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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccttcaagatgttataacattgccaaggaattattgtgattcatgtttttttcatcccattctttcaatctaaaccctcctgctgctatttgttgacattcctttacccaatcctagATATTTTTCGCCCATTTGTGGGGTATAAAGAAGTAAGACTCGTGAGCAAAGAATCCAAGCAT

Basic information

species Vitis vinifera
transcript Vv18s0166g00240.t01
intron # 5
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0166g00240.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA20G30540.2 (Glycine max), 3'ss of exon 3
-----------------------------------gtatccttcaagatgttataacattgccaaggaat-tattgtgattcatgtttttttcatcccattctttcaatctaaaccctcctgc--tgctatttgttgacattcctttac--ccaatcctagATATTTTTCGCCCATTTGTGGGGTATAAAGAAGTAAGACTCGTGAGCAAAGAATCCAAGCAT
                                   ||||  |   |  |   |     ||| ||    || |||| | | | |  | |||||  || ||     |  ||   ||   |  ||   | || |    || | |  | |||    || |  |||||||||||||||| ||||| || |||| |||||||||||| ||||||||||||||||| |||
gtatcctttttgttctcagatactgtataggaattgtataatcatactttcaactgtcttgtcacttcatatattttaaattacctatttttgttctcagatactgtataggaattgtattgtcatactttcaactgtcttgtccttaatgtcatttttagATATTTTTCGCCCTTTTGTTGGATATAGAGAAGTAAGACTTGTGAGCAAAGAATCCAAACAT

upper sequence: Vv18s0166g00240.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA02G09230.2 (Glycine max), 3'ss of exon 2
gtatccttcaagatgttataacattgccaaggaattattgtgattcatgtttttttcatcccattctttcaatctaaaccctcctgctgctatttgt-tgacattcctttacccaatcctagATATTTTTCGCCCATTTGTGGGGTATAAAGAAGTAAGACTCGTGAGCAAAGAATCCAAGCAT
||||||||     | | ||  || |||  ||||||| |  |   |    |||| |  ||  |    ||||| |    |   |  | | | ||||  | | | ||||||| ||   | | |||||||||||||||| ||||| ||||||| |||||| ||||| ||||||||||||||||| |||
gtatccttttcattttgatg-caatgcttaggaatt-tcat--cttgctttttatctatttctgagtttcatt---gatattagttcagttattcatatcatattccttaacatcaccttagATATTTTTCGCCCTTTTGTTGGGTATAGAGAAGTTAGACTTGTGAGCAAAGAATCCAAACAT

upper sequence: Vv18s0166g00240.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA20G30540.4 (Glycine max), 3'ss of exon 3
gtatccttcaagatgttataacattgccaaggaattattgtgattcatgttt----ttttcatcccattctttcaatctaaaccctcctgctgctatttgttgacattcctttac-ccaatcctagATATTTTTCGCCCATTTGTGGGGTATAAAGAAGTAAGACTCGTGAGCAAAGAATCCAAGCAT
||||||||   | | | |    | ||   | ||||| |       ||  ||     |||  |      | | |||   | |    |  |  | |||  | || | ||||||| |  ||| |  |||||||||||||||| ||||| || |||| ||||||||| || ||||||||||||||||| |||
gtatccttttggttctca-gttactgtttaagaattgtatcatcacacattcacactttcaactgtgctttgtcagcttcatttattttaat-ctagctattcaaattccttaatgccatttttagATATTTTTCGCCCTTTTGTTGGATATAGAGAAGTAAGGCTTGTGAGCAAAGAATCCAAACAT

upper sequence: Vv18s0166g00240.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA10G37100.1 (Glycine max), 3'ss of exon 2
-----------------------------------------gtatccttcaagatgttataacattgccaaggaattattgtgattcatgtttttttcatcccattctttcaatctaaaccctcctgctgctatttgttgacattcctttacccaatcctagATATTTTTCGCCCATTTGTGGGGTATAAAGAAGTAAGACTCGTGAGCAAAGAATCCAAGCAT
                                           || |||| |  | |  |  || | |      ||||   | |   || || || |||     |   |   |  |  | | || | ||   |  |||     | | |     || |  |||||||||||||||| || || || |||| |||||||||||| ||||||||||||||||| |||
gcatcctttttgttctcagatactggataggaattttatattgatacttccaactatcttgtcacttcatttatattaa-attacctattttgttctcagatactgtatgggaattgtatcgtcatactttcaactgtct-tgtccttaatgtcatttttagATATTTTTCGCCCTTTCGTTGGATATAGAGAAGTAAGACTTGTGAGCAAAGAATCCAAACAT

upper sequence: Vv18s0166g00240.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA16G28620.2 (Glycine max), 3'ss of exon 3
gtatccttcaagatgttataacattgccaaggaattattgtgattcatgtttttttcatcccattctttcaatctaaaccctcctgctgctatttgttgacattcctttacccaatcctagATATTTTTCGCCCATTTGTGGGGTATAAAGAAGTAAGACTCGTGAGCAAAGAATCCAAGCAT
||||||||     | | ||  || |||  |||||||       ||||| ||  |||    | ||| | | | | | |    |  |  | | | || || | ||||||| |||  | | |||||||||| ||||| ||||| ||||||| |||||| ||||| |||||||||||||| || |||
gtatccttttcattttgatg-caatgcttaggaatt-------ttcatcttgcttttcatctatt-tctgagtttcattgattttagttc-agttatttatattccttaacctcaccttagATATTTTCCGCCCTTTTGTTGGGTATAGAGAAGTTAGACTTGTGAGCAAAGAATCGAAACAT

upper sequence: Vv18s0166g00240.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA10G37090.1 (Glycine max), 3'ss of exon 3
gtatccttcaagatgttataacattgccaagg---aattattgtgattcatgtttttttcatcccattctttcaatctaaaccctcctgctgctatttgttgacattcctttac-ccaatcctagATATTTTTCGCCCATTTGTGGGGTATAAAGAAGTAAGACTCGTGAGCAAAGAATCCAAGCAT
||||||||   | | | ||  |   |  |  |   ||| ||||| |         |||  ||     | | |||   | |    |  |  |  ||  | || | ||||||| |  | | |  ||||||||||||| || ||||| || |||| |||||| ||||| ||||||||||||||||| |||
gtatcctttttgttctcatttctcagttattgtttaataattgt-accatcacactttcaattatgctttgtcagcttcatttattttagt-ttagctattcaaattccttaatgctatttttagATATTTTTCGGCCTTTTGTTGGATATAGAGAAGTGAGACTTGTGAGCAAAGAATCCAAACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcaatctaaaccctcctgctgctatttgttgacattcctttacccaatcctagATATTTTTCGCCCATTTGTGGGGTATAAAGAAGTAAGACTCGTGAGCAAAGAATCCAAGCAT
 ttcctttac  putative branch site 
                                    ttcctttaccc  putative PPT
                        tatttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatccttcaagatgttataacattgccaaggaattattgtgattcatgtttttttcatcccattctttcaatctaaaccctcctgctgctatttgttgacattcctttacccaatcctagATATTTTTCGCCCATTTGTGGGGTATAAAGAAGTAAGACTCGTGAGCAAAGAATCCAAGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA