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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtggcatttaatgcattgtatatagcatgctttttaaaataaaaggtgttttttctaattgttttctctttaccccctaacatccttttgtacatgcagAGTTTTGTTGGCCATGGGGACTCGATTAATGAAATCAGGACTCAGGCACTGAGACCATCACTTGTGGTGTCTGCAAGCAAA

Basic information

species Vitis vinifera
transcript Vv19s0014g05210.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0014g05210.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA10G02690.3 (Glycine max), 3'ss of exon 2
----agtggcatttaatgcattgtatatagcatgctttttaaaataaaaggtgttttttctaattgttttctctttaccccctaacatccttttgtacatgcagAGTTTTGTTGGCCATGGGGACTCGATTAATGAAATCAGGACTCAGGCACTGAGACCATCACTTGTGGTGTCTGCAAGCAAA
    |||   |  ||||   ||| ||  |  ||  | || |||||  |  |    | | |||||   |    ||      | | |  ||||  |  || |||||||||||||||||||||| |||||  | |||||||||||||||||  || | |  |||||||||||| | ||||||||||||
taaaagtcttaaataattttttgaattca--ataatgttaaaaatgtattgatcgtgtactaatccctgctgctacctgacatgatgtcctcct-cac-tgcagAGTTTTGTTGGCCATGGAGACTCCGTAAATGAAATCAGGACTCAAACATTAAAGCCATCACTTGTGATCTCTGCAAGCAAA

upper sequence: Vv19s0014g05210.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA02G17110.1 (Glycine max), 3'ss of exon 3
----agtggcatttaatgcattgtatatagcatgctttttaaaataaaaggtgttttttctaattgttttctctttaccccctaacatccttttgtacatgcagAGTTTTGTTGGCCATGGGGACTCGATTAATGAAATCAGGACTCAGGCACTGAGACCATCACTTGTGGTGTCTGCAAGCAAA
    |||   |  ||||   ||| ||  |  ||  | || |||||| |  |  ||| | |||||   |    ||      | | |  ||||  |  || |||||||||||||||||||||| |||||  | |||||||||||||| ||  || | |  |||||||||||| | ||||||||||||
taaaagtcttaaataattttttgaattca--ataatgttgaaaatatattgattttgtactaatccctgctgctaactgacatgatgtcctcct-cac-tgcagAGTTTTGTTGGCCATGGAGACTCCGTAAATGAAATCAGGACCCAAACATTAAAGCCATCACTTGTGATCTCTGCAAGCAAA

upper sequence: Vv19s0014g05210.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA13G36310.1 (Glycine max), 3'ss of exon 3
----agtggcatttaatgcattgtatatagcatgctttttaaaataaaaggtgttttttctaattgttttctctttaccccctaacatccttttgtacatgcagAGTTTTGTTGGCCATGGGGACTCGATTAATGAAATCAGGACTCAGGCACTGAGACCATCACTTGTGGTGTCTGCAAGCAAA
    | || | ||||||   || | |||   ||  | || |||||  |  |  | |    ||||   |    || |    | |||   |||  | |   |||||||||||||||||||||| ||||| || |||||| |||   ||||   | | |  |||||||| ||||| || |||||||||
ggtgaatgtc-tttaatatttttt-tattcaataatgttgaaaatgtactggttatgcattaatacgtgctgctatgttacataaagccctcctctg--tgcagAGTTTTGTTGGCCATGGAGACTCCATAAATGAAGTCAAAGCTCAAATATTAAATCCATCACTCGTGGTATCGGCAAGCAAA

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|71864778|gb|DT013833.1|DT013833
EST:     TCAATGGTATAATTCGTATCATTGATACTGGCAATGAGAAGATACACAAG                         AGTTTTGTTGGCCATGGGGACTCGATTAATGAAATCAGGACTCAGGCACTG
genomic: TCAATGGTATAATTCGTATCATTGATACTGGCAATGAGAAGATACACAAGgtactatttt ... gtacatgcagAGTTTTGTTGGCCATGGGGACTCGATTAATGAAATCAGGACTCAGGCACTG
EST: gi|161719190|gb|FC065436.1|FC065436
EST:     TCAATGGTATAATTCGTATCATTGATACTGGCAATGAGAAGATACACAAG                         AGTTTTGTTGGCCATGGGGACTCGATTAATGAAATCAGGACTCAGGCACTG
genomic: TCAATGGTATAATTCGTATCATTGATACTGGCAATGAGAAGATACACAAGgtactatttt ... gtacatgcagAGTTTTGTTGGCCATGGGGACTCGATTAATGAAATCAGGACTCAGGCACTG
EST: gi|351053554|gb|FQ459301.1|FQ459301
EST:     TCAATGGTATAATTCGTATCATTGATACTGGCAATGAGAAGATACACAAG                         AGTTTTGTTGGCCATGGGGACTCGATTAATGAAATCAGGACTCAGGCACTG
genomic: TCAATGGTATAATTCGTATCATTGATACTGGCAATGAGAAGATACACAAGgtactatttt ... gtacatgcagAGTTTTGTTGGCCATGGGGACTCGATTAATGAAATCAGGACTCAGGCACTG
EST: gi|351036699|gb|FQ457412.1|FQ457412
EST:     TCAATGGTATAATTCGTATCATTGATACTGGCAATGAGAAGATACACAAG                         AGTTTTGTCGGCCATGGGGACTCGATTAATGAAATCAGGACTCAGGCACTG
genomic: TCAATGGTATAATTCGTATCATTGATACTGGCAATGAGAAGATACACAAGgtactatttt ... gtacatgcagAGTTTTGTTGGCCATGGGGACTCGATTAATGAAATCAGGACTCAGGCACTG
EST: gi|351043856|gb|FQ452650.1|FQ452650
EST:     TCAATGGTATAATTCGTATCATTGATACTGGCAATGAGAAGATACACAAG                         AGTTTTGTTGGCCATGGGGACTCGATTAATGAAATCAGGACTCAGGCACTG
genomic: TCAATGGTATAATTCGTATCATTGATACTGGCAATGAGAAGATACACAAGgtactatttt ... gtacatgcagAGTTTTGTTGGCCATGGGGACTCGATTAATGAAATCAGGACTCAGGCACTG
EST: gi|352791431|gb|FQ481010.1|FQ481010
EST:     TCAATGGTATAATTCGTATCATTGATACTGGCAATGAGAAGATACACAAG                         AGTTTTGTTGGCCATGGGGACTCGATTAATGAAATCAGGACTCAGGCACTG
genomic: TCAATGGTATAATTCGTATCATTGATACTGGCAATGAGAAGATACACAAGgtactatttt ... gtacatgcagAGTTTTGTTGGCCATGGGGACTCGATTAATGAAATCAGGACTCAGGCACTG
EST: gi|161711022|gb|FC059448.1|FC059448
EST:     TCAATGGTATAATTCGTATCATTGATACTGGCAATGAGAAGATACACAAG                         AGTTTTGTTGGCCATGGGGACTCGATTAATGAAATCAGGACTCAGGCACTG
genomic: TCAATGGTATAATTCGTATCATTGATACTGGCAATGAGAAGATACACAAGgtactatttt ... gtacatgcagAGTTTTGTTGGCCATGGGGACTCGATTAATGAAATCAGGACTCAGGCACTG
EST: gi|294965480|gb|GW839051.1|GW839051
EST:     TCAATGGTATAATTCGTATCATTGATACTGGCAATGAGAAGATACACAAG                         AGTTTTGTTGGCCATGGGGACTCGATTAATGAAATCAGGACTCAGGCACTG
genomic: TCAATGGTATAATTCGTATCATTGATACTGGCAATGAGAAGATACACAAGgtactatttt ... gtacatgcagAGTTTTGTTGGCCATGGGGACTCGATTAATGAAATCAGGACTCAGGCACTG
EST: gi|351033874|gb|FQ447912.1|FQ447912
EST:     TCAATGGTATAATTCGTATCATTGATACTGGCAATGAGAAGATACACAAG                         AGTTTTGTTGGCCATGGGGACTCGATTAATGAAATCAGGACTCAGGCACTG
genomic: TCAATGGTATAATTCGTATCATTGATACTGGCAATGAGAAGATACACAAGgtactatttt ... gtacatgcagAGTTTTGTTGGCCATGGGGACTCGATTAATGAAATCAGGACTCAGGCACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtgttttttctaattgttttctctttaccccctaacatccttttgtacatgcagAGTTTTGTTGGCCATGGGGACTCGATTAATGAAATCAGGACTCAGGCACTGAGACCATCACTTGTGGTGTCTGCAAGCAAA
                              ccctaac  putative branch site (score: 2)
                                      tccttttgt  CT-rich tract
     tttttctaattgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtggcatttaatgcattgtatatagcatgctttttaaaataaaaggtgttttttctaattgttttctctttaccccctaacatccttttgtacatgcagAGTTTTGTTGGCCATGGGGACTCGATTAATGAAATCAGGACTCAGGCACTGAGACCATCACTTGTGGTGTCTGCAAGCAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- -ggcattt
- - - - - - tgcattg
- - - - - - - - - - - - -gcatgct
- - - - - - - - - - - - - - - - - - aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catcctt