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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggctaaaaggaatgagttccttctgccaatatctatgtgaaattcacaattcttttccacagcagtgtcatgtttaacaattctttcattggttttgtagGTTTAGAGACCCACAACCTGATTATTCTGCTTTCCGGGAAGCCAGTTATGGGCATTCCACATTGGAAATAAAAAACAGGACACATGCATTCTACCGCTGG

Basic information

species Vitis vinifera
transcript Vv11s0118g00240.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0118g00240.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA17G11790.1 (Glycine max), 3'ss of exon 8
ggctaaaaggaatgagttccttctgccaatatctatgtgaaattcacaattcttttccaca-gcagtgtcatgtt--taacaattctttcattggttttgtagGTTTAGAGACCCACAACCTGATTATTCTGCTTTCCGGGAAGCCAGTTATGGGCATTCCACATTGGAAATAAAAAACAGGACACATGCATTCTACCGCTGG
   ||||   ||  |      |||   || |||  | |  |||  |  ||| | |   | | |   |||||| |   |   |||||| || |||||  || ||||||   || ||||| || || ||||||||||| || ||||| || || || ||||||||| |||| |||||||| ||||| |||||  |||||| ||||
--gtaaattaaacaaaccatatct---aaaatccttcttgaat--atgattatgtcaaagatgtcttgtcatataggttttaattctatccttggtcatgcagGTTTTTGGATCCACAGCCAGAATATTCTGCTTTTCGAGAAGCAAGCTACGGACATTCCACACTGGAGATAAAAAATAGGACCCATGCTATCTACCACTGG
















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|30296687|gb|CB973481.1|CB973481
EST:     GTTTATATAACTGTTGGCGATGGAGGAAATCAGGAAGGTTTAGCTGGAAG                         GTTTAGAGACCCACAACCTGATTATTTTGCTTTCCGGGAAGCCAGTTATGG
genomic: GTTTATATAACTGTTGGCGATGGAGGAAATCAGGAAGGTCTAGCTGGAAGgtgagctaaa ... ggttttgtagGTTTAGAGACCCACAACCTGATTATTCTGCTTTCCGGGAAGCCAGTTATGG
EST: gi|351023069|gb|FQ430944.1|FQ430944
EST:     GTTTATATAACTGTTGGCGATGGAGGAAATCAGGAAGGTCTAGCTGGAAG                         GTTTAGAGACCCACAACCTGATTATTCTGCTTTCCGGGAAGCCAGTTATGG
genomic: GTTTATATAACTGTTGGCGATGGAGGAAATCAGGAAGGTCTAGCTGGAAGgtgagctaaa ... ggttttgtagGTTTAGAGACCCACAACCTGATTATTCTGCTTTCCGGGAAGCCAGTTATGG
EST: gi|30136888|gb|CB922226.1|CB922226
EST:     GTTTATATAACTGTTGGCGATGGAGGAAATCAGGAAGGTCTAGCTGGAAG                         GTTTAGAGACCCACAACCTGATTATTCTGCTTTCCGGGAAGCCAGTTATGG
genomic: GTTTATATAACTGTTGGCGATGGAGGAAATCAGGAAGGTCTAGCTGGAAGgtgagctaaa ... ggttttgtagGTTTAGAGACCCACAACCTGATTATTCTGCTTTCCGGGAAGCCAGTTATGG
EST: gi|30296755|gb|CB973549.1|CB973549
EST:     GTTTATATAACTGTTGGCGATGGAGGAAATCAGGAAGGTCTAGCTGGAAG                         GTTTAGAGACCCACAACCTGATTATTCTGCTTTCCGGGAAGCCAGTTATGG
genomic: GTTTATATAACTGTTGGCGATGGAGGAAATCAGGAAGGTCTAGCTGGAAGgtgagctaaa ... ggttttgtagGTTTAGAGACCCACAACCTGATTATTCTGCTTTCCGGGAAGCCAGTTATGG
EST: gi|110372208|gb|EC936360.1|EC936360
EST:     GTTTATATAACTGTTGGCGATGGAGGAAATCAGGAAGGTCTAGCTGGAAG                         GTTTAGAGACCCACAACCTGATTATTCTGCTTTCCGGGAAGCCAGTTATGG
genomic: GTTTATATAACTGTTGGCGATGGAGGAAATCAGGAAGGTCTAGCTGGAAGgtgagctaaa ... ggttttgtagGTTTAGAGACCCACAACCTGATTATTCTGCTTTCCGGGAAGCCAGTTATGG
EST: gi|110416678|gb|EC982675.1|EC982675
EST:     GTTTATATAACTGTTGGCGATGGAGGAAATCAGGAAGGTCTAGCTGGAAG                         GTTTAGAGACCCACAACCTGATTATTCTGCTTTCCGGGAAGCCAGTTATGG
genomic: GTTTATATAACTGTTGGCGATGGAGGAAATCAGGAAGGTCTAGCTGGAAGgtgagctaaa ... ggttttgtagGTTTAGAGACCCACAACCTGATTATTCTGCTTTCCGGGAAGCCAGTTATGG
EST: gi|34362933|gb|CF404518.1|CF404518
EST:     GTTTATATAACTGTTGGCGATGGAGGAAATCAGGAAGGTCTAGCTGGAAG                         GTTTAGAGACCCCCAACCTGATTATTCTGCTTTCCGGGAAGCCAGTTATGG
genomic: GTTTATATAACTGTTGGCGATGGAGGAAATCAGGAAGGTCTAGCTGGAAGgtgagctaaa ... ggttttgtagGTTTAGAGACCCACAACCTGATTATTCTGCTTTCCGGGAAGCCAGTTATGG
EST: gi|349810110|gb|FQ401556.1|FQ401556
EST:     TTTATATAACTGTTGGCGATGGAGGAAATCAGGAAGGTCTAGCCTGGAAG                         -TTTAGAGACCC
genomic: TTTATATAACTGTTGGCGATGGAGGAAATCAGGAAGGTCTAGC-TGGAAGgtgagctaaa ... ggttttgtagGTTTAGAGACCC
EST: gi|351032759|gb|FQ462473.1|FQ462473
EST:     GTTTATATAACTGTTGGCGATGGAGGAAATCANGAAGGTCTAGCTGGAAG                         GTTTAGAGACCCACAA
genomic: GTTTATATAACTGTTGGCGATGGAGGAAATCAGGAAGGTCTAGCTGGAAGgtgagctaaa ... ggttttgtagGTTTAGAGACCCACAA
EST: gi|351036359|gb|FQ458734.1|FQ458734
EST:     GTTTATATAACTGTTGGCGATGGAGGAAATCAGGAAGGTCTAGCTGGAAA                         GTTTAGAGACCCACAACCTGATT
genomic: GTTTATATAACTGTTGGCGATGGAGGAAATCAGGAAGGTCTAGCTGGAAGgtgagctaaa ... ggttttgtagGTTTAGAGACCCACAACCTGATT
EST: gi|110380934|gb|EC946237.1|EC946237
EST:     GTTTATATAACTGTTGGCGATGGAGGAAATCAGGAAGGTCTAGCTGGAAG                         GTTTAGAGACCCACAACCTGATTATTCTGCTTTCCGGGAAGCCAGTTATGG
genomic: GTTTATATAACTGTTGGCGATGGAGGAAATCAGGAAGGTCTAGCTGGAAGgtgagctaaa ... ggttttgtagGTTTAGAGACCCACAACCTGATTATTCTGCTTTCCGGGAAGCCAGTTATGG
EST: gi|30134430|gb|CB919768.1|CB919768
EST:     GTTTATATAACTGTTGGCGATGGAGGAAATCAGGAAGGTCTAGCTGGAAG                         GTTTAGAGACCCACAACCTGATTATTCTGCTTTCCGGGAAGCCAGTTATGG
genomic: GTTTATATAACTGTTGGCGATGGAGGAAATCAGGAAGGTCTAGCTGGAAGgtgagctaaa ... ggttttgtagGTTTAGAGACCCACAACCTGATTATTCTGCTTTCCGGGAAGCCAGTTATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaattcttttccacagcagtgtcatgtttaacaattctttcattggttttgtagGTTTAGAGACCCACAACCTGATTATTCTGCTTTCCGGGAAGCCAGTTATGGGCATTCCACATTGGAAATAAAAAACAGGACACATGCATTCTACCGCTGG
                          gtttaac  putative branch site (score: 3)
                           tttaacaattcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggctaaaaggaatgagttccttctgccaatatctatgtgaaattcacaattcttttccacagcagtgtcatgtttaacaattctttcattggttttgtagGTTTAGAGACCCACAACCTGATTATTCTGCTTTCCGGGAAGCCAGTTATGGGCATTCCACATTGGAAATAAAAAACAGGACACATGCATTCTACCGCTGG

- - -aaaggaa
- - - - - - - - - - -tctgcca
- - - - - - - - - - - - - - - - ctatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacaatt