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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcattaattttactttccctttttctattctgtaattttttgacctcttgggcatttattgcattagttattgaaaatctacaactactaaaactaatacctattatcggagtatattttcttagggtttttgtcttcccttctaaatcaccccttgacttttattttgcatcatctgttaaaaaacatacagGTTGTTCCAGAGACCTTGGAACCAAGTCTGCAGTTAGCTGCTGCTGTTCTTGCACAG

Basic information

species Vitis vinifera
transcript Vv15s0046g03390.t01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: LOC_Os04g58620.1 (Oryza sativa), 3'ss of exon 18
gtatcattaattttactttccctttttctattctgtaattttttgacctcttgggcatttattgcattagttattgaaaatctacaactactaaaactaatacctattatcggagtatattttcttagggtttttgtcttcccttctaaatcaccccttgacttttattttgcatcatctgttaaaaaacatacagGTTGTTCCAGAGACCTTGGAACCAAGTCTGCAGTTAGCTGCTGCTGTTCTTGCACAG
                                                                                 | |    | ||    || || | |||  |     |||||  | |      || | ||  |  ||  | |  ||    |     |     | ||||  || ||||          |||||| || |||||||||||||||||||| ||||| |||||||||||||||||||||
-----------------------------------------------------------------------------gggccca----ttctttgtcttatgcatatccttttgttatatactgta-----ttctatcaccgatttaataatactatctcctaatggaactacatctacttttaa----------gGTTGTCCCTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAG

upper sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA09G39770.1 (Glycine max), 3'ss of exon 21
gtatcattaattttactttccctttttctattctgtaattttttgacctcttgggcatttattgcattagttattgaaaatctacaactactaaaactaatacctattatcggagtatattttct-tagggtttttgtcttcccttctaaatcaccccttgacttttattttgcatcatctgttaaaaaacatacagGTTGTTCCAGAGACCTTGGAACCAAGTCTGCAGTTAGCTGCTGCTGTTCTTGCACAG
                                                                                              ||  | |   | || |       |  ||| | |||     |||         || |           |   ||| | |  |  |  |  |   |  ||| |||||||| ||||||||||||||||||||||| ||  |||| |||||||| ||| | |||
----------------------------------------------------------------------------------------------aaagagt-tttgttgtttagtcttgctttttgtagcaaaattgaaacaaaaacttaccattagtgaaatgcttactctagagaactttctgcca--catgcagGTTGTCCCAGAGACCTTGGAACCAAGTCTTCAACTAGCAGCTGCTGTGCTTTCTCAG

upper sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA07G08030.1 (Glycine max), 3'ss of exon 17
gtatcattaattttactttccctttttctattctgtaattttttgacctcttgggcatttattgcattagttattgaaaatctacaactactaaaactaatacctattatcggagtatattttcttagggtttttgtcttcccttctaaatcaccccttgacttttattttgcatcatctgttaaaaaacatacagGTTGTTCCAGAGACCTTGGAACCAAGTCTGCAGTTAGCTGCTGCTGTTCTTGCACAG
       |||| || || |  | ||||||||| || ||| || |||   | |       ||| | || | ||    |   | |     |||||| ||  ||    |||     |  ||| | | |||            ||   |||   | | | ||| |  | |    ||| || |   ||        | |||||||| ||||||||||||||||||||||| ||  |||| || || || ||||| |||
------gtaatatt-ctattaccttttctattatg-aatgttatgattgcct-------tatggtataattttggaagtgtttttctttactaatacatatttagatttagccaaaatactctgttaa-----------tcttctctgtcttatctctttatctct---ctgcctcttgcatt--------tgcagGTTGTCCCAGAGACCTTGGAACCAAGTCTTCAACTAGCAGCCGCCGTGCTTGCTCAG

upper sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA18G46420.1 (Glycine max), 3'ss of exon 25
gtatcattaattttactttccctttttctattctgtaattttttgacctcttgggcatttattgcattagttattgaaaatctacaactactaaaactaatacctattatcggagtatattttcttagggtttttgtcttcccttctaaatcaccccttgacttttattttgcatcatctgttaaaaaacatacagGTTGTTCCAGAGACCTTGGAACCAAGTCTGCAGTTAGCTGCTGCTGTTCTTGCACAG-
                                                                                            || | |  |   | || | |   |   ||||  |||     |||         || |  ||    |  | |  |  | |  |  |  |  |   |  | | |||||||| || |||||||||||||||||||| ||  |||| |||||||| ||| | ||| 
--------------------------------------------------------------------------------------------aagagttttgt-tgttttagtcttgc-tttttgtagcaaaattgaaagaaaaactta-ccattagtgaaatgcttatctagagaactttctgcca--cttgcaggTTGTCCCGGAGACCTTGGAACCAAGTCTTCAACTAGCAGCTGCTGTGCTTTCTCAGG

upper sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: AT4G00630.1 (Arabidopsis thaliana), 3'ss of exon 17
gtatcattaattttactttccctttttctattctgtaattttttgacctcttgggcatttattgcattagttattgaaaatctacaactactaaaactaatacctattatcggagtatattttcttagggtttttgt-cttcccttctaaatcaccccttgacttttattttgcatcatctgttaaaaaacatacagGTTGTTCCAGAGACCTTGGAACCAAGTCTGCAGTTAGCTGCTGCTGTTCTTGCACAG
                                                                                               | |||   | |  |      | |||| || |   ||  |||  |  |  ||  |||  |  |  ||| |   || | |   ||      ||||  | |  |||||||||| |||||  ||||||||||||| |||||||| ||||||||||||||||||
---------------------------------------------------------------------------------------------gtaataacttccacaacttt--tctattctccttctgtcattgcacaacattttcaaagtaaac--tgattaaaatctcgataca------aaaactcgt-tagGTTGTTCCTGAGACGCTGGAACCAAGTCTTCAGTTAGCAGCTGCTGTTCTTGCACAG

upper sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: EFJ07595 (Selaginella moellendorffii), 3'ss of exon 15
gtatcattaattttactttccctttttctattctgtaattttttgacctcttgggcatttattgcattagttattgaaaatctacaactactaaaactaatacctattatcggagtatattttcttagggtttttgtcttcccttctaaatcaccccttgacttttattttgcatcatctgttaaaaaacatacagGTTGTTCCAGAGACCTTGGAACCAAGTCTGCAGTTAGCTGCTGCTGTTCTTGCACAG
                                                                                                                  |||  |    || |         ||||    | |||   | |||||  ||||  || ||||                ||||||||||||| ||||| |||||||| || |||||||| || || || || |||||  ||
------------------------------------------------------------------------------------------------------------------gtaagtcgctttggc-------ccttctacgcaaaaagtcaccttgggttttggttggcat----------------tacagGTTGTTCCCGAGACGTTGGAACCGAGCCTGCAGTTGGCGGCAGCAGTACTTGCCGAG

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|351045387|gb|FQ447652.1|FQ447652
EST:     CTCATGATGTTGATCATGGCCTTAATTTGGAAAAGGCTGGGGCAACAGCG                         GTTGTTCCAGAGACCTTGGAACCAAGTCTGCAGTTAGCTGCTGCTGTTCTT
genomic: CTCATGATGTTGATCATGGCCTTAATTTGGAAAAGGCTGGGGCAACAGCGgtatcattaa ... aaacatacagGTTGTTCCAGAGACCTTGGAACCAAGTCTGCAGTTAGCTGCTGCTGTTCTT
EST: gi|110407685|gb|EC973295.1|EC973295
EST:     GAAAAGGCTGGGGCAACAGCG                         GTTGTTCCAGAGACCTTGGAACCAAGTCTGCAGTTAGCTGCTGCTGTTCTT
genomic: GAAAAGGCTGGGGCAACAGCGgtatcattaa ... aaacatacagGTTGTTCCAGAGACCTTGGAACCAAGTCTGCAGTTAGCTGCTGCTGTTCTT
EST: gi|110425477|gb|EC991862.1|EC991862
EST:     CTCATGATGTTGATCATGGCCTTAATTTGGAAAAGGCTGGGGCAACAGCG                         GTTGTTCCAGAGACCTTGGAACCAAGTCTGCAGTTAGCAGCTGCTGTTCTT
genomic: CTCATGATGTTGATCATGGCCTTAATTTGGAAAAGGCTGGGGCAACAGCGgtatcattaa ... aaacatacagGTTGTTCCAGAGACCTTGGAACCAAGTCTGCAGTTAGCTGCTGCTGTTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttctaaatcaccccttgacttttattttgcatcatctgttaaaaaacatacagGTTGTTCCAGAGACCTTGGAACCAAGTCTGCAGTTAGCTGCTGCTGTTCTTGCACAG
                ttgacttttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcattaattttactttccctttttctattctgtaattttttgacctcttgggcatttattgcattagttattgaaaatctacaactactaaaactaatacctattatcggagtatattttcttagggtttttgtcttcccttctaaatcaccccttgacttttattttgcatcatctgttaaaaaacatacagGTTGTTCCAGAGACCTTGGAACCAAGTCTGCAGTTAGCTGCTGCTGTTCTTGCACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT