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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcttttatttaatattgtttaaaagcatatcaaatctttagcttgctcctttgtgcagcaatagccctataactagtgttgattcttttgaggtttgtgacttgcagGCCATTGATTTTCTTGATAAGCTCCTTCGATATGATCATCAGGACAGGCTGACAGCAAGAGAGGCAATG

Basic information

species Vitis vinifera
transcript Vv07s0129g00410.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0129g00410.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA11G05340.1 (Glycine max), 3'ss of exon 8
gtcttttatttaatattgtttaaaagcatatcaaatctttagcttgctcctttgtgcagcaatagccctataactagtgttgattc---ttttgaggtt----tgtgacttgcagGCCATTGATTTTCTTGATAAGCTCCTTCGATATGATCATCAGGACAGGCTGACAGCAAGAGAGGCAATG
                                 | |||| || || |   | ||    ||| |  || |  |  |||| | ||||    |||     ||    | ||||  | |||| ||||||||||||||||||||||||||||||||||| ||||||||||| ||||| ||||| ||||||
------------------------------gtgactcttcagttttcctatctg----gcattgaccttgcatttagtatagattgcaatttaacaattcttgtatgacacgtagGCAATTGATTTTCTTGATAAGCTCCTTCGATATGATCACCAGGACAGGCTAACAGCTAGAGAAGCAATG

upper sequence: Vv07s0129g00410.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA01G39950.1 (Glycine max), 3'ss of exon 8
gtcttttatttaatattgtttaaaagcatatcaaatctttagcttgctcctttgtgcagcaatagccctataactagtgttgattct--tttgaggttt-----gtgacttgcagGCCATTGATTTTCTTGATAAGCTCCTTCGATATGATCATCAGGACAGGCTGACAGCAAGAGAGGCAATG
                                 |||||| || || |   | ||    ||| |  || |  |  |||| | || |    ||| |  |||      |||| || |||| ||||||||||||||||||||||||||||||||||| ||||||||||| ||||| ||||| ||||||
------------------------------gtgaatcttcagttttcctatctg----gcattgaccttgcatttagtatggactgcaatttaacatttcttgtatgacatgtagGCAATTGATTTTCTTGATAAGCTCCTTCGATATGATCACCAGGACAGGCTAACAGCTAGAGAAGCAATG

upper sequence: Vv07s0129g00410.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA17G17790.1 (Glycine max), 3'ss of exon 8
gtcttttatttaatattgtttaaaagcat----atcaaatct-ttagcttgctcctttgtgcagcaatagccctataactagtgttgattcttttgaggtttgtgacttgcagGCCATTGATTTTCTTGATAAGCTCCTTCGATATGATCATCAGGACAGGCTGACAGCAAGAGAGGCAATG
||  |||| |  || ||     |   |||    | | || |  |||| ||   |  |  |  | ||||  | |  | |   || || ||| |||  |  | |  ||| ||||||| ||||||||||||||||| ||||||||||| ||||| ||||||||||| ||||||||||| ||||||
gtaatttaatccatgttccaacatgtcattgggacctaaccaattagtttatactgtaatttaacaatt-ctccgttatcggttttaattatttcaatatatcggacatgcagGCAATTGATTTTCTTGATAAACTCCTTCGATACGATCACCAGGACAGGCTAACAGCAAGAGAAGCAATG

upper sequence: Vv07s0129g00410.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA05G22250.1 (Glycine max), 3'ss of exon 8
gtcttttatttaatattgtttaaaagcat----atcaaatct-ttagcttgctcctttgtgcagcaatagccctataactagtgttgattcttttgaggtttgtgacttgcagGCCATTGATTTTCTTGATAAGCTCCTTCGATATGATCATCAGGACAGGCTGACAGCAAGAGAGGCAATG
||  |||| |  || ||     |   |||    | | || |  |||| ||   |  |  |  | ||||  |  | | | | || || ||| |||  |  | |  ||| ||||||| ||||||||||||||||| ||||||||||| ||||| ||||||||| | ||||||||||| ||||||
gtaatttaatccatgttccaacatgtcattcggacctaaccaattagtttatactgtaatttatcaatt-ctttgttattggttttaattatttcaatatatcggacatgcagGCAATTGATTTTCTTGATAAACTCCTTCGATACGATCACCAGGACAGGTTAACAGCAAGAGAAGCAATG

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|30305031|gb|CB981825.1|CB981825
EST:     CATGGTCCAAATTTATCCATGCAGACAATCAGCATCTAGTTTCTCCAGAG                         GCCATTGATTTTCTTGATAAGCTCCTTCGATATGATCATCAGGACAGGCTT
genomic: CGTGGTCCAAATTTATCCATGCAGACAATCAGCATCTAGTTTCTCCAGAGgtcttttatt ... tgacttgcagGCCATTGATTTTCTTGATAAGCTCCTTCGATATGATCATCAGGACAGGCTG
EST: gi|110729560|gb|EE105636.1|EE105636
EST:     CATGGTCCAAATTTATCCATGCAGACAATCAGCATCTAGTTTCTCCAGAG                         GCCATTGATTTTCTTGATAAGCTCCTTCGATATGATCATCAGGACAGGCTT
genomic: CGTGGTCCAAATTTATCCATGCAGACAATCAGCATCTAGTTTCTCCAGAGgtcttttatt ... tgacttgcagGCCATTGATTTTCTTGATAAGCTCCTTCGATATGATCATCAGGACAGGCTG
EST: gi|37187892|gb|CF607243.1|CF607243
EST:     CGTGGTCCAAATTTATCCATGCAGACAATCAGCATCTAGTTTCTCCAGAG                         GCCATTGATTTTCTTGATAAGCTCCTTCGATATGATCATCAGGACAGGCTG
genomic: CGTGGTCCAAATTTATCCATGCAGACAATCAGCATCTAGTTTCTCCAGAGgtcttttatt ... tgacttgcagGCCATTGATTTTCTTGATAAGCTCCTTCGATATGATCATCAGGACAGGCTG
EST: gi|30127890|gb|CB913229.1|CB913229
EST:     CGTGGTCCAAATTTATCCATGCAGACAATCAGCATCTAGTTTCTCCAGAG                         GCCATTGATTTTCTTGATAAGCTCCTTCGATATGATCATCAGGACAGGCTG
genomic: CGTGGTCCAAATTTATCCATGCAGACAATCAGCATCTAGTTTCTCCAGAGgtcttttatt ... tgacttgcagGCCATTGATTTTCTTGATAAGCTCCTTCGATATGATCATCAGGACAGGCTG
EST: gi|110364239|gb|EC923655.1|EC923655
EST:     CATGGTCCAAATTTATCCATGCAGACAATCAGCATCTAGTTTCTCCAGAG                         GCCATTGATTTTCTTGATAAGCTCCTTCGATATGATCATCAGGACAGGCTG
genomic: CGTGGTCCAAATTTATCCATGCAGACAATCAGCATCTAGTTTCTCCAGAGgtcttttatt ... tgacttgcagGCCATTGATTTTCTTGATAAGCTCCTTCGATATGATCATCAGGACAGGCTG
EST: gi|110365854|gb|EC929354.1|EC929354
EST:     CATGGTCCAAATTTATCCATGCAGACAATCAGCATCTAGTTTCTCCAGAG                         GCCATTGATTTTCTTGATAAGCTCCTTCGATATGATCATCAGGACAGGCTT
genomic: CGTGGTCCAAATTTATCCATGCAGACAATCAGCATCTAGTTTCTCCAGAGgtcttttatt ... tgacttgcagGCCATTGATTTTCTTGATAAGCTCCTTCGATATGATCATCAGGACAGGCTG
EST: gi|351030908|gb|FQ438944.1|FQ438944
EST:     CGTGGTCCAAATTTATCCATGCAGACAATCAGCATCTAGTTTCTCCAGAA                         GCCATTGATTTTCTTGATAAGCTCCTTCGATATGATCATCAGGACAGGCTG
genomic: CGTGGTCCAAATTTATCCATGCAGACAATCAGCATCTAGTTTCTCCAGAGgtcttttatt ... tgacttgcagGCCATTGATTTTCTTGATAAGCTCCTTCGATATGATCATCAGGACAGGCTG
EST: gi|110417189|gb|EC983224.1|EC983224
EST:     CATGGTCCAAATTTATCCATGCAGACAATCAGCATCTAGTTTCTCCAGAG                         GCCATTGATTTTCTTGATAAGCTCCTTCGATATGATCATCAGGACAGGCTT
genomic: CGTGGTCCAAATTTATCCATGCAGACAATCAGCATCTAGTTTCTCCAGAGgtcttttatt ... tgacttgcagGCCATTGATTTTCTTGATAAGCTCCTTCGATATGATCATCAGGACAGGCTG
EST: gi|30304903|gb|CB981697.1|CB981697
EST:     CATGGTCCAAATTTATCCATGCAGACAATCAGCATTTAGTTTCTCCAGAG                         GCCATTGATTTTCTTGATAAGCTCCTTCGATATGATCATCAGGACAGGCTT
genomic: CGTGGTCCAAATTTATCCATGCAGACAATCAGCATCTAGTTTCTCCAGAGgtcttttatt ... tgacttgcagGCCATTGATTTTCTTGATAAGCTCCTTCGATATGATCATCAGGACAGGCTG
EST: gi|110423934|gb|EC990287.1|EC990287
EST:     CATGGTCCAAATTTATCCATGCAGACAATCAGCATCTAGTTTCTCCAGAG                         GCCATTGATTTTCTTGATAAGCTCCTTCGATATGATCATCAGGACAGGCTT
genomic: CGTGGTCCAAATTTATCCATGCAGACAATCAGCATCTAGTTTCTCCAGAGgtcttttatt ... tgacttgcagGCCATTGATTTTCTTGATAAGCTCCTTCGATATGATCATCAGGACAGGCTG
EST: gi|110731135|gb|EE109011.1|EE109011
EST:     CATGGTCCAAATTTATCCATGCAGACAATCAGCATCTAGTTTCTCCAGAG                         GCCATTGATTTTCTTGATAAGCTCCTTCGATATGATCATCAGGACAGGCTT
genomic: CGTGGTCCAAATTTATCCATGCAGACAATCAGCATCTAGTTTCTCCAGAGgtcttttatt ... tgacttgcagGCCATTGATTTTCTTGATAAGCTCCTTCGATATGATCATCAGGACAGGCTG
EST: gi|110374218|gb|EC938850.1|EC938850
EST:     CATGGTCCAAATTTATCCATGCAGACAATCAGCATCTAGTTTCTCCAGAG                         GCCATTGATTTTCTTGATAAGCTCCTTCGATATGATCATCAGGACAGGCTT
genomic: CGTGGTCCAAATTTATCCATGCAGACAATCAGCATCTAGTTTCTCCAGAGgtcttttatt ... tgacttgcagGCCATTGATTTTCTTGATAAGCTCCTTCGATATGATCATCAGGACAGGCTG
EST: gi|110692539|gb|EE071897.1|EE071897
EST:     CATGGTCCAAATTTATCCATGCAGACAATCAGCATCTAGTTTCTCCAGAG                         GCCATTGATTTTCTTGATAAGCTCCTTCGATATGATCATCAGGACAGGCTT
genomic: CGTGGTCCAAATTTATCCATGCAGACAATCAGCATCTAGTTTCTCCAGAGgtcttttatt ... tgacttgcagGCCATTGATTTTCTTGATAAGCTCCTTCGATATGATCATCAGGACAGGCTG
EST: gi|110361331|gb|EC924797.1|EC924797
EST:     CATGGTCCAAATTTATCCATGCAGACAATCAGCATCTAGTTTCTCCAGAG                         GCCATTGATTTTCTTGATAAGCTCCTTCGATATGATCATCAGGACAGGCTT
genomic: CGTGGTCCAAATTTATCCATGCAGACAATCAGCATCTAGTTTCTCCAGAGgtcttttatt ... tgacttgcagGCCATTGATTTTCTTGATAAGCTCCTTCGATATGATCATCAGGACAGGCTG
EST: gi|110384058|gb|EC948472.1|EC948472
EST:     CATGGTCCAAATTTATCCATGCAGACAATCAGCATCTAGTTTCTCCAGAG                         GCCATTGATTTTCTTGATAAGCTCCTTCGATATGATCATCAGGACAGGCTT
genomic: CGTGGTCCAAATTTATCCATGCAGACAATCAGCATCTAGTTTCTCCAGAGgtcttttatt ... tgacttgcagGCCATTGATTTTCTTGATAAGCTCCTTCGATATGATCATCAGGACAGGCTG
EST: gi|254915687|gb|GR905118.1|GR905118
EST:     CGTGGTCCAAATTTATCCATGCAGACAATCAGCATCTAGTTTCTCCAGAG                         GCCATTGATTTTCTTGATAAGCTCCTTCGATATGATCATCAGGACAGGCTG
genomic: CGTGGTCCAAATTTATCCATGCAGACAATCAGCATCTAGTTTCTCCAGAGgtcttttatt ... tgacttgcagGCCATTGATTTTCTTGATAAGCTCCTTCGATATGATCATCAGGACAGGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgcagcaatagccctataactagtgttgattcttttgaggtttgtgacttgcagGCCATTGATTTTCTTGATAAGCTCCTTCGATATGATCATCAGGACAGGCTGACAGCAAGAGAGGCAATG
               tataacta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcttttatttaatattgtttaaaagcatatcaaatctttagcttgctcctttgtgcagcaatagccctataactagtgttgattcttttgaggtttgtgacttgcagGCCATTGATTTTCTTGATAAGCTCCTTCGATATGATCATCAGGACAGGCTGACAGCAAGAGAGGCAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG