGGACAACTGGTTCTGTTGCCATG

upper sequence: Vv08s0007g07460.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA02G07910.1 (Glycine max), 3'ss of exon 6
----ttgcatcttttcttca---tcaagggatgca--tatccaagaagaac-aatctatgcatgtggtatggcgatgtatgaactgaa---ccagttt---gtttcttgcttgcagACTTATGGTTTTGAAAATCAGCTCAAAGTTTGAACTGCGGCGATTTTGCCGTACAACTGGAGCTGTTGCAGTT
     || |   ||| | ||   |    || |  |  | ||    |  |   |||  ||        |||  |     || |  |      | |  ||     ||| |||||  || ||||||||| ||||||||||||||||||||||||| || ||||||||||| ||||| ||  |||||||  | 
gtatgtgaagtctttatccatgtttggtggttttaattgtctcttactattgaattaatatgaacattataactgcacattagattgttttctaacttcaaaattcctgcttttagGCTTATGGTTCTGAAAATCAGCTCAAAGTTTGAACTACGTCGATTTTGCCGGACAACCGGCTCTGTTGCCATG

upper sequence: Vv08s0007g07460.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT3G03960.1 (Arabidopsis thaliana), 3'ss of exon 6
ttgcatcttttcttcatcaagggatgcatatccaagaagaacaatctatgcatgtggtatggcgatgtatgaactgaaccagtttgtttcttgcttgcagACTTATGGTTTTGAAAATCAGCTCAAAGTTTGAACTGCGGCGATTTTGCCGTACAACTGGAGCTGTTGCAGTT
               ||     ||  ||||||     | |    |||  ||   || |||     ||| || | |     |     ||| ||  | ||||  | ||||| ||||||||||||||||||||||||||| |||| |||||||||||| | || ||||| ||   |
-------------gtatgtgtagac-catatcatgttatactcgtcttagctattgttat-----tgtctgcattctgataccccattttttcttggcagGATAATGGTATTGAAAATCAGCTCAAAGTTTGAACTGAGGCGTTTTTGCCGTACAGCGGGGGCTGTCGCCCAT

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|71859802|gb|DT008857.1|DT008857
EST:     AGTGGAGGGGCAGTTGGAGAGATGGCATTGCATTTCTGTGAGCGATACAA                         ACTTATGGTTTTGAAAATCAGCTCAAAGTTTGAACTGC
genomic: AGTGGAGGGGCAGTTGGAGAGATGGCATTGCATTTCTGTGAGCGATACAAgtacattatt ... ttgcttgcagACTTATGGTTTTGAAAATCAGCTCAAAGTTTGAACTGC
EST: gi|110687426|gb|EE064824.1|EE064824
EST:     AGTGGAGGGGCAGTTGGAGAGATGGCATTGCATTTCTGTGAGCGATACAA                         ACTTATGGTTTTGAAAATCAGCTCAAAGTTTGAACTGCGGCGATTTTGCCG
genomic: AGTGGAGGGGCAGTTGGAGAGATGGCATTGCATTTCTGTGAGCGATACAAgtacattatt ... ttgcttgcagACTTATGGTTTTGAAAATCAGCTCAAAGTTTGAACTGCGGCGATTTTGCCG
EST: gi|110701079|gb|EE078296.1|EE078296
EST:     AGTGGAGGGGCAGTTGGAGAGATGGCATTGCATTTCTGTGAGCGATACAA                         ACTTATGGTTTTGAAAATCAGCTCAAAGTTTGAACTGCGGCGATTTTGCCG
genomic: AGTGGAGGGGCAGTTGGAGAGATGGCATTGCATTTCTGTGAGCGATACAAgtacattatt ... ttgcttgcagACTTATGGTTTTGAAAATCAGCTCAAAGTTTGAACTGCGGCGATTTTGCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatgcatgtggtatggcgatgtatgaactgaaccagtttgtttcttgcttgcagACTTATGGTTTTGAAAATCAGCTCAAAGTTTGAACTGCGGCGATTTTGCCGTACAACTGGAGCTGTTGCAGTT
                                     tttgtttcttgctt  CT-rich tract
                                     tttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgcatcttttcttcatcaagggatgcatatccaagaagaacaatctatgcatgtggtatggcgatgtatgaactgaaccagtttgtttcttgcttgcagACTTATGGTTTTGAAAATCAGCTCAAAGTTTGAACTGCGGCGATTTTGCCGTACAACTGGAGCTGTTGCAGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
-tgcatct
- - - - - - -tcatcaa
- - - - - - - - - - -ggatgca
- - - - - - - - - - - - - - - - - -gaagaac
- - - - - - - - - - - - - - - - - - - - - - -ctatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgaacc