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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaattcattctgatatgaggatgcttttatctgaggttgcaattactcagagtgagaagaatttgtttgttaccaatattggaaatttcctcttgtacagGTAATGGCTCGATCTTCACCATTGGATAAGCATATCCTTGTGAAACACTTGAGAACTGCATTGGAAGAAGTTGTTGCAGTGACTGGGGATGGTACAAATG

Basic information

species Vitis vinifera
transcript Vv18s0001g09150.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g09150.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA06G04900.1 (Glycine max), 3'ss of exon 3
aaattcattctgatatgaggatgcttttatctgaggttgcaattactcagagtgagaagaatt----tgtttgttaccaatattggaaatttcctcttgtacagGTAATGGCTCGATCTTCACCATTGGATAAGCATATCCTTGTGAAACACTTGAGAACTGCATTGGAAGAAGTTGTTGCAGTGACTGGGGATGGTACAAATG
    | |   |    || | |    || | |   |   |  |    |  ||       ||  |    |  |  | ||  | | |  |   |||    | | ||||||||||| |||||||||||| |||||||||||| ||| |||||||||||||| ||  ||||  |||| |||||| |||| ||||| |||||||||||||
----ttagagtatactgggtaactcttgaaccttgaaagtgagggtttggacctttgggacctacactactcttcactgagaataaattcttctatatctgcagGTAATGGCCCGATCTTCACCAATGGATAAGCATACCCTGGTGAAACACTTGAGGACAACATTTCAAGAGGTTGTTTCAGTAACTGGTGATGGTACAAATG

upper sequence: Vv18s0001g09150.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA04G04810.1 (Glycine max), 3'ss of exon 3
aaattcattctgatatgaggatgcttttatctgaggttgca--attactcagagtgagaagaatttgtttgttaccaatattggaaatttcctcttgtacagGTAATGGCTCGATCTTCACCATTGGATAAGCATATCCTTGTGAAACACTTGAGAACTGCATTGGAAGAAGTTGTTGCAGTGACTGGGGATGGTACAAATG
  |||| |       |||   |     | |  ||   | ||  | |  |||   |||  | ||||  | |   | || | |  || || ||    | | ||||||||||| |||||||||||  |||||||||||| ||| |||||||||||||| ||  ||||  |||| |||||| |||| ||||| |||||||||||||
tgattc-tcgaaccttgaaagtaagggtttgggaacctacattactcttcactatgaaga-aattcttctacaatcattttatgatatgtctatatctgcagGTAATGGCCCGATCTTCACCCATGGATAAGCATACCCTGGTGAAACACTTGAGGACAACATTTCAAGAGGTTGTTTCAGTAACTGGTGATGGTACAAATG
















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|32250063|gb|CD715882.1|CD715882
EST:     TTCGTGAGAAGAGTGAGGAGGAATTGCAAAAACTAATTCCAAAAATTCAG                         GTAATGGCTCGATCTTCACCATTGGATAAGCATATCCTTGTGAAACACTTG
genomic: TTCGTGAGAAGAGTGAGGAGGAATTGCAAAAACTAATTCCAAAAATTCAGgtgcatttcc ... tcttgtacagGTAATGGCTCGATCTTCACCATTGGATAAGCATATCCTTGTGAAACACTTG
EST: gi|27580854|gb|CB003549.1|CB003549
EST:     TTCGTGAGAAGAGTGAGGAGGAATTGCAAAAACTAATTCCAAAAATTCAG                         GTAATGGCTCGATCTTCACCATTGGATAAGCATATCCTTGTGAAACACTTG
genomic: TTCGTGAGAAGAGTGAGGAGGAATTGCAAAAACTAATTCCAAAAATTCAGgtgcatttcc ... tcttgtacagGTAATGGCTCGATCTTCACCATTGGATAAGCATATCCTTGTGAAACACTTG
EST: gi|110689058|gb|EE064960.1|EE064960
EST:     TTCGTGAGAAGAGTGAGGAGGAATTGCAAAAACTAATTCCAAAAATTCAG                         GTAATGGCTCGATCTTCACCATTGGATAAGCATATCCTTGTGAAACACTTG
genomic: TTCGTGAGAAGAGTGAGGAGGAATTGCAAAAACTAATTCCAAAAATTCAGgtgcatttcc ... tcttgtacagGTAATGGCTCGATCTTCACCATTGGATAAGCATATCCTTGTGAAACACTTG
EST: gi|18458580|gb|BM436858.1|BM436858
EST:     TTCGTGAGAAGAGTGAGGAGGAATTGCAAAAACTAATTCCAAAAATTCAG                         GTAATGGCTCGATCTTCACCATTGGATAAGCATATCCTTGTGAAACACTTG
genomic: TTCGTGAGAAGAGTGAGGAGGAATTGCAAAAACTAATTCCAAAAATTCAGgtgcatttcc ... tcttgtacagGTAATGGCTCGATCTTCACCATTGGATAAGCATATCCTTGTGAAACACTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcagagtgagaagaatttgtttgttaccaatattggaaatttcctcttgtacagGTAATGGCTCGATCTTCACCATTGGATAAGCATATCCTTGTGAAACACTTGAGAACTGCATTGGAAGAAGTTGTTGCAGTGACTGGGGATGGTACAAATG
                                        tttcctcttgt  CT-rich tract
                             aatattggaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaattcattctgatatgaggatgcttttatctgaggttgcaattactcagagtgagaagaatttgtttgttaccaatattggaaatttcctcttgtacagGTAATGGCTCGATCTTCACCATTGGATAAGCATATCCTTGTGAAACACTTGAGAACTGCATTGGAAGAAGTTGTTGCAGTGACTGGGGATGGTACAAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - -cattctg
- - - - - - - - - ggatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - agaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -accaata