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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagcatctggttctttttctgggattttttttaattaatttatgattttgaacatggaatatttgaagaagctttatcgtctagcagccagtgtctggtgaatggtgggcccattttctgggtgaaccattaactctactgtcaagtagtgattgctaatgaattgttttgatcaattggcagTGAAAACATCATCTGGAAGGCTTTTAGCCCCACCACTATTAATAGTGGTCGTGGAGCTGAATTTGAAGGTGCTGTTATTGCTCTCTTCCATCTGCTAATA

Basic information

species Vitis vinifera
transcript Vv00s1338g00020.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s1338g00020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os09g17840.1 (Oryza sativa), 3'ss of exon 2
gttagcatctggttctttttctgggattttttttaattaatttatgattttgaacatggaatatttgaagaagctttatcgtctagcagccagtgtctggtgaatggtgggcccattttctgggtgaaccattaactctactgtcaagtag-tgattgctaatgaattgttttgatcaattggcagTGAAAACATCATCTGGAAGGCTTTTAGCCCCACCACTATTAATAGTGGTCGTGGAGCTGAATTTGAAGGTGCTGTTATTGCTCTCTTCCATCTGCTAATA
                                                                                        |  ||  ||   | ||         | || ||| | |||      |  | |   |  |  ||| | |||  |  |||| | |  || |  |    |||||| || |||||||||||||| ||||||||||| || || || ||||| ||||| ||||||||||||||                               
----------------------------------------------------------------------------------------gtaagcatcc--taaac------ttctttctcttgctgatgtgaca-ttttgtcgcaatttagCTTATTATTGGTGAACT-TGCTGTTGCA----CAGTGAGAATATCATCTGGAAGGCGTTTAGCCCCACAACCATCAACAGTGGGCGTGGTGCTGAATTTGAAGGA------------------------------

upper sequence: Vv00s1338g00020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os09g17830.1 (Oryza sativa), 3'ss of exon 2
gttagcatctggttctttttctgggattttttttaattaatttatgattttgaacatggaatatttgaagaagctttatcgtctagcagccagtgtctggtgaatggtgggcccattttctgggtgaaccattaactctactgtcaagtag-tgattgctaatgaattgttttgatcaattggcagTGAAAACATCATCTGGAAGGCTTTTAGCCCCACCACTATTAATAGTGGTCGTGGAGCTGAATTTGAAGGTGCTGTTATTGCTCTCTTCCATCTGCTAATA
                                                                                        |  ||  |||      |  |   |  |  ||||   |||      |  | |  |   |  ||| | |||  |  |||| | |  || |  |    |||||| || |||||||||||||| ||||||||||| || || || ||||| ||||| ||||||||||||||                               
----------------------------------------------------------------------------------------gtaagcatcttaaatttctttatcttacattcttactgatgtgaca-ttttgttacaatttagCTTATTATTGGTGAACT-TGCTGTTGCA----CAGTGAGAATATCATCTGGAAGGCGTTTAGCCCCACAACCATCAACAGTGGGCGTGGTGCTGAATTTGAAGGA------------------------------

upper sequence: Vv00s1338g00020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os03g11440.1 (Oryza sativa), 3'ss of exon 3
gttagcatctggttctttttctgggattttttttaattaatttatgattttgaacatggaatatttgaagaagctttatcgtctagcagccagtgtctggtgaatggtgggcccattttctgggtgaaccattaac-tctactgtcaagtagtgattgctaatgaattgttttgatcaattggcagTGAAAACATCATCTGGAAGGCTTTTAGCCCCACCACTATTAATAGTGGTCGTGGAGCTGAATTTGAAGGTGCTGTTATTGCTCTCTTCCATCTGCTAATA
                                                                                                   ||||       |  | || |     |  |   || || | | || |  |    ||| |  ||  ||| | |||       |  | ||||| || |||||||||||||| ||||||||||| ||||| || ||||| ||||| ||||| || || || ||||| |||||  | ||||||||| | || 
---------------------------------------------------------------------------------------------------gtgagcacattgaactttgttcttctctattgttgacattttctattcaact-tgact--tatggaaatctttc------tctgtagTGAGAATATCATCTGGAAGGCATTTAGCCCCACAACTATCAACAGTGGCCGTGGTGCTGAGTTCGAGGGGGCTGTCATTGCATTGTTCCATCTGTTGATT

upper sequence: Vv00s1338g00020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G130987_T02 (Zea mays), 3'ss of exon 3
gttagcatctggttctttttctgggattttttttaattaatttatgattttgaacatggaatatttgaagaagctttatcgtctagcagccagtgtctggtgaatggtgggcccattttctgggtgaaccattaactctactgtcaagtagtgattgctaatgaattgttttgatcaattggcagTGAAAACATCATCTGGAAGGCTTTTAGCCCCACCACTATTAATAGTGGTCGTGGAGCTGAATTTGAAGGTGCTGTTATTGCTCTCTTCCATCTGCTAATA
                                                                           | | | | | | |   | |   |  | | || ||     |||   | | || |   ||  || | |     |||     ||   |    | || ||| ||      | ||||| || |||||||||||||| ||||||||||| || || || ||||||||||| |||||||| ||||| ||||| ||||| || ||||||||| | || 
--------------------------------------------------------------------------gtaagcatgttggatttaatcctt--ttattgatgttgatattagattgatgtaatgtt--ctgttccacttagtc----ttataataagactgctttcat------gtagTGAGAATATCATCTGGAAGGCATTTAGCCCCACAACCATCAACAGTGGTCGTGGCGCTGAATTCGAAGGGGCTGTCATTGCACTGTTCCATCTGTTGATT

upper sequence: Vv00s1338g00020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G073498_T02 (Zea mays), 3'ss of exon 2
gttagcatctggttctttttctgggattttttttaattaatttatgattttgaacatggaatatttgaagaagctttatcgtctagcagccagtgtctggtgaatggtgggcccattttctgggtgaaccattaactctactgtcaagtagtgattgctaatgaattgttttgatcaattggcagTGAAAACATCATCTGGAAGGCTTTTAGCCCCACCACTATTAATAGTGGTCGTGGAGCTGAATTTGAAGGTGCTGTTATTGCTCTCTTCCATCTGCTAATA
                                                                                        |  ||  ||| |    |  |     | |||| | | ||  |  ||    ||  || ||  ||  | ||   |    | |  ||| ||      | || || || |||||||||||||| ||||||||||| || || || ||||||||||| |||||||||||||| ||||| ||||| || || |||||| | || 
----------------------------------------------------------------------------------------gtaagcatcttggacttaat-----ccttttattgatgtgctgtt----ctgttg-cacttaaagcttataataagaattctttcat------gtagCGAGAATATCATCTGGAAGGCATTTAGCCCCACAACCATCAACAGTGGTCGTGGTGCTGAATTTGAAGGGGCTGTCATTGCACTGTTTCATCTGTTGATT

upper sequence: Vv00s1338g00020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G307252_T02 (Zea mays), 3'ss of exon 2
gttagcatctggttctttttctgggattttttttaattaatttatgattttgaacatggaatatttgaagaagctttatcgtctagcagccagtgtctggtgaatggtgggcccattttctgggtgaaccattaactctactgtcaagtagtgattgctaatgaattgttttgatcaattggcagTGAAAACATCATCTGGAAGGCTTTTAGCCCCACCACTATTAATAGTGGTCGTGGAGCTGAATTTGAAGGTGCTGTTATTGCTCTCTTCCATCTGCTAATA
                                                                                ||    ||   ||   |     ||    || || |  | |    |    |||| | |   || |   |||      ||| | |      |    || ||  | ||||| || |||||||||||||| |||||||| || || || || ||||| ||||| |||||||||||||| || || |||||  | ||||||||  | || 
-------------------------------------------------------------------------------tgtggcacatttagccacaaaccaaaca-ggccctaaatgccacatc--tcattgatta-gctattctgtatgtgcggcttacggtaaactcatgtccat--gtagTGAGAATATCATCTGGAAGGCGTTTAGCCCAACAACCATCAACAGTGGGCGTGGTGCTGAATTTGAAGGGGCAGTCATTGCATTGTTCCATCTATTGATT

upper sequence: Vv00s1338g00020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S323_56V6.1 (Physcomitrella patens), 3'ss of exon 3
gttagcatctggttctttttctgggattttttttaattaatttatgattttgaacatggaatatttgaagaagctttatcgtctagcagccagtgtctggtgaatggtgggcccattttctgggtgaaccattaactctactgtcaagtagtgattgctaatgaattgttttgatcaattggcagTGAAAACATCATCTGGAAGGCTTTTAGCCCCACCACTATTAATAGTGGTCGTGGAGCTGAATTTGAAGGTGCTGTTATTGCTCTCTTCCATCTGCTAATA
                                                                        ||   | |  ||    |  | ||||||    |||    |   |||||||   || |  |||   |||   |||   ||   | | |   |     ||||||  |     ||||||| |||||||| ||||| |  || || || ||||| || || |||||||||||||| || ||||| || |||||||||||||||||||| || ||  | 
------------------------------------------------------------------------gcacaacctcct----gtaactgtctga-agatgcattgttgattttcttc-tggagtatt---tcttacgtcggttaacaagttcctttctccggttttgtcct----gcagTGAGAACATCATTTGGAAAGGATTCAGTCCGACCACCATCAACAGTGGTCGTGGAGCAGAGTTTGAGGGAGCTGTTATTGCTCTCTTCCACCTTCTGTTC

upper sequence: Vv00s1338g00020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S114_48V6.1 (Physcomitrella patens), 3'ss of exon 3
gttagcatctggttctttttctgggattttttttaattaatttatgattttgaacatggaatatttgaagaagctttatcgtctagcagccag----tgtctggtgaatggtgggcccattttctgggtgaaccattaactctactgtcaagtagtgattgctaatgaattgttttgatcaattggcagTGAAAACATCATCTGGAAGGCTTTTAGCCCCACCACTATTAATAGTGGTCGTGGAGCTGAATTTGAAGGTGCTGTTATTGCTCTCTTCCATCTGCTAATA
                                                                                |   ||||   |     | | | |  |   || | ||   |       |||   | | | |  ||||   |   |    ||||||||  ||| |||       | ||||||||||||||||||||||||| |||||||| || ||||| || ||||||||||||||||| || || || |||||||||||||||||||| || ||  | 
------------------------------------------------------------------------------cagcgcagcaattacattttatttaggtacacgtagtcctggtcctc---tgatttacttagtgaactgatcaagggaatctgctaatg--ttgattt------ctcgcagTGAAAACATCATCTGGAAGGCATTTAGCCCAACTACTATCAACAGTGGTCGTGGAGCTGAGTTCGAGGGCGCTGTTATTGCTCTCTTCCACCTTCTTTTC

upper sequence: Vv00s1338g00020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ11193 (Selaginella moellendorffii), 3'ss of exon 2
gttagcatctggttctttttctgggattttttttaattaatttatgattttgaacatggaatatttgaagaagctttatcgtctagcagccagtgtctggtgaatggtgggcccattttctgggtgaaccattaactctactgtcaagtagtgattgctaatgaattgttttgatcaattggcagTGAAAACATCATCTGGAAGGCTTTTAGCCCCACCACTATTAATAGTGGTCGTGGAGCTGAATTTGAAGGTGCTGTTATTGCTCTCTTCCATCTGCTAATA
                                                                                                                        || | ||| | ||   | |  | |||||   |||||  |  |  ||||| |   |     | |||||| ||||||||||||||||| ||||| || || || || || ||||| ||||||||||| || || || ||| | |||||||| ||||| ||  | || 
-----------------------------------------------------------------------------------------------------------------------gtgagagaaacctt---tttcttttcaagctctgattttt--tctattgtatctgt-----gacagTGAGAACATCATCTGGAAGGCGTTTAGTCCGACTACCATCAACAGTGGCCGTGGAGCTGAGTTCGAGGGAGCTATCATTGCTCTGTTCCACCTCTTGATC

upper sequence: Vv00s1338g00020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ15673 (Selaginella moellendorffii), 3'ss of exon 2
gttagcatctggttctttttctgggattttttttaattaatttatgattttgaacatggaatatttgaagaagctttatcgtctagcagccagtgtctggtgaatggtgggcccattttctgggtgaaccattaactctactgtcaagtagtgattgctaatgaattgttttgatcaattggcagTGAAAACATCATCTGGAAGGCTTTTAGCCCCACCACTATTAATAGTGGTCGTGGAGCTGAATTTGAAGGTGCTGTTATTGCTCTCTTCCATCTGCTAATA
                                                                                                                        || | ||| | ||   |    | || ||   |||||  |       | || |||     || |||||| | ||||||||||||||| ||||| || || || || || ||||| ||||||||||| ||||| || ||| | |||||||||||||| ||  | || 
-----------------------------------------------------------------------------------------------------------------------gtgagagaaacctt---ttccttttccagctctgattattt-----ctattgtgactg--tgacagTGAGACCATCATCTGGAAGGCGTTTAGTCCGACTACCATCAACAGTGGCCGTGGAGCTGAGTTTGAGGGAGCTATCATTGCTCTCTTCCACCTCTTGATC

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|351028747|gb|FQ433177.1|FQ433177
EST:     GGATATGGCCTTGGCTCTGGAATTTCTCTTTTCATAGCAACTAATATCTG                         TGAAAACATCATCTGGAAGGCTTTTAGCCC-ACCACTATTAATAGTGGTCG
genomic: GGATATGGCCTTGGCTCTGGAATTTCTCTTTTCATAGCAACTAATATCTGgttagcatct ... caattggcagTGAAAACATCATCTGGAAGGCTTTTAGCCCCACCACTATTAATAGTGGTCG
EST: gi|349832293|gb|FQ420854.1|FQ420854
EST:     GGATATGGCCTTGGCTCTGGAATTTCTCTTTTCATAGCAACTAATATCTG                         TGAAAACATCATCTGGAAGGCTTTTAGCCCCACCACTATTAATAGTGGTCG
genomic: GGATATGGCCTTGGCTCTGGAATTTCTCTTTTCATAGCAACTAATATCTGgttagcatct ... caattggcagTGAAAACATCATCTGGAAGGCTTTTAGCCCCACCACTATTAATAGTGGTCG
EST: gi|110718605|gb|EE095630.1|EE095630
EST:     GGATATGGCCTTGGCTCTGGAATTTCTCTTTTCATAGCAACTAATATCTG                         TGAAAACATCATCTGGAAGGCTTTTAGCCCCAC-ACTATTAATAATGGTCC
genomic: GGATATGGCCTTGGCTCTGGAATTTCTCTTTTCATAGCAACTAATATCTGgttagcatct ... caattggcagTGAAAACATCATCTGGAAGGCTTTTAGCCCCACCACTATTAATAGTGGTCG
EST: gi|110689014|gb|EE067912.1|EE067912
EST:     GGATATGGCCTTGGCTCTGGAATTTCTCTTTTCATAGCA-CTAATATCTG                         TGAAAACATCATCTGGAANGGCTTTTAGCCCCACCACTATTAATAGTGGTC
genomic: GGATATGGCCTTGGCTCTGGAATTTCTCTTTTCATAGCAACTAATATCTGgttagcatct ... caattggcagTGAAAACATCATCTGGAA-GGCTTTTAGCCCCACCACTATTAATAGTGGTC
EST: gi|110701078|gb|EE078295.1|EE078295
EST:     GGATATGGCCTTGGCTCTGGAATTTCTCTTTTCATAGCAACTAATATCTG                         TGAAAACATCATCTGGAAGGCTTTTAGCCCC-CCACTATTAATAGTGGTCG
genomic: GGATATGGCCTTGGCTCTGGAATTTCTCTTTTCATAGCAACTAATATCTGgttagcatct ... caattggcagTGAAAACATCATCTGGAAGGCTTTTAGCCCCACCACTATTAATAGTGGTCG
EST: gi|161717695|gb|FC067907.1|FC067907
EST:     GGATATGGCCTTGGCTCTGGAATTTCTCTTATCATAGCAACTAATATCTG                         TGAAAACATCATCTGGAAGGCTTATAGCCCCACCACTATTAATAGTGGTC
genomic: GGATATGGCCTTGGCTCTGGAATTTCTCTTTTCATAGCAACTAATATCTGgttagcatct ... caattggcagTGAAAACATCATCTGGAAGGCTTTTAGCCCCACCACTATTAATAGTGGTC
EST: gi|34549670|gb|CF517902.1|CF517902
EST:     GGATATGGCCTTGGCTCTGGAATTTCTCTTTTCATAGCAACTAATATCTG                         TGAAAACATCATCTGGAAGGCTTTTAGCCCCACCACTATTAATAGTGGGCG
genomic: GGATATGGCCTTGGCTCTGGAATTTCTCTTTTCATAGCAACTAATATCTGgttagcatct ... caattggcagTGAAAACATCATCTGGAAGGCTTTTAGCCCCACCACTATTAATAGTGGTCG
EST: gi|161718391|gb|FC067285.1|FC067285
EST:     GGATATGGCCTTGGCTCTGGAATTTCTCTTTTCATAGCAACTAATATCTG                         TGAAAACATCATCTGGAAGGCTTTTAGCCCCACCACTATTAATAGTGGTCG
genomic: GGATATGGCCTTGGCTCTGGAATTTCTCTTTTCATAGCAACTAATATCTGgttagcatct ... caattggcagTGAAAACATCATCTGGAAGGCTTTTAGCCCCACCACTATTAATAGTGGTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attaactctactgtcaagtagtgattgctaatgaattgttttgatcaattggcagTGAAAACATCATCTGGAAGGCTTTTAGCCCCACCACTATTAATAGTGGTCGTGGAGCTGAATTTGAAGGTGCTGTTATTGCTCTCTTCCATCTGCTAATA
                            taatgaattgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagcatctggttctttttctgggattttttttaattaatttatgattttgaacatggaatatttgaagaagctttatcgtctagcagccagtgtctggtgaatggtgggcccattttctgggtgaaccattaactctactgtcaagtagtgattgctaatgaattgttttgatcaattggcagTGAAAACATCATCTGGAAGGCTTTTAGCCCCACCACTATTAATAGTGGTCGTGGAGCTGAATTTGAAGGTGCTGTTATTGCTCTCTTCCATCTGCTAATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT