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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagatacacactcaatacatgtatatggttcttgtggatttgtttttcatcatttattttctgagttttaatggacttttcagTTTAAACAAGCTGAAGAAACAGCTGTGAAGCTTGATTTGGATGGCCTACTTGTCATTGGTGGAGATGACTCAAACACAAATGCTTGCCTTCTTGCTGAAA

Basic information

species Vitis vinifera
transcript Vv10s0116g00360.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 4
--------------------gtg-agatacacactcaatacatgtatatggttcttgtgga----------tttgtt------tttcatca-----tttattttctgagttttaatggactttt---cagTTTAAACAAGCTGAAGAAACAGCTGTGAAGCTTGATTTGGATGGCCTACTTGTCATTGGTGGAGATGACTCAAACACAAATGCTTGCCTTCTTGCTGAAA
                    ||| | || |  | | ||| | | ||| ||  | |   ||           ||||||      |||||  |     ||  | || | | || |        |||   ||||| || ||||||||||| || |     || |||||||||||||| ||  ||||||||||||| ||||| ||||||||||| || ||||||||||||||  
gtatatctttgcgcttttatgtgcaaatgcttatttaatccctttatctgcctttcagggtatttggctattttgttgcctagtttcactagcattttcttattttaaattctgtcatgtatttgagcagTTCAAGCAAGCTGAAGACACTGTAAACAAACTTGATTTGGATGGGCTTGTTGTCATTGGTGGTGATGATTCAAACACAAACGCATGCCTTCTTGCTGAGT

upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 4
------------------gtgagatacacactcaa-tacatgtatatggttcttgt----ggatttgtt---tttcatcatttattttctgagttttaatg--------gacttttcagTTTAAACAAGCTGAAGAAACAGCTGTGAAGCTTGATTTGGATGGCCTACTTGTCATTGGTGGAGATGACTCAAACACAAATGCTTGCCTTCTTGCTGAAA
                  |  |  |  |   |||| | | | |  |      ||||    ||||||  |    |  ||||||| || ||       ||||         |  | | |||||||| ||||||||||| || ||    ||||||||||||||||| ||  ||||||||||||| ||||| |||||||| ||||| ||||| |||| |||| 
gtatgtctctgggctctggccatgtttatgttcaaatgcttatgaaaaaactttgttactggatttcctaatctcgatcattttttctcaactacctaatacctgtgttggttgtgcagTTTAAGCAAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTTGTCATTGGTGGTGATGATTCAAACACCAATGCCTGCCTCCTTGGTGAAT

upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA07G39380.1 (Glycine max), 3'ss of exon 4
-gtgagatacacactcaatac------atgtatatggttcttgtggatttgt-----ttttcatcatttattttctgagtt---ttaatggac-ttttcagTTTAAACAAGCTGAAGAAACAGCTGTGAAGCTTGATTTGGATGGCCTACTTGTCATTGGTGGAGATGACTCAAACACAAATGCTTGCCTTCTTGCTGAAA
  ||   ||         | |      || || ||  ||| | |  | |  |     | ||| |||   | | |  |   |   ||| |  || | | |||||||||||||||||||||||||    ||||||  | ||||| |||||  |||| ||||||||||||||||||||||||||||| ||||| ||||||||  
gttggcctatttctctgctgctttgctatatagattattcatttcaactcttacacatcttcgtcaacgagtatggggaataatttattttacatgtacagTTTAAACAAGCTGAAGAAACAGTGCAGAAGCTAAACTTGGACGGCCTTGTTGTTATTGGTGGAGATGACTCAAACACAAATGCATGCCTCCTTGCTGAGC

upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 2
--------------gtg-agatacacactcaatacatgt-atatgg-ttcttgtggatttgtttttcatcatttattttctgagttttaatggactttt-cagTTTAAACAAGCTGAAGAAACAGCTGTGAAGCTTGATTTGGATGGCCTACTTGTCATTGGTGGAGATGACTCAAACACAAATGCTTGCCTTCTTGCTGAAA
               || ||||   |  | || |    | |||||   ||||||    ||     || |||  |||     |   |||| |   | | | |||||||||||||||||||||||||    |||||| || ||||| |||||  |||| ||||||||||||||||| ||||||||||| ||||| ||||||||  
gttggcctatttctctgcagatttgctataaagattgatcatatgaactcttgtactattacacatcttcaagtatggggagtaatttattttgcatgtacagTTTAAACAAGCTGAAGAAACAGTGCAGAAGCTAGACTTGGACGGCCTTGTTGTTATTGGTGGAGATGACTCGAACACAAATGCATGCCTCCTTGCTGAGC

upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 4
---------gtgaga-tacacactcaatacatgtatatggttcttgtggatttgtttttcatcatttattttctgagt----tttaatggactt------ttcagTTTAAACAAGCTGAAGAAACAGCTGTGAAGCTTGATTTGGATGGCCTACTTGTCATTGGTGGAGATGACTCAAACACAAATGCTTGCCTTCTTGCTGAAA
         |||||  ||||   | | || | |  ||      ||| | | |||| | || || || |  |    ||     || | || ||||      |  ||||||| ||||| ||||||||||||  |||||| || |||||||| ||  |||| |||||||| |||||||||||||| ||||| |||||||||||||| |
gtgagttttgtgaggctacatgtttactatacgattaattaatttgagcacttgtgtatcttctttcaagtctaaagactaattcagtgtacttgcatggtatagTTTAAGCAAGCGGAAGAAACAGCTAAGAAGCTAGACTTGGATGGGCTCGTTGTTATTGGTGGTGATGACTCAAACACCAATGCGTGCCTTCTTGCTGAGA

upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA15G11890.1 (Glycine max), 3'ss of exon 4
---------gtgaga-tacacactcaatacatgtatat----ggttcttgtggatttgtttttca--tcatttattttctgagttttaatggacttttcagTTTAAACAAGCTGAAGAAACAGCTGTGAAGCTTGATTTGGATGGCCTACTTGTCATTGGTGGAGATGACTCAAACACAAATGCTTGCCTTCTTGCTGAAA
         |||||  ||||   | | || | |  ||         |||||  || |  || | |   ||   | |   | |||||   |  |   |  ||||||| ||||| ||||||||||||  |||||| || |||||||| ||  |||| |||||||| |||||||||||||| ||||| ||||| |||||||| |
gtgagttttgtgaggctacatgtttactatacgattaatttgaacgcttgtatatcttcttataagtccaaagagtaattcagtttacttacatggtatagTTTAAGCAAGCGGAAGAAACAGCTAAGAAGCTAGACTTGGATGGGCTCGTTGTTATTGGTGGTGATGACTCAAACACCAATGCATGCCTCCTTGCTGAGA

upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgagatacacactcaatacatgtatatggttcttgtggatttgtttttcatcatttattttctg--------agttttaatggactttt-----cagTTTAAACAAGCTGAAGAAACAGCTGTGAAGCTTGATTTGGATGGCCTACTTGTCATTGGTGGAGATGACTCAAACACAAATGCTTGCCTTCTTGCTGAAA
||   |||     |       || | | | |  ||||  | |  ||    | | | |||||  ||        | || ||   | || |      ||||||||||||||||||||||||||   ||||||||||||||||||  |  | || || ||||||||||| || ||||| ||||||||||||||||||||||
gttgaatatttttttgtggtttgaaaa-gatatttgtt-actgcttccaaagcctctatttcgtgcagtgagtaattatatatgcctctcatgtgcagTTTAAACAAGCTGAAGAAACAGCAAAGAAGCTTGATTTGGATGGGTTGGTGGTTATCGGTGGAGATGATTCCAACACCAATGCTTGCCTTCTTGCTGAAA

upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT4G04040.1 (Arabidopsis thaliana), 3'ss of exon 4
gt-gagatacaca-ctcaatacatgtatatggttcttgtggatttgtttttcatca---tttattttctgagttttaatggacttttcagTTTAAACAAGCTGAAGAAACAGCTGTGAAGCTTGATTTGGATGGCCTACTTGTCATTGGTGGAGATGACTCAAACACAAATGCTTGCCTTCTTGCTGAAA
|| || ||      || |||   | | |||||  |   | |||   ||| ||       ||  || | |    |||  |  | |||  ||||||| ||||||||||| || | |   ||| | ||||| ||||| ||  | || ||||||||||||||||| || || |||||||| || ||||||||| 
gtagaaatgtttttcttaatgttt-tgtatggcgcgcattgatgcttttatcgatggacttagttatattcagtttggtacattttgtagTTTAAGCAAGCTGAAGAGACTGTTACAAAGATGGATTTAGATGGTCTTGTGGTAATTGGTGGAGATGACTCCAATACTAATGCTTGTCTCCTTGCTGAAC

upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ13842 (Selaginella moellendorffii), 3'ss of exon 4
gtgagatacacactcaatacatgtatatggttcttgtgg-atttgtttttcatcatttattttctgagttttaatggacttttcagTTTAAACAAGCTGAAGAAACAGCTGTGAAGCTTGATTTGGATGGCCTACTTGTCATTGGTGGAGATGACTCAAACACAAATGCTTGCCTTCTTGCTGAAA
                 | | ||| | |  |||   | | | |  |   ||     | | |   || |||||      |||| ||||| || ||||| ||||| || ||||||||||| || ||||| ||| |  | || |||||||| || ||||| ||||| ||||| ||||||||||| ||  
---------------gtttcttgtgttt--ttccaatagcagtaatggctctcagctcaatcaatgtgtttttgc---ctttgcagTTCAAGCAAGCGGAAGACACGGCTGTGAAGCTCGACTTGGACGGCATTGTAGTTATTGGTGGGGACGACTCCAACACGAATGCCTGCCTTCTTGCGGAGT

upper sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ12684 (Selaginella moellendorffii), 3'ss of exon 4
gtgagatacacactcaatacatgtatatggttcttgtggatttgtttttcatcatttattttctgagttttaatggacttttcagTTTAAACAAGCTGAAGAAACAGCTGTGAAGCTTGATTTGGATGGCCTACTTGTCATTGGTGGAGATGACTCAAACACAAATGCTTGCCTTCTTGCTGAAA
             |   | | | | |    |    ||     ||  | |||    | | |   ||  ||||  ||   ||| ||||| || ||||| ||||| || ||||||||||| || ||||| ||| |  | || |||||||| || ||||| ||||| ||||| ||||||||||| ||  
-----------gtttcttgcgtttttccaatagcagtaa---tggctctca--gctcaatcaatgtatttt--tgccttttgcagTTCAAGCAAGCGGAAGACACGGCTGTGAAGCTCGACTTGGACGGCATTGTAGTTATTGGTGGGGACGACTCCAACACGAATGCCTGCCTTCTTGCGGAGT

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|351027672|gb|FQ446839.1|FQ446839
EST:     GTTTTGATATGATCTGCAGTGGGAGAGACAAGATTGAAACTCCAGAACAG                         TTTAAACAAGCTGAAGAAACAGCTGTGAAGCTTGATTTGGATGGGCTTCTT
genomic: GTTTTGATATGATCTGCAGTGGGAGAGACAAGATTGAAACTCCAGAACAGgtgagataca ... gacttttcagTTTAAACAAGCTGAAGAAACAGCTGTGAAGCTTGATTTGGATGGCCTACTT
EST: gi|349820950|gb|FQ408658.1|FQ408658
EST:     GTTTTGATATGATCTGCAGTGGGAGAGACAAGATTGAAACTCCAGAACAG                         TTTAAACAAGCTGAAGAAACAGCTGTGAAGCTTGATTTGGATGGGCTTCTT
genomic: GTTTTGATATGATCTGCAGTGGGAGAGACAAGATTGAAACTCCAGAACAGgtgagataca ... gacttttcagTTTAAACAAGCTGAAGAAACAGCTGTGAAGCTTGATTTGGATGGCCTACTT
EST: gi|110689257|gb|EE065321.1|EE065321
EST:     GTTTTGATATGATCTGCAGTGGGAGAGACAAGATTGAAACTCCAGAACAG                         TTTAAACAAGCTGAAGAAACAGCTGTGAAGCTTGATTTGGATGGGCTTCTT
genomic: GTTTTGATATGATCTGCAGTGGGAGAGACAAGATTGAAACTCCAGAACAGgtgagataca ... gacttttcagTTTAAACAAGCTGAAGAAACAGCTGTGAAGCTTGATTTGGATGGCCTACTT
EST: gi|110730531|gb|EE107719.1|EE107719
EST:     ACAAGATTGAAACTCCAGAACAG                         TTTAAACAAGCTGAAGAAACAGCTGTGAAGCTTGATTTGGATGGGCTTCTT
genomic: ACAAGATTGAAACTCCAGAACAGgtgagataca ... gacttttcagTTTAAACAAGCTGAAGAAACAGCTGTGAAGCTTGATTTGGATGGCCTACTT
EST: gi|71865073|gb|DT014128.1|DT014128
EST:     GTTTTGATATGATCTGCAGTGGGAGAGACAAGATTGAAACTCCAGAACAG                         TTTAAACAAGCTGAAGAAACAGCTGTGAAGCTTGATTTGGATGGGCTTCTT
genomic: GTTTTGATATGATCTGCAGTGGGAGAGACAAGATTGAAACTCCAGAACAGgtgagataca ... gacttttcagTTTAAACAAGCTGAAGAAACAGCTGTGAAGCTTGATTTGGATGGCCTACTT
EST: gi|110698469|gb|EE075999.1|EE075999
EST:     GTTTTGATATGATCTGCAGTGGGAGAGACAAGATTGAAACTCCAGAACAG                         TTTAAACAAGCTGAAGAAACAGCTGTGAAGCTTGATTTGGATGGGCTTCTT
genomic: GTTTTGATATGATCTGCAGTGGGAGAGACAAGATTGAAACTCCAGAACAGgtgagataca ... gacttttcagTTTAAACAAGCTGAAGAAACAGCTGTGAAGCTTGATTTGGATGGCCTACTT
EST: gi|349808365|gb|FQ405533.1|FQ405533
EST:     GTTTTGATATGATCTGCAGTGGGAGAGACAAGATTGAAACTCCAGAACAG                         TTTAAACAAGCTGAAGAAACAGCTGTGAAGCTTGATTTGGATGGGCTTCTT
genomic: GTTTTGATATGATCTGCAGTGGGAGAGACAAGATTGAAACTCCAGAACAGgtgagataca ... gacttttcagTTTAAACAAGCTGAAGAAACAGCTGTGAAGCTTGATTTGGATGGCCTACTT
EST: gi|351029574|gb|FQ427414.1|FQ427414
EST:     GTTTTGATATGATCTGCANTGGGAGAGACAAGATTGAAACTCCAGAACAT                         TTTAAACAAGCTGAAGAAACAGCTGTGAAACTTGAT
genomic: GTTTTGATATGATCTGCAGTGGGAGAGACAAGATTGAAACTCCAGAACAGgtgagataca ... gacttttcagTTTAAACAAGCTGAAGAAACAGCTGTGAAGCTTGAT
EST: gi|349833359|gb|FQ416737.1|FQ416737
EST:     GTTTTGATATGATCTGCAGTGGGAGAGACAAGATTGAAACTCCAGAACAG                         TTTAAACAAGCTGAAGAAACAGCTGTGAAGCTTGATTTGGATGGGCTTCTT
genomic: GTTTTGATATGATCTGCAGTGGGAGAGACAAGATTGAAACTCCAGAACAGgtgagataca ... gacttttcagTTTAAACAAGCTGAAGAAACAGCTGTGAAGCTTGATTTGGATGGCCTACTT
EST: gi|351034089|gb|FQ448007.1|FQ448007
EST:     GTTTTGATATGATCTGCAGTGGGAGAGACAAGATTGAAACTCCAGAACAG                         TTTAAACAAGCTGAAGAAACAGCTGTGAAGCTTGATTTGGATGGGCTTCTT
genomic: GTTTTGATATGATCTGCAGTGGGAGAGACAAGATTGAAACTCCAGAACAGgtgagataca ... gacttttcagTTTAAACAAGCTGAAGAAACAGCTGTGAAGCTTGATTTGGATGGCCTACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttgtggatttgtttttcatcatttattttctgagttttaatggacttttcagTTTAAACAAGCTGAAGAAACAGCTGTGAAGCTTGATTTGGATGGCCTACTTGTCATTGGTGGAGATGACTCAAACACAAATGCTTGCCTTCTTGCTGAAA
                                     ttttaat  putative branch site (score: 3)
                                               cttttc  putative PPT
         atttgtttttcatcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagatacacactcaatacatgtatatggttcttgtggatttgtttttcatcatttattttctgagttttaatggacttttcagTTTAAACAAGCTGAAGAAACAGCTGTGAAGCTTGATTTGGATGGCCTACTTGTCATTGGTGGAGATGACTCAAACACAAATGCTTGCCTTCTTGCTGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG