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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagaaattattattttcctatgaaatttgtccccctttttccttcatctctctcaaccgagtcgatagaatgtttgtgaattaaccataaatttacatttggtcaattctttgcctgaacagATAATTTCTGGCGTGGAGTACTGCCACAGGAATATGGTAGTTCACAGAGATCTTAAACCTGAGAACTTGCTTTTGGATTCCAAATGCAATGTGAAGATTG

Basic information

species Vitis vinifera
transcript Vv14s0108g01230.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0108g01230.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os05g45420.3 (Oryza sativa), 3'ss of exon 3
gtagaaattattattttcctatga--aatttgtccccctttttccttcatctctctcaaccgagtcgatagaatgtttgtgaattaaccataaatttacatttggtcaattctttgcctgaacagATAATTTCTGGCGTGGAGTACTGCCACAGGAATATGGTAGTTCACAGAGATCTTAAACCTGAGAACTTGCTTTTGGATTCCAAATGCAATGTGAAGATTG
              || |  || |   |||||      ||||   | |||    || |   |  ||  |  |   |  | | ||        ||||| | |||| |  || |||||    |  |||| || ||||| || || || ||||| || || ||||| |||||  | |||||||| || |||||| | |||||||| |||||||||||||| |||||||
------------gcttccgcattacagatttggtaattttttatatgcattgtactgatatgcttcagtt-agcatccgaggat--------aattttcttttgtttgat-ctttg---aattagATCATATCTGGTGTTGAATATTGCCATAGAAACATGGTGGTTCATCGTGATCTTAAGCCAGAGAACCTTCTTTTGGACTCCAAATGCAATGTTAAGATTG

upper sequence: Vv14s0108g01230.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA18G49770.1 (Glycine max), 3'ss of exon 4
gtagaaattattattttcctatgaaatttgtccccctttttccttcatctctctcaaccgagtcgatagaatgtttgtgaattaaccataaatttacatttggtcaattctttgcct---gaacagATAATTTCTGGCGTGGAGTACTGCCACAGGAATATGGTAGTTCACAGAGATCTTAAACCTGAGAACTTGCTTTTGGATTCCAAATGCAATGTGAAGATTG
                                              ||   |  | |    ||  |  |||   || ||   |   || | ||||   |   |  ||||  |    |    | |||||||| ||||| ||||||||||| |||||||||||||| ||||| |||||| | || |||||||| || |||||||| |||||||| ||||| |||||||
-----------------------------------------gtaggattgtttactattttgtgtagtgaagacttttg--cttgtcacagatttt--tcaagctaatttctgattttggaagcagATAATCTCTGGGGTGGAGTACTGTCACAGGAATATGGTGGTTCATAGAGATTTGAAGCCTGAGAATTTACTTTTGGACTCCAAATGTAATGTCAAGATTG

upper sequence: Vv14s0108g01230.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA08G26180.1 (Glycine max), 3'ss of exon 3
gtagaaattattattttcctatgaaatttgtccccctttttccttcatctctctcaaccgagtcgatagaatgtttgtgaattaaccataaatttacatttggtcaattctttgcct---gaacagATAATTTCTGGCGTGGAGTACTGCCACAGGAATATGGTAGTTCACAGAGATCTTAAACCTGAGAACTTGCTTTTGGATTCCAAATGCAATGTGAAGATTG
                                      |    ||  |  || |     | ||   ||  |   || |  ||    || | |||| |     |  ||||  |    |    | |||||||| ||||| ||||||||||| |||||||||||||| ||||| |||||| | || |||||||| || |||||||| |||||||| ||||| |||||||
-------------------------------------gtaggattgtttactatt--ttgtgtaattaagagactttttcat--gtcacagattttc--caagctaatttctgattttggaagcagATAATCTCTGGTGTGGAGTACTGTCACAGGAATATGGTGGTTCATAGAGATTTGAAGCCTGAGAATTTACTTTTGGACTCCAAATGTAATGTCAAGATTG

upper sequence: Vv14s0108g01230.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA13G05700.2 (Glycine max), 3'ss of exon 3
gtagaaattattattttcctatgaaatttgtccccctttttccttcatctctctcaaccgagtcgatagaatgtttgtgaattaaccataaatttacatttggtcaattctttgcctgaacagATAATTTCTGGCGTGGAGTACTGCCACAGGAATATGGTAGTTCACAGAGATCTTAAACCTGAGAACTTGCTTTTGGATTCCAAATGCAATGTGAAGATTG-----------------------------
                                      | |  ||  |     |     | ||   |   |  ||||||   |  ||| |   ||  ||       ||  | ||    |||||||||||||||| ||||||||||| |||||||||||||| ||||| ||||| || || |||||||| || || ||||| || ||||  ||  | |||||||                             
-------------------------------------gtataatttgtaatattt--ttgtgtgcttcagagatttgtg--cttgccacattattgaatccaacttatgttatga--aaacagataatttctggtgtggagtactgtcacagGAATATGGTGGTTCATAGAGACCTGAAGCCTGAGAATTTACTCTTGGACTCAAAATTTAACATCAAGATTGCTGATTTTGGGTTGAGCAACATCATGCGT

upper sequence: Vv14s0108g01230.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA13G05700.1 (Glycine max), 3'ss of exon 3
gtagaaattattattttcctatgaaatttgtccccctttttccttcatctctctcaaccgagtcgatagaatgtttgtgaattaaccataaatttacatttggtcaattctttgcctgaacagATAATTTCTGGCGTGGAGTACTGCCACAGGAATATGGTAGTTCACAGAGATCTTAAACCTGAGAACTTGCTTTTGGATTCCAAATGCAATGTGAAGATTG
                                      | |  ||  |     |     | ||   |   |  ||||||   |  ||| |   ||  ||       ||  | ||    |||||||||||||||| ||||||||||| |||||||||||||| ||||| ||||| || || |||||||| || || ||||| || ||||  ||  | |||||||
-------------------------------------gtataatttgtaatattt--ttgtgtgcttcagagatttgtg--cttgccacattattgaatccaacttatgttatga--aaacagATAATTTCTGGTGTGGAGTACTGTCACAGGAATATGGTGGTTCATAGAGACCTGAAGCCTGAGAATTTACTCTTGGACTCAAAATTTAACATCAAGATTG

upper sequence: Vv14s0108g01230.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT3G01090.2 (Arabidopsis thaliana), 3'ss of exon 3
gtagaaattattattttcctatgaaatttgtccccctttttccttcatctctctcaaccgagtcgatagaatgtttgtgaattaaccataaatttacatttggtcaattctttgcctgaacagATAATTTCTGGCGTGGAGTACTGCCACAGGAATATGGTAGTTCACAGAGATCTTAAACCTGAGAACTTGCTTTTGGATTCCAAATGCAATGTGAAGATTG
        |||  ||||  | |  | ||| ||  | | |  | |||    |   ||  ||| |  |||  || |||| || ||||  || |  |   | ||||      |||||       ||||||| || || ||||| ||||||||  | || ||||| ||||||||||| || || ||||| |||||||||||||| || ||||||||||| |||||||
-------gtatgtttttatttt--attttatcaacatgtaactttccaagcaaccattcgattttatattatatttgagagttaagaattagct---acttgg------ctttgat---gtagATAATATCAGGAGTGGAATACTGCCATCGAAACATGGTGGTTCACAGAGACCTCAAGCCTGAAAACTTGCTTTTGGACTCTAAATGCAATGTAAAGATTG

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|161721802|gb|FC071139.1|FC071139
EST:     TAGAGAAGGGCAGGCTACAGGAGGAAGAAGCTCGTAACTTTTTTCAACAG                         ATAATTTCTGGCGTGGAGTACTGCCACAGGAATATGGTATTTCACAGAGAT
genomic: TAGAGAAGGGCAGGCTACAGGAGGAAGAAGCTCGTAACTTTTTTCAACAGgtagaaatta ... gcctgaacagATAATTTCTGGCGTGGAGTACTGCCACAGGAATATGGTAGTTCACAGAGAT
EST: gi|161720814|gb|FC070953.1|FC070953
EST:     TAGAGAAGGGCAGGCTACAGGAGGAAGAAGCTCGTAACTTTTTTCAACAG                         ATAATTTCTGGCGTGGAGTACTGCCACAGGAATATGGTAGTTCACAGAGAT
genomic: TAGAGAAGGGCAGGCTACAGGAGGAAGAAGCTCGTAACTTTTTTCAACAGgtagaaatta ... gcctgaacagATAATTTCTGGCGTGGAGTACTGCCACAGGAATATGGTAGTTCACAGAGAT
EST: gi|161715840|gb|FC067437.1|FC067437
EST:     TAGAGAAGGGCAGGCTACAGGAGGAAGAAGCTCGTAACTTTTTTCAACAG                         ATAATTTCTGGCGTGGAGTACTGCCACAGGAATATGGTAGTTCACAGAGAT
genomic: TAGAGAAGGGCAGGCTACAGGAGGAAGAAGCTCGTAACTTTTTTCAACAGgtagaaatta ... gcctgaacagATAATTTCTGGCGTGGAGTACTGCCACAGGAATATGGTAGTTCACAGAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatgtttgtgaattaaccataaatttacatttggtcaattctttgcctgaacagATAATTTCTGGCGTGGAGTACTGCCACAGGAATATGGTAGTTCACAGAGATCTTAAACCTGAGAACTTGCTTTTGGATTCCAAATGCAATGTGAAGATTG
           aattaac  putative branch site (score: 2)
                                       ttctttgcct  putative PPT
           aattaaccataaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagaaattattattttcctatgaaatttgtccccctttttccttcatctctctcaaccgagtcgatagaatgtttgtgaattaaccataaatttacatttggtcaattctttgcctgaacagATAATTTCTGGCGTGGAGTACTGCCACAGGAATATGGTAGTTCACAGAGATCTTAAACCTGAGAACTTGCTTTTGGATTCCAAATGCAATGTGAAGATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA