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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttcttttcctgaattttctcggcaaccaaacaaaggaataggtgttttatttaattcctgaatctattgattctgaaatgggttcgtttgggcgcagTTTCACCAGTACCAGGTGGTAGGGAGGGCCCTTCCTTCGGAATCGGATGAGCATCCGAGGATCTACAGGATGAAGCTTTGGGCTACGAACGAGGTTCGTG

Basic information

species Vitis vinifera
transcript Vv19s0135g00100.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0135g00100.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA14G03380.1 (Glycine max), 3'ss of exon 1
tttttcttttcctgaattttctcggcaaccaaacaaaggaataggtgttttatttaattcc-----tgaatctattgattctgaaatgggttcgtt-------tgggcgcagTTTCACCAGTACCAGGTGGTAGGGAGGGCCCTTCCTTCGGAATCGGATGAGCATCCGAGGATCTACAGGATGAAGCTTTGGGCTACGAACGAGGTTCGTG
                     | || ||      || ||  |  |||||| ||||| ||       ||| | | | || | | | ||| |   ||        | |  |||||||||||||||||||||||| || ||||| |||||| | ||||| ||||||||||| | ||||||| | ||||| || ||||| || |||||||| ||||
--------------------gtgggtaat--gttaatggtttttgtgtttgatttagtttgcagagtgagtttgtggaatttaacatgtgaatgtgattatggttgaagcagTTTCACCAGTACCAGGTGGTGGGAAGGGCTCTTCCTACCGAATCCGATGAGCATCCTAAGATCTACCGCATGAAACTCTGGGCCACCAACGAGGTCCGTG

upper sequence: Vv19s0135g00100.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA15G10220.1 (Glycine max), 3'ss of exon 1
tttttcttttcctgaattttctcggcaaccaaacaaaggaataggtgttttatttaattcctgaatctattgattctgaaatgggtt-cgtttgggcgcagTTTCACCAGTACCAGGTGGTAGGGAGGGCCCTTCCTTCGGAATCGGATGAGCATCCGAGGATCTACAGGATGAAGCTTTGGGCTACGAACGAGGTTCGTG
         | |  ||  ||| |  ||          |   |     ||||  |   ||  ||| | |   ||    |   |  |||  || |    |||||||||||||||||||||||| |||||||| |||||  ||||| | ||| |||| || | ||||||| | |||||||| ||||| || ||||||||||| |
--------gtgcgtaagattcacaccatttggtgttcgattt---cattttcctctgttaatgatttttacgaggtggtgttttgttatgtgtatttgcagTTTCACCAGTACCAGGTGGTTGGGAGGGCTCTTCCCACGGAAGCAGATCAGCACCCCAAGATCTACCGAATGAAGCTCTGGGCCACCAACGAGGTTCGCG

upper sequence: Vv19s0135g00100.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA02G45430.1 (Glycine max), 3'ss of exon 1
tttttcttttcctgaattttctcggcaaccaaacaaaggaataggtgttttatttaattcc-----tgaatctattgattctgaaatgggttcgtt-------tgggcgcagTTTCACCAGTACCAGGTGGTAGGGAGGGCCCTTCCTTCGGAATCGGATGAGCATCCGAGGATCTACAGGATGAAGCTTTGGGCTACGAACGAGGTTCGTG
                     |  | ||      || || ||  |||||| ||||  ||       ||| | | | |||| | |  || | | ||        | |  ||||||||| |||||||||||||| || ||||| |||||| | ||||| ||||||||||| | ||||||| | ||||| || ||||| || |||||||| ||||
--------------------gtgagtaat--gttaatggtatttgtgtttgattttgtttggagagtgagtttgtggattttaacgtgtgattgtgattatggttgaagcagTTTCATCAGTACCAGGTGGTGGGAAGGGCTCTTCCTACCGAATCCGATGAGCATCCTAAGATCTACCGCATGAAACTCTGGGCAACTAACGAGGTCCGTG

upper sequence: Vv19s0135g00100.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA18G13270.1 (Glycine max), 3'ss of exon 1
-tttttcttttcctgaattttctcgg-caaccaaacaaaggaataggtgtttt-atttaattcctgaatctattgattctgaaatgggttcgtttgggcgcagTTTCACCAGTACCAGGTGGTAGGGAGGGCCCTTCCTTCGGAATCGGATGAGCATCCGAGGATCTACAGGATGAAGCTTTGGGCTACGAACGAGGTTCGTG-
  |||| ||    |   |||||| |  ||        | |   |  ||||    | || ||    ||   || || || |    | |||  |||  |   |||||||||||||||||||| || || ||||| |||||  | ||| | |||| |||||| | |||||||||||||||||| ||||| || || ||||| |||| 
ccttttattaattttgcttttctagttcatttttctgatgctgtgagtgtgaagagttcataatggatgataatgttttttt--ttggtatgtt--gaatcagtTTCACCAGTACCAGGTTGTTGGAAGGGCTCTTCCCACTGAAACTGATGTGCATCCTAAGATCTACAGGATGAAGCTGTGGGCCACCAATGAGGTCCGTGC

upper sequence: Vv19s0135g00100.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S101_218V6.1 (Physcomitrella patens), 3'ss of exon 1
tttttcttttcctgaattttctcggcaaccaaacaaaggaataggtgtttt-atttaa-------ttcctgaatctattgattctgaa---atgggttcgtttgggc--gcagTTTCACCAGTACCAGGTGGTAGGGAGGGCCCTTCCTTCGGAATCGGATGAGCATCCGAGGATCTACAGGATGAAGCTTTGGGCTACGAACGAGGTTCGTG
             |  |     ||| |   ||    ||    |  ||| |  ||||||       |  |||  | |  | | |||||     |  || || ||||     ||||||||||||||||||||||| ||| ||||||| ||  | |   |  ||||   ||| | |  |||| | |||||  | ||||| |||||||| || || |
-------------gcgtcgagccggtaggaaagtggagattgaattgtctccatttaaaggcttctatctgcgtgtgattactctgattgtgtttgtgcgcttggtacaacagTTTCACCAGTACCAGGTGGTGGGGCGGGCCCTCCCAACAGCTACCAATGAAACTCCCAAGGCCTACCGCATGAAATTATGGGCGACGAACGAAGTGCGCG

upper sequence: Vv19s0135g00100.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S5_178V6.1 (Physcomitrella patens), 3'ss of exon 1
tttttcttttcctgaattttctcggcaaccaaacaaaggaataggtgttttatttaattcctgaatctattgattctgaaatgggt-----tcgtttgggcgcagTTTCACCAGTACCAGGTGGTAGGGAGGGCCCTTCCTTCGGAATCGGATGAGCATCCGAGGATCTACAGGATGAAGCTTTGGGCTACGAACGAGGTTCGTG
 |||  | |   ||||   |    |      |      ||||     |||| |||    |||   ||| ||| ||||||  ||| |     |   |||    ||||||||||| ||||||||||| ||| ||||||||||  | | | |  |||||   || |     ||| | |||||||||||||| || || || || || |
atttggtgtcattgaaaaatggtcgtg----agtttttgaatgtcctttttttttccccccttcttct-ttggttctgatttggttcattattccttgtcaacagTTTCACCAATACCAGGTGGTGGGGCGGGCCCTTCCAACTGCAACCAATGAGGCCCCTAAAGCTTACCGCATGAAGCTTTGGGCGACCAATGAAGTCCGCG

upper sequence: Vv19s0135g00100.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S56_243V6.3 (Physcomitrella patens), 3'ss of exon 1
tttttcttttcctgaattttctcggcaaccaaacaaaggaatag-gtgttttatttaattcctgaatctattgattctgaaatgggttcgtttgggcgcagTTTCACCAGTACCAGGTGGTAGGGAGGGCCCTTCCTTCGGAATCGGATGAGCATCCGAGGATCTACAGGATGAAGCTTTGGGCTACGAACGAGGTTCGTG---------
        ||   |  | ||   |       | ||  |    || ||  ||| | | |    |||   |  ||||    |  | |  || | |      |||||||||||||||||||||||||| ||||||| ||  | |   |  |||||   |||| |   ||| | |||||||| ||||| || ||||| || || |         
--------ttttcgggtctttctgtttgttcatcatggtttcagtgtactttttctgaaatttgatgatgctgatc--aaggtcgtgtcttgttccaatagtttcaccagTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAGACCCCGAAGGCTTACCGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGA

upper sequence: Vv19s0135g00100.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S56_243V6.1 (Physcomitrella patens), 3'ss of exon 1
---------------------tttttcttttcctgaattttctcggcaaccaaacaaaggaatag-gtgttttatttaattcctgaatctattgattctgaaatgggttcgtttgggcgcagTTTCACCAGTACCAGGTGGTAGGGAGGGCCCTTCCTTCGGAATCGGATGAGCATCCGAGGATCTACAGGATGAAGCTTTGGGCTACGAACGAGGTTCGTG
                           ||||   |  | ||   |       | ||  |    || ||  ||| | | |    |||   |  ||||    |  | |  || | |      |||||||||||||||||||||||||| ||||||| ||  | |   |  |||||   |||| |   ||| | |||||||| ||                    
tagttaagacggagtgaaagtgggagtttttttcgggtctttctgtttgttcatcatggtttcagtgtactttttctgaaatttgatgatgctgatc--aagGTCGTGTCTTGTTCCAATAGTTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAGACCCCGAAGGCTTACCGCATGAAGCTATG--------------------

upper sequence: Vv19s0135g00100.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S56_243V6.2 (Physcomitrella patens), 3'ss of exon 1
-tttttcttttcctgaattttctcggcaaccaaacaaaggaatag-gtgttttatttaattcctgaatctattgattctgaaatgggttcgtttgggcgcagTTTCACCAGTACCAGGTGGTAGGGAGGGCCCTTCCTTCGGAATCGGATGAGCATCCGAGGATCTACAGGATGAAGCTTTGGGCTACGAACGAGGTTCGTG
       ||||   |  | ||   |       | ||  |    || ||  ||| | | |    |||   |  ||||    |  | |  || | |      |||||||||||||||||||||||||| ||||||| ||  | |   |  |||||   |||| |   ||| | |||||||| ||||| || ||||| || || |
tgggagtttttttcgggtctttctgtttgttcatcatggtttcagtgtactttttctgaaatttgatgatgctgatc--aaggtcgtgtcttgttccaatagTTTCACCAGTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAGACCCCGAAGGCTTACCGCATGAAGCTATGGGCCACTAACGAAGTGCGCG

upper sequence: Vv19s0135g00100.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S44_13V6.1 (Physcomitrella patens), 3'ss of exon 1
tttttcttttcctgaattttctcggcaaccaa-acaaaggaataggtgtt--ttatttaattcctgaatctattgattctgaaatgggttcgtttgggc---gcagTTTCACCAGTACCAGGTGGTAGGGAGGGCCCTTCCTTCGGAATCGGATGAGCATCCGAGGATCTACAGGATGAAGCTTTGGGCTACGAACGAGGTTCGTG
     |   ||     |||||  ||| |   |     ||   | ||| ||  | |     |||||     |  | ||||  || ||  || | ||        ||||||||||||||||||||||| ||| | ||||||||  |        |||||   || | |   ||| | |||||| | ||||| ||| |||| || || |
-----cgcatcgaagtttttcagggccattgacgtttagctcttggttttcgtgacgcctttccttggcgtggt-attcacaagtgatttggatttatttttacagTTTCACCAGTACCAGGTGGTTGGGCGAGCCCTTCCAACCCCGGGCAATGAGACCCCCAAGGCTTACCGCATGAAGTTGTGGGCCACGGACGAAGTGCGCG

upper sequence: Vv19s0135g00100.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ31458 (Selaginella moellendorffii), 3'ss of exon 1
tttttcttttcctgaattttctcggcaaccaaacaaaggaataggtgttttatttaattcctgaatctattgattctgaaatgggttcgtttgggcgcagTTTCACCAGTACCAGGTGGTAGGGAGGGCCCTTCCTTCGGAATCGGATGAGCATCCGAGGATCTACAGGATGAAGCTTTGGGCTACGAACGAGGTTCGTG
                                      | |    |       |  |   ||  ||| || ||||    |       | ||    ||||||||||||||||||||||||| || || ||   |||  |        ||||||| || | ||| ||| |||||||||| |||||     |||| || || |
--------------------------------------gtaagaattcgcagctcgagcgctcgatccatcgatt---gatccctcccattgtctcgcagTTTCACCAGTACCAGGTGGTCGGAAGAGCTACTCCCACTCCCGACAATGAGCACCCAAAGATGTACCGGATGAAGCTCTGGGCCGGCGACGAAGTGCGCG

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|30135992|gb|CB921330.1|CB921330
EST:     GGAAGCTGCTCCTGAGCTTGTCTCTTATCGCCAAAATGGTTACTTTTAAG                         TTTCACCAGTACCAGGTGGTAGGGAGGGCCCTTCCTTCGGAACCGGATGAG
genomic: GGAAGCTGCTCCTGAGCTTGTCTCTTATCGCCAAAATGGTTACTTTCAAGgtctgtatga ... ttgggcgcagTTTCACCAGTACCAGGTGGTAGGGAGGGCCCTTCCTTCGGAATCGGATGAG
EST: gi|51990043|gb|CV179498.1|CV179498
EST:     CTCCTGAGCTTGTCTCTTATCGCCAAAATGGTTACTTTCAAG                         TTTCACCAGTACCAGGTGGTAGGGAGGGCCCTCCCTTCGGAATCGGATGAG
genomic: CTCCTGAGCTTGTCTCTTATCGCCAAAATGGTTACTTTCAAGgtctgtatga ... ttgggcgcagTTTCACCAGTACCAGGTGGTAGGGAGGGCCCTTCCTTCGGAATCGGATGAG
EST: gi|294966449|gb|GW839556.1|GW839556
EST:     GGAAGCTGCTCCTGAGCTTGTCTCTTATCGCCAAAATGGTTACTTTCAAG                         TTTCACCAGTACCAGGTGGTAGGGAGGGCCCTTCCTTCGGAATCGGATGAG
genomic: GGAAGCTGCTCCTGAGCTTGTCTCTTATCGCCAAAATGGTTACTTTCAAGgtctgtatga ... ttgggcgcagTTTCACCAGTACCAGGTGGTAGGGAGGGCCCTTCCTTCGGAATCGGATGAG
EST: gi|71875043|gb|DT024098.1|DT024098
EST:     GGAAGCTGCTCCTGAGCTTGTCTCTTATCGCCAAAATGGTTACTTTCAAG                         TTTCACCAGTACCAGGTGGTAGGGAGGGCCCTTCCTTCGGAATCGGATGAG
genomic: GGAAGCTGCTCCTGAGCTTGTCTCTTATCGCCAAAATGGTTACTTTCAAGgtctgtatga ... ttgggcgcagTTTCACCAGTACCAGGTGGTAGGGAGGGCCCTTCCTTCGGAATCGGATGAG
EST: gi|71869765|gb|DT018820.1|DT018820
EST:     GGAAGCTGCTCCTGAGCTTGTCTCTTATCGCCAAAATGGTTACTTTCAAG                         TTTCACCAGTACCAGGTGGTAGGGAGGGCCCTTCCTTCGGAATCGGATGAG
genomic: GGAAGCTGCTCCTGAGCTTGTCTCTTATCGCCAAAATGGTTACTTTCAAGgtctgtatga ... ttgggcgcagTTTCACCAGTACCAGGTGGTAGGGAGGGCCCTTCCTTCGGAATCGGATGAG
EST: gi|71875150|gb|DT024205.1|DT024205
EST:     AGCTGCTCCTGAGCTTGTCTCTTATCGCCAAAATGGTTACTTTCAAG                         TTTCACCAGTACCAGGTGGTAGGGAGGGCCCTCCCTTCGGAATCGGATGAG
genomic: AGCTGCTCCTGAGCTTGTCTCTTATCGCCAAAATGGTTACTTTCAAGgtctgtatga ... ttgggcgcagTTTCACCAGTACCAGGTGGTAGGGAGGGCCCTTCCTTCGGAATCGGATGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttttatttaattcctgaatctattgattctgaaatgggttcgtttgggcgcagTTTCACCAGTACCAGGTGGTAGGGAGGGCCCTTCCTTCGGAATCGGATGAGCATCCGAGGATCTACAGGATGAAGCTTTGGGCTACGAACGAGGTTCGTG
                      tattgat  putative branch site (score: 3)
                                        ttcgttt  putative PPT
     tatttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttcttttcctgaattttctcggcaaccaaacaaaggaataggtgttttatttaattcctgaatctattgattctgaaatgggttcgtttgggcgcagTTTCACCAGTACCAGGTGGTAGGGAGGGCCCTTCCTTCGGAATCGGATGAGCATCCGAGGATCTACAGGATGAAGCTTTGGGCTACGAACGAGGTTCGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - ttcctga
- - - - - - - - - - - - - - - aaacaaa
- - - - - - - - - - - - - - - - - - -ggaatagg