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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaacttcttatgcctctcatatacatatatatatatgaatttctcattggagcactctctgatgctaattgtacctacttcttaaactgcagTTTATCCTGATGGACGAGTTTGCATATCAATTTTACATCCTCCTGGTGAGGACCCAAATGGCTATGAGCTTGCAAGTGAGCGTTGGACACCTGTCCACAC

Basic information

species Vitis vinifera
transcript Vv08s0007g00120.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g00120.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os01g62244.3 (Oryza sativa), 3'ss of exon 1
gttaacttcttatgcctctcatatacatatatatatatgaatttctcattggagcactctctgatgctaattgtacctacttcttaaactgcagTTTATCCTGATGGACGAGTTTGCATATCAATTTTACATCCTCCTGGTGAGGACCCAAATGGCTATGAGCTTGCAAGTGAGCGTTGGACACCTGTCCACAC
|| | |||      |   |  ||     || | | | | | |   | ||          | | |  |  |   ||  || |  | ||    |||||||||| |||||||| || ||||| || ||| | ||||| |||||||| || || ||||| ||||||||||| ||||||||||||||||| || || ||
gtcagctttc----ctcattgtaacttcatgtttctgtaactccatgatccataa---ttttaacac--agcataa-tattggtcaattgccagTTTATCCGGATGGACGTGTATGCATTTCTATTCTTCATCCGCCTGGTGATGATCCCAATGGTTATGAGCTTGCGAGTGAGCGTTGGACACCAGTGCATAC

upper sequence: Vv08s0007g00120.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G012052_T01 (Zea mays), 3'ss of exon 3
gttaacttcttatgcctctcatatacatatatatatatgaatttctcattggagcactctctgatgctaattgtacctacttcttaaactgcagTTTATCCTGATGGACGAGTTTGCATATCAATTTTACATCCTCCTGGTGAGGACCCAAATGGCTATGAGCTTGCAAGTGAGCGTTGGACACCTGTCCACAC
          || || || |    |  | | | | ||  | ||  ||||   |    |||     |  |||| |   |  || | ||    ||||||||||||||||||| |||||||| || ||| | ||||| |||||||| || || ||||| |||||||||||||| || || |||||||| || |||||
---------gtaagcatcgctatcatgtct-tgtctactatttgatcatgccaaagttct-----gacaattctttttgttt-tgaattctcagTTTATCCTGATGGACGTGTTTGCATTTCTATTCTTCATCCACCTGGTGAAGATCCCAATGGTTATGAGCTTGCAAGCGAACGATGGACACCAGTGCACAC

upper sequence: Vv08s0007g00120.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G085600_T03 (Zea mays), 3'ss of exon 3
gttaacttcttatgcctctcatatacatatatatatatgaatttctcattggagcactctctgatgctaattgtacctacttcttaaactgcagTTTATCCTGATGGACGAGTTTGCATATCAATTTTACATCCTCCTGGTGAGGACCCAAATGGCTATGAGCTTGCAAGTGAGCGTTGGACACCTGTCCACAC
|| | ||| ||||   |   |  |  || ||| ||  | |  | |   |  |     | |||||    |    ||     |    ||||  |||| ||||||||||| || ||||| || || ||| | ||||| |||||||| || ||||| || |||||||| ||||||||||| ||||||||||| |||||
gtcagctttttattagtgaaaattgtatttatttacttcatctgcagttctg----ttttctgacatcatgcataatatttgaggaaacgccagTCTATCCTGATGGGCGGGTTTGTATCTCTATTCTTCATCCACCTGGTGAAGATCCAAACGGTTATGAGCTCGCAAGTGAGCGATGGACACCTGTGCACAC

upper sequence: Vv08s0007g00120.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G007300_T02 (Zea mays), 3'ss of exon 3
gttaacttcttatgcctctcatatacatatatatatatgaatttctcattggagcactctctgatgctaattgtacctacttcttaaactgcagTTTATCCTGATGGACGAGTTTGCATATCAATTTTACATCCTCCTGGTGAGGACCCAAATGGCTATGAGCTTGCAAGTGAGCGTTGGACACCTGTCCACAC
|| |  || ||||   |     | |  | ||| ||| |   ||   |  ||      | |||||    |    ||     |    |||   |||||||| | ||||| |  || || || || ||| | ||||| |||||||| || |||| ||| |||||||| ||||||||||||||||||||||| || ||
gtaagatttttattagtg----aaagttgtatttatttagtttatccgctgttatgttttctgacatcatgcatattatttggggaaatgccagTTTATTCAGATGGGCTGGTGTGTATCTCTATTCTTCATCCACCTGGTGAAGATCCAAGTGGTTATGAGCTCGCAAGTGAGCGTTGGACACCTGTGCATAC

upper sequence: Vv08s0007g00120.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G007276_T03 (Zea mays), 3'ss of exon 3
gttaacttcttatgcctctcatatacatatatatatatgaatttctcattggagcactctctgatgctaattgtacctact-tcttaaactg-cagTTTATCCTGATGGACGAGTTTGCATATCAATTTTACATCCTCCTGGTGAGGACCCAAATGGCTATGAGCTTGCAAGTGAGCGTTGGACACCTGTCCACAC
          || || || | |||     | ||   |||  | |   ||  || ||        | || |   | | || | | || || |  |||||||||| ||||| || |||||||| || ||| | ||||| |||||||| || || | ||| |||||||||||||| || || |||||||| || |||||
---------gtaagcttcac-tatcggactgtactcatg--tctactatctgatcatgtcaaagttctgacaattcttattattttgaattctcagTTTATCCGGATGGGCGTGTTTGCATTTCTATTCTTCATCCACCTGGTGAAGATCCCAGTGGTTATGAGCTTGCAAGCGAACGGTGGACACCAGTGCACAC

upper sequence: Vv08s0007g00120.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S75_236V6.1 (Physcomitrella patens), 3'ss of exon 5
--gttaacttct-tatgcctctcatatacatatatatatatgaatttctcattggagcactct-ctgatgctaattgta---cctacttcttaaactgcagTTTATCCTGATGGACGAGTTTGCATATCAATTTTACATCCTCCTGGTGAGGACCCAAATGGCTATGAGCTTGCAAGTGAGCGTTGGACACCTGTCCACAC
     ||||    | || |||| | || ||   || |   | ||||| || ||       ||| || ||    ||   |   | |   | || |  ||||||||||||||||||||| |||||||| |||||| ||||| |||||||||| || |||||||| |||||  | || |||||||||||| | || || || ||
gaaagaactctggtttgactctga-atgcactcatgtgacttaatttttctttacgatgttctgcttatttccataccaatccttgacttttcatgtgcagTTTATCCTGATGGACGGGTTTGCATTTCAATTCTACATGCTCCTGGTGATGATCCAAATGGTTATGAATTGGCGAGTGAGCGTTGGTCTCCCGTGCATAC

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|37190149|gb|CF609498.1|CF609498
EST:     CAACAGTCCTCCATCAGTGAGGTTTACCTCAGATATGTGGCATCCTAATG                         TTTATCCTGATGGACGAGTTTGCATATCAATTTTACATCCGCCTGGTGAGG
genomic: CAACAGTCCTCCATCAGTGAGGTTTACCTCGGATATGTGGCATCCTAATGgttaacttct ... taaactgcagTTTATCCTGATGGACGAGTTTGCATATCAATTTTACATCCTCCTGGTGAGG
EST: gi|71855236|gb|DT004291.1|DT004291
EST:     CAACAGTCCTCCATCAGTGAGGTTTACCTCGGATATGTGGCATCCTAATG                         TTTATCCTGATGGACGAGTTTGCATATCAATTTTACATCCTCCTGGTGAGG
genomic: CAACAGTCCTCCATCAGTGAGGTTTACCTCGGATATGTGGCATCCTAATGgttaacttct ... taaactgcagTTTATCCTGATGGACGAGTTTGCATATCAATTTTACATCCTCCTGGTGAGG
EST: gi|110406248|gb|EC971815.1|EC971815
EST:     CAACAGTCCTCCATCAGTGAGGTTTACCTCGGATATGTGGCATCCTAATG                         TTTATCCTGATGGACGAGTTTGCATATCAATTTTACATCCTCCTGGTGAGG
genomic: CAACAGTCCTCCATCAGTGAGGTTTACCTCGGATATGTGGCATCCTAATGgttaacttct ... taaactgcagTTTATCCTGATGGACGAGTTTGCATATCAATTTTACATCCTCCTGGTGAGG
EST: gi|110411536|gb|EC977255.1|EC977255
EST:     CAACAGTCCTCCATCAGTGAGGTTTACCTCGGATATGTGGCATCCTAATG                         TTTATCCTGATGGACGAGTTTGCATATCAATTTTACATCCTCCTGGTGAGG
genomic: CAACAGTCCTCCATCAGTGAGGTTTACCTCGGATATGTGGCATCCTAATGgttaacttct ... taaactgcagTTTATCCTGATGGACGAGTTTGCATATCAATTTTACATCCTCCTGGTGAGG
EST: gi|110408770|gb|EC974411.1|EC974411
EST:     CAACAGTCCTCCATCAGTGAGGTTTACCTCGGATATGTGGCATCCTAATG                         TTTATCCTGATGGACGAGTTTGCATATCAATTTTACATCCTCCTGGTGAGG
genomic: CAACAGTCCTCCATCAGTGAGGTTTACCTCGGATATGTGGCATCCTAATGgttaacttct ... taaactgcagTTTATCCTGATGGACGAGTTTGCATATCAATTTTACATCCTCCTGGTGAGG
EST: gi|71855279|gb|DT004334.1|DT004334
EST:     CAACAGTCCTCCATCAGTGAGGTTTACCTCGGATATGTGGCATCCTAATG                         TTTATCCTGATGGACGAGTTTGCATATCAATTTTACATCCTCCTGGTGAGG
genomic: CAACAGTCCTCCATCAGTGAGGTTTACCTCGGATATGTGGCATCCTAATGgttaacttct ... taaactgcagTTTATCCTGATGGACGAGTTTGCATATCAATTTTACATCCTCCTGGTGAGG
EST: gi|161706746|gb|FC055086.1|FC055086
EST:     CAACAGTCCTCCATCAGTGAGGTTTACCTCGGATATGTGGCATCCTAATG                         TTTATCCTGATGGACGAGTTTGCATATCAATTTTACATCCTCCTGGTGAAG
genomic: CAACAGTCCTCCATCAGTGAGGTTTACCTCGGATATGTGGCATCCTAATGgttaacttct ... taaactgcagTTTATCCTGATGGACGAGTTTGCATATCAATTTTACATCCTCCTGGTGAGG
EST: gi|110404984|gb|EC970511.1|EC970511
EST:     CAACAGTCCTCCATCAGTGAGGTTTACCTCGGATATGTGGCATCCTAATG                         TTTATCCTGATGGACGAGTTTGCATATCAATTTTACATCCTCCTGGTGAGG
genomic: CAACAGTCCTCCATCAGTGAGGTTTACCTCGGATATGTGGCATCCTAATGgttaacttct ... taaactgcagTTTATCCTGATGGACGAGTTTGCATATCAATTTTACATCCTCCTGGTGAGG
EST: gi|161707423|gb|FC057350.1|FC057350
EST:     CAACAGTCCTCCATCAGTGAGGTTTACCTCGGATATGTGGCATCCTAATG                         TTTATCCTGATGGACGAGT
genomic: CAACAGTCCTCCATCAGTGAGGTTTACCTCGGATATGTGGCATCCTAATGgttaacttct ... taaactgcagTTTATCCTGATGGACGAGT
EST: gi|110375077|gb|EC940034.1|EC940034
EST:     CAACAGTCCTCCATCAGTGAGGTTTACCTCGGATATGTGGCATCCTAATG                         TTTATCCTGATGGACGAGTTTGCATATCAATTTTACATCCTCCTGGTGAGG
genomic: CAACAGTCCTCCATCAGTGAGGTTTACCTCGGATATGTGGCATCCTAATGgttaacttct ... taaactgcagTTTATCCTGATGGACGAGTTTGCATATCAATTTTACATCCTCCTGGTGAGG
EST: gi|37183655|gb|CF603009.1|CF603009
EST:     CAACAGTCCTCCATCAGTGAGGTTTACCTCGGATATGTGGCATCCTAATG                         TTTATCCTGATGGACGAGTTTGCATATCAATTTTACATCCTCCTGGTGAGG
genomic: CAACAGTCCTCCATCAGTGAGGTTTACCTCGGATATGTGGCATCCTAATGgttaacttct ... taaactgcagTTTATCCTGATGGACGAGTTTGCATATCAATTTTACATCCTCCTGGTGAGG
EST: gi|161710953|gb|FC058612.1|FC058612
EST:     CAACAGTCCTCCATCAGTGAGGTTTACCTCGGATATGTGGCATCCTAATG                         TTTATCCTGATGGACGAGTTTGCATATCAATTTTACATCCTCCTGGTGAGG
genomic: CAACAGTCCTCCATCAGTGAGGTTTACCTCGGATATGTGGCATCCTAATGgttaacttct ... taaactgcagTTTATCCTGATGGACGAGTTTGCATATCAATTTTACATCCTCCTGGTGAGG
EST: gi|110409487|gb|EC975150.1|EC975150
EST:     CAACAGTCCTCCATCAGTGAGGTTTACCTCGGATATGTGGCATCCTAATG                         TTTATCCTGATGGACGAGTTTGCATATCAATTTTACATCCTCCTGGTGAGG
genomic: CAACAGTCCTCCATCAGTGAGGTTTACCTCGGATATGTGGCATCCTAATGgttaacttct ... taaactgcagTTTATCCTGATGGACGAGTTTGCATATCAATTTTACATCCTCCTGGTGAGG
EST: gi|110398671|gb|EC965142.1|EC965142
EST:     CAACAGTCCTCCATCAGTGAGGTTTACCTCGGATATGTGGCATCCTAATG                         TTTATCCTGATGGACGAGTTTGCATATCAATTTTACATCCTCCTGGTGAGG
genomic: CAACAGTCCTCCATCAGTGAGGTTTACCTCGGATATGTGGCATCCTAATGgttaacttct ... taaactgcagTTTATCCTGATGGACGAGTTTGCATATCAATTTTACATCCTCCTGGTGAGG
EST: gi|110411501|gb|EC977218.1|EC977218
EST:     CAACAGTCCTCCATCAGTGAGGTTTACCTCGGATATGTGGCATCCTAATG                         TTTATCCTGATGGACGAGTTTGCATATCAATTTTACATCCTCCTGGTGAGG
genomic: CAACAGTCCTCCATCAGTGAGGTTTACCTCGGATATGTGGCATCCTAATGgttaacttct ... taaactgcagTTTATCCTGATGGACGAGTTTGCATATCAATTTTACATCCTCCTGGTGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttctcattggagcactctctgatgctaattgtacctacttcttaaactgcagTTTATCCTGATGGACGAGTTTGCATATCAATTTTACATCCTCCTGGTGAGGACCCAAATGGCTATGAGCTTGCAAGTGAGCGTTGGACACCTGTCCACAC
                         tgctaat  putative branch site (score: 2)
                                    cctacttctt  putative PPT
                            taattgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaacttcttatgcctctcatatacatatatatatatgaatttctcattggagcactctctgatgctaattgtacctacttcttaaactgcagTTTATCCTGATGGACGAGTTTGCATATCAATTTTACATCCTCCTGGTGAGGACCCAAATGGCTATGAGCTTGCAAGTGAGCGTTGGACACCTGTCCACAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT