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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttatgtttcttctatggctatttgctaaatccctataaatttaggttggtgcacgaaaatcttatctattgcccttatgctagGTGTTGAGATTGTCATTGCTACACCTGGACGATTAATAGATATGCTGGAGGCTCAACATACAAACCTGCGAAGAGTGACTTACCTTGTATTAGATGAGGC

Basic information

species Vitis vinifera
transcript Vv17s0000g09130.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g09130.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g68320.3 (Oryza sativa), 3'ss of exon 4
gtacttatgtttcttctatggctatttgctaaatccctataaatttaggttggtgcacgaaaatcttatctattgccctta-tgctagGTGTTGAGATTGTCATTGCTACACCTGGACGATTAATAGATATGCTGGAGGCTCAACATACAAACCTGCGAAGAGTGACTTACCTTGTATTAGATGAGGC
       | ||| | | ||   ||      ||||   | |  |  || | |  || | |  ||     ||| ||||   || | | ||| ||||||||||||||||| |||||||| || || || ||||||||||| | |   || || |||||||||||||| || ||||| ||  | ||||||||
------gtatttgtcccatc-ttaccga--aaataattttggacataaggttttgtaggctaa----gtctcttgcgtctacttccagGGGTTGAGATTGTCATTGCAACACCTGGTCGGTTGATCGATATGCTGGAAGGTGGTCACACTAACCTGCGAAGAGTAACATACCTCGTCCTGGATGAGGC

upper sequence: Vv17s0000g09130.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G362850_T01 (Zea mays), 3'ss of exon 5
gtacttatgtttcttctatggctatttgctaaatccctataaatttaggttggtgcacgaaaatcttatctattgccctta-tgctagGTGTTGAGATTGTCATTGCTACACCTGGACGATTAATAGATATGCTGGAGGCTCAACATACAAACCTGCGAAGAGTGACTTACCTTGTATTAGATGAGGC
|||| |       |    || | | ||  ||| ||  | || ||  | |    |  |    |||   |||| |       | |  |||| ||||| ||||||||||| || ||||| || || || ||||||||||| |||   || |||||||| || |||||||| |||||||| || ||||||||
gtacctgcacacatc---tgtccactt--taattctttttagatgaatgccttttaaactcaatgcaatctgtcatttgcacttttagGAGTTGAAATTGTCATTGCAACTCCTGGCCGGTTGATTGATATGCTGGAAGCTGGTCACACAAACCTACGTAGAGTGACATACCTTGTGTTGGATGAGGC

upper sequence: Vv17s0000g09130.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AC209019.3_FGT003 (Zea mays), 3'ss of exon 2
------gtacttatgtttcttctatggctatttgctaaatccctataaatttaggttggtgcacgaaaatcttatctattgcccttatgctagGTGTTGAGATTGTCATTGCTACACCTGGACGATTAATAGATATGCTGGAGGCTCAACATACAAACCTGCGAAGAGTGACTTACCTTGTATTAGATGAGGC
      | ||  || | ||  || |   | |||  || ||   |     || |  |   ||||      |  | ||  |||| |||    |||| ||||| ||||||||||| || ||||| || || || ||||||||||| |||   || |||||||| || |||||||| |||||||| || ||||||||
gtacctgcacacatctgtccactttaattcttt-ttagatgaatgccttttaaactcaatgca------ttctgtcatttgcactt---ttagGAGTTGAAATTGTCATTGCAACTCCTGGCCGGTTGATTGATATGCTGGAAGCTGGTCACACAAACCTACGTAGAGTGACGTACCTTGTGTTGGATGAGGC

upper sequence: Vv17s0000g09130.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G059020_T01 (Zea mays), 3'ss of exon 6
------gtacttatgtttcttctatggctatttgctaaatccctataaatttaggttggtgcacgaaaatcttatctattgcccttatgctagGTGTTGAGATTGTCATTGCTACACCTGGACGATTAATAGATATGCTGGAGGCTCAACATACAAACCTGCGAAGAGTGACTTACCTTGTATTAGATGAGGC
      | ||  || | ||  || |   | |||  || ||   |     || |  |   ||||      |  | ||  |||| |||    |||| ||||| ||||||||||| || ||||| || || || |||||| |||| |||   || |||||||| || |||||||| |||||||| || ||||||||
gtacctgcacacatctgtccactttaattcttt-ttagatgaatgccttttaaactcaatgca------ttctgtcatttgcactt---ttagGAGTTGAAATTGTCATTGCAACTCCTGGCCGGTTGATTGATATGATGGAAGCTGGTCACACAAACCTACGTAGAGTGACATACCTTGTGTTGGATGAGGC

upper sequence: Vv17s0000g09130.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA17G09270.1 (Glycine max), 3'ss of exon 4
gtacttatgtttctt--ctatggctatttgctaaatccctataaatttaggttggtgcacgaaaatcttatctattgcccttatgctagGTGTTGAGATTGTCATTGCTACACCTGGACGATTAATAGATATGCTGGAGGCTCAACATACAAACCTGCGAAGAGTGACTTACCTTGTATTAGATGAGGC
|||| |   || |||  || | |   |||| |||     | |  | | |     |  || ||  |   || || |||    | ||  ||| || || || || |||||||||||||| ||  ||||||||||| |||| ||||| || || |||||||| ||||||||||||||||| |||||||| ||
gtacatggtttacttgccttttgtactttgataataatttttggaataa--ccagaacatgatgac--taacttttgatgct-tgacagGCGTCGAAATAGTTATTGCTACACCTGGTCGTCTAATAGATATGTTGGAAGCTCAGCACACGAACCTGCGGAGAGTGACTTACCTTGTCTTAGATGAAGC

upper sequence: Vv17s0000g09130.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA05G02590.1 (Glycine max), 3'ss of exon 4
gtacttatgtttctt--ctatggctatttgctaaatccctataaatttaggttggtgcacgaaaatcttatctattgcccttatgctagGTGTTGAGATTGTCATTGCTACACCTGGACGATTAATAGATATGCTGGAGGCTCAACATACAAACCTGCGAAGAGTGACTTACCTTGTATTAGATGAGGC
|||| |   || |||  |||| ||  |||| ||| |   | |  | | |  |  |  || ||  |   || || |||    | ||| ||| ||||| || || |||||||||||||| ||  ||||||||||| |||| ||||| || |||||||||   ||||||||||||||||| || ||||| ||
gtacatggtttacttgcctattgcactttgataa-taattttggaataacat--gaacatgatgaa--taacttttggtgct-tgccagGCGTTGAAATAGTTATTGCTACACCTGGTCGTCTAATAGATATGTTGGAAGCTCAGCACACAAACCTGAAGAGAGTGACTTACCTTGTCTTGGATGAAGC

upper sequence: Vv17s0000g09130.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G63120.1 (Arabidopsis thaliana), 3'ss of exon 4
gtacttatgtttcttctatggctatttgctaaatccctataaatttaggttggtgcacgaaaatcttatctattgccctta---tgctagGTGTTGAGATTGTCATTGCTACACCTGGACGATTAATAGATATGCTGGAGGCTCAACATACAAACCTGCGAAGAGTGACTTACCTTGTATTAGATGAGGC
||| || | ||| ||    |  || ||   |  ||    |   | | || |||  ||  ||| | ||||  ||     ||    ||  ||||||||||||||| |||||||||||||| || || || |||||| ||||   |||||| || ||  ||   |||||||||||||||||| | ||||||||
gtattt-tattttttaatagtgtagttttcatgtc----tggttcttggatggaacatcaaagt-ttatgaatcatgattggcttgtcagGTGTTGAGATTGTAATTGCTACACCTGGTCGTTTGATTGATATGTTGGAATGTCAACACACTAATTTGAAGAGAGTGACTTACCTTGTACTGGATGAGGC

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|37188613|gb|CF607962.1|CF607962
EST:     CATTTATGGTGGTGCTCCAAAGGGACCACAGATTCGTGATCTTCAAAGAG                         GTGTTGAGATTGTCATTGCTACACCTGGACGATTAATAGATATGCTGGAGG
genomic: CATTTATGGTGGTGCTCCAAAGGGACCACAGATTCGTGATCTTCAAAGAGgtacttatgt ... cttatgctagGTGTTGAGATTGTCATTGCTACACCTGGACGATTAATAGATATGCTGGAGG
EST: gi|161712720|gb|FC062292.1|FC062292
EST:     CATTTATGGTGGTGCTCCAAAGGGACCACAGATTCGTGATCTTCAAAGAG                         GTGTTGAGATTGTCATTGCTACACCTGGACGATTAATAGATATGCTGGAGG
genomic: CATTTATGGTGGTGCTCCAAAGGGACCACAGATTCGTGATCTTCAAAGAGgtacttatgt ... cttatgctagGTGTTGAGATTGTCATTGCTACACCTGGACGATTAATAGATATGCTGGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atccctataaatttaggttggtgcacgaaaatcttatctattgcccttatgctagGTGTTGAGATTGTCATTGCTACACCTGGACGATTAATAGATATGCTGGAGGCTCAACATACAAACCTGCGAAGAGTGACTTACCTTGTATTAGATGAGGC
                                        ttgccctt  CT-rich tract
                           aaaatcttatctatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttatgtttcttctatggctatttgctaaatccctataaatttaggttggtgcacgaaaatcttatctattgcccttatgctagGTGTTGAGATTGTCATTGCTACACCTGGACGATTAATAGATATGCTGGAGGCTCAACATACAAACCTGCGAAGAGTGACTTACCTTGTATTAGATGAGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA