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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagctggaaatttgttctctgtttgtgaatgattttgtgtttttttttttttttgggtggggggggggggggggtggggtgggggagtatgggagttcaggccatttgggttcactgaaactgatggtttgttgcatttccagGGAGGAATGTGTGTGTAATGGGGTCCGCTATTTTGCCATCTTGTCTATGCAAAGATCCGGGAGTGGATGGTTTGAGACATTGTTAAATAGTCATATTAAT

Basic information

species Vitis vinifera
transcript Vv18s0001g11050.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g11050.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G142507_T02 (Zea mays), 3'ss of exon 3
gtagctggaaatttgttctctgtttgtgaatgattttgtgtttttttttttttttgggtggggggggggggggggtggggtgggggagtatgggagttcaggccattt--gggttcac-tgaaactgatggtttgttgcatttccagGGAGGAATGTGTGTGTAATGGGGTCCGCTATTTTGCCATCTTGTCTATGCAAAGATCCGGGAGTGGATGGTTTGAGACATTGTTAAATAGTCATATTAAT
                                                         ||   |  |         ||||    | || | |     |||     ||||   ||||    |   |||      || ||    |   ||| | ||||||| ||| |  |||||  | |  ||||| |||||||| ||||| || ||||||||||||||| ||||||| ||||| ||||| |||  ||||
---------------------------------------------------------gtaatgaagatatatac-tgggtcatgtgattttcctttttctatttatttccaggttagtgtctgacttgcatgttctttgtctgttagGAAAGAATGTGCGTGCACAGGGGTTAGGTTCTTTGCTATCTTGTCAATGCAGAGGTCCGGGAGTGGATGGGTTGAGACGTTGTTGAATAGCCATCCTAAT

upper sequence: Vv18s0001g11050.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM5G877077_T01 (Zea mays), 3'ss of exon 2
gtagctggaaatttgttctctgtttgtgaatgattttgtgtttttttttttttttgggtggggggggggggggggtggggtgggggagtatgggagttcaggccatttgggttcac--tgaaactgatggtttgttgcattt-ccagGGAGGAATGTGTGTGTAATGGGGTCCGCTATTTTGCCATCTTGTCTATGCAAAGATCCGGGAGTGGATGGTTTGAGACATTGTTAAATAGTCATATTAAT-----
                                                                    |    |  |   |   |     |  || ||       ||  ||||        |  ||  ||| |  |   | |   ||| | ||||||| ||| |  |||||  | |  ||||| || ||||| ||||| || || |||||||||||| ||||||||||||| ||||| |||  ||||     
--------------------------------------------------------------------gtaacgaagatatactgtgtcctctgattttgcctttttcaggttagtgactgacttgtgggtgttctttgtctgttaggaaagAATGTGCGTGCACGGGGGTTAGGTTCTTTGCTATATTGTCAATGCAGAGGTCAGGGAGTGGATGGGTTGAGACATTGTTGAATAGCCATCCTAATATTAG

upper sequence: Vv18s0001g11050.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM5G877077_T02 (Zea mays), 3'ss of exon 2
gtagctggaaatttgttctctgtttgtgaatgattttgtgtttttttttttttttgggtggggggggggggggggtggggtgggggagtatgggagttcaggccatttgggtt--cactgaaactgatggtttgttgcattt-ccagGGAGGAATGTGTGTGTAATGGGGTCCGCTATTTTGCCATCTTGTCTATGCAAAGATCCGGGAGTGGATGGTTTGAGACATTGTTAAATAGTCATATTAAT
                                                                    |    |  |   |   |     |  || ||       ||  ||||        |  ||  ||| |  |   | |   ||| | ||||||| ||| |  |||||  | |  ||||| || ||||| ||||| || || |||||||||||| ||||||||||||| ||||| |||  ||||
--------------------------------------------------------------------gtaacgaagatatactgtgtcctctgattttgcctttttcaggttagtgactgacttgtgggtgttctttgtctgttagGAAAGAATGTGCGTGCACGGGGGTTAGGTTCTTTGCTATATTGTCAATGCAGAGGTCAGGGAGTGGATGGGTTGAGACATTGTTGAATAGCCATCCTAAT

upper sequence: Vv18s0001g11050.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA17G36300.1 (Glycine max), 3'ss of exon 1
gtagctggaaatttgttctctgtttgtgaatgattttgtgtttttttttttttttgggtggggggggggggggggtggggtgggggagtatgggagttcaggc-catttgggt--tcactgaaactgatggtttgttgcatttccagGGAGGAATGTGTGTGTAATGGGGTCCGCTATTTTGCCATCTTGTCTATGCAAAGATCCGGGAGTGGATGGTTTGAGACATTGTTAAATAGTCATATTAAT
                                               |   | |    || ||  |         |    |      | |    | |||| |  | ||||  |  | | | | | |||  | ||| || ||   ||| ||||| ||||  || |||   || || | ||||| ||| ||| | ||||||||||| |||||||||||||||||||| ||||| || |||||||| |||
-----------------------------------------------tgcatatgctttgaggaagaaattttttttaattttccatgaacattaattcatgtgcgtttgattaattagttatattgaatgattggtgaatgagcagAGAGGAGTGTGCTTGCAATCCTGTACGGTTTTTTGTCATATTGACAATGCAAAGATCGGGGAGTGGATGGTTTGAGACGTTGTTGAACAGTCATATGAAT

upper sequence: Vv18s0001g11050.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA04G03960.1 (Glycine max), 3'ss of exon 2
gtagctggaaatttgttctctgtttgtgaatgattttgtgtttttttttttttttgggtggggggggggggggggtggggtgggggagtatgggagttcaggccatttgggttcactgaaactgatggtttgttgcatttccagGGAGGAATGTGTGTGTAATGGGGTCCGCTATTTTGCCATCTTGTCTATGCAAAGATCCGGGAGTGGATGGTTTGAGACATTGTTAAATAGTCATATTAAT
                        | |  ||   | | ||||   | |||  |||   |       |        |    ||||   || ||| | |  |     | | |  | | |||    ||| ||   |||      ||| || || ||||  || |||   || |  | |||   |||  |||| ||||||||||| ||||| || |||||||||||||| || || ||||||||||||
------------------------tatatatatatatatgttcggtctttaattttaatatttctag--------ttatatgggttggtttggtaatgta-----tatagagtgattga---cgattgtgcattgtg----cagAGAAGAGTGTGCTTGCAATCCTGTTCTGTTTTTCTGCATTGTGTCAATGCAAAGATCTGGGAGCGGTTGGTTTGAGACATTTTTGAACAGTCATATTAAT

upper sequence: Vv18s0001g11050.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA14G08870.1 (Glycine max), 3'ss of exon 2
gtagctggaaatttgttctctgtttgtgaatgattttgtgtttttttttttttttgggtggggggggggggggggtggggtgggggagtatgggagttcaggccatttgggttcactgaaactgatggtttgttgcatttccagGGAGGAATGTGTGTGTAATGGGGTCCGCTATTTTGCCATCTTGTCTATGCAAAGATCCGGGAGTGGATGGTTTGAGACATTGTTAAATAGTCATATTAAT
                                           |   | |  |||| |    |            |  | |       | ||  | ||  |     ||   |  |   | | |||  | ||| || ||   ||| ||||| ||||  || |||   ||||| | |||| |||| ||| | ||||||||||| || ||||||||||||||||| ||||| || |||||||| |||
------------------------------------------atgcatatgctttgtggaatgcaaatttttcaatttgctacaaatatttgttatttgggtttgattatat--agctatattgaatgattggtgaatgagcagAGAGGAGTGTGCTTGCAATCCTGTCCGGTTTTTTACCATATTGACAATGCAAAGATCAGGTAGTGGATGGTTTGAGACGTTGTTGAACAGTCATATGAAT

upper sequence: Vv18s0001g11050.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA06G04120.1 (Glycine max), 3'ss of exon 2
gtagctggaaatttgttctctgtttgtgaatgattttgtgtttttttttttttttgggtggggggggggggggggtggggtgggggagtatgggagttcaggccatttgggttcactgaaactgatggtttgttgcatttccagGGAGGAATGTGTGTGTAATGGGGTCCGCTATTTTGCCATCTTGTCTATGCAAAGATCCGGGAGTGGATGGTTTGAGACATTGTTAAATAGTCATATTAAT
                      | | |  ||  ||   ||||   | |||  |||   |       |    ||| |||  ||    | ||||            |  | |  | | |||    ||   |   |||      ||| || || ||||  || |||   || |  | |||   |||  |||| ||||||||||| ||||| || |||||||| ||||| || || ||||||||||||
----------------------tatatagattgttgattgttcggtctttaattttaatttttctagttacgggttggtttg----attatg-----------tacatagagtgattga---cgaatctacattgtg----cagAGAAGAGTGTGCTTGCAATCCTGTTCTGTTTTTCTGCATTGTGTCAATGCAAAGATCTGGGAGCGGTTGGTTTGAAACATTTTTGAACAGTCATATTAAT

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|294964137|gb|GW837940.1|GW837940
EST:     CCGTGGGAGATTCCCTATGTGCATTACCCAAAACCCAAAACCCATAGCAG                         GGAGGAATGTGTGTGTAATGGGGTCCGCTATTTTGCCATCTTGTCTATGCA
genomic: CCGTGGGAGATTCCCTATGTGCATTACCCAAAACCCAAAACCCATAGCAGgtagctggaa ... gcatttccagGGAGGAATGTGTGTGTAATGGGGTCCGCTATTTTGCCATCTTGTCTATGCA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgggagttcaggccatttgggttcactgaaactgatggtttgttgcatttccagGGAGGAATGTGTGTGTAATGGGGTCCGCTATTTTGCCATCTTGTCTATGCAAAGATCCGGGAGTGGATGGTTTGAGACATTGTTAAATAGTCATATTAAT
                              aactgat  putative branch site (score: 3)
                                              catttcc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagctggaaatttgttctctgtttgtgaatgattttgtgtttttttttttttttgggtggggggggggggggggtggggtgggggagtatgggagttcaggccatttgggttcactgaaactgatggtttgttgcatttccagGGAGGAATGTGTGTGTAATGGGGTCCGCTATTTTGCCATCTTGTCTATGCAAAGATCCGGGAGTGGATGGTTTGAGACATTGTTAAATAGTCATATTAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA