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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaaaaatgcacagggacaatttcatttgtgttctgtgctgactaaaatgatgatgcttctttgcaattgaatatgacgtttggcacttctccttgtcagATAATGAGAGATCCTGATACAGGAAATTCTCGTGGTTTTGGTTTCGTTAGCTATGACTCTTTTGAGGCATCTGATGCAGCTATTGAG

Basic information

species Vitis vinifera
transcript Vv04s0023g01470.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g01470.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os10g31900.1 (Oryza sativa), 3'ss of exon 6
ttaaaaatgcacagggacaatttcatttgtgttctgtgctgac--taaaat---gatgatgcttctttgcaattgaatatgacgtttggcacttctccttgtcagATAATGAGAGATCCTGATACAGGAAATTCTCGTGGTTTTGGTTTCGTTAGCTATGACTCTTTTGAGGCATCTGATGCAGCTATTGAG
   || ||| ||     ||||    ||    | | ||| | |   |  | |     || ||       | ||||   | |||  |||   | || || || | |||||||| |||||||||| || |||||||| || || ||||| || || ||||||||||| |||||  ||||||||  |||||| |||
---aacatgtactacttcaatcgt-ttaccatgcagtgttaatagtgtatttccagtgttggcatacagtaatttgctttgattttttttatttatctttat-agATAATGCGAGATCCTGAAACTGGAAATTCACGAGGCTTTGGCTTTGTGAGCTATGACTCCTTTGAATCATCTGATCAAGCTATAGAG

upper sequence: Vv04s0023g01470.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G102639_T02 (Zea mays), 3'ss of exon 4
-----ttaaaaatg-cacagggacaatttcatttgtgttctgtgctgactaaaatgatgatgcttctttgcaattgaatatgacgtttggcacttctccttgtcagATAATGAGAGATCCTGATACAGGAAATTCTCGTGGTTTTGGTTTCGTTAGCTATGACTCTTTTGAGGCATCTGATGCAGCTATTGAG
     |||  | |  |||  |  |  || ||   |||| ||||  |    | ||  ||  |  |    |||| |  ||| |   | |       | |  ||   |||||||| |||||||||| |||||||||||| | || ||||| || || |||||||| || |||||  |||||||   ||| || |||
tggtgttaggagtaacacctgatctgttgca---gtgt-ctgttattttaagaagcatagttgtcacctgcagt--aatgtattgatctttttcttttgtttgaagATAATGCGAGATCCTGAAACAGGAAATTCTAGAGGCTTTGGCTTTGTGAGCTATGAGTCCTTTGAATCATCTGACCAAGCAATAGAG

upper sequence: Vv04s0023g01470.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA12G36950.1 (Glycine max), 3'ss of exon 6
-ttaaaaatgcacagggacaatttcatttgtgttctgtgctgactaaaatgatgatgctt--ctttgca-attgaatatgacgtttggcacttctccttgtcagATAATGAGAGATCCTGATACAGGAAATTCTCGTGGTTTTGGTTTCGTTAGCTATGACTCTTTTGAGGCATCTGATGCAGCTATTGAG
  ||  || || ||  |||||||  |  |     |    ||||    | | ||    ||   | ||    ||   || |||  ||     ||| |  ||| ||||| |||||||||||||| ||||||||||| ||||||||||| ||| |||||||||| || ||||||||||||||| |||| ||||||
ggtatcaa-gc-caatgacaattaaaaataaccaccac-ctgaaaggattcatttcactcaacattatgtatatgatctgatattcaaggctttttgttg-cagATCATGAGAGATCCTGAGACAGGAAATTCCCGTGGTTTTGGCTTCATTAGCTATGATTCATTTGAGGCATCTGATTCAGCCATTGAG

upper sequence: Vv04s0023g01470.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA09G00310.1 (Glycine max), 3'ss of exon 6
----ttaaaaatgcacagggacaatttcatttgtgttctgtgctgactaaaatgatgatgcttctttgcaattgaatatgacgtttggcacttctccttgtcagATAATGAGAGATCCTGATACAGGAAATTCTCGTGGTTTTGGTTTCGTTAGCTATGACTCTTTTGAGGCATCTGATGCAGCTATTGAG
     |     |    |   ||||   |     |   |||    || | |  | ||        | || |  ||| | | || |      |||    ||| ||||| |||||||||||||| ||||||||||| ||||||||||| ||| ||||||| || || ||||||||||||||| |||| ||||||
tagtctcttgttctttaaacacaacccc-cccatac-ctgaaaggattcattttattcaaacattatgtatatga-tctaacatacaaggctttgtgttg-cagATCATGAGAGATCCTGACACAGGAAATTCCCGTGGTTTTGGCTTCATTAGCTACGATTCATTTGAGGCATCTGATTCAGCCATTGAG

upper sequence: Vv04s0023g01470.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT2G18510.1 (Arabidopsis thaliana), 3'ss of exon 6
--------------------------ttaaaaatgcacagggacaatttcatttgtgttctgt-gctgact------aaaatgatgatgcttc-----tttgcaattgaatatgacgtttggcacttctccttgtcagATAATGAGAGATCCTGATACAGGAAATTCTCGTGGTTTTGGTTTCGTTAGCTATGACTCTTTTGAGGCATCTGATGCAGCTATTGAG
                          |     |||      ||    || || ||| | ||||  | || |       |||| | ||| | ||     |   |  | ||  || |   || | |  | | | | |||||||||||||||||| ||||| ||||| || || |||||||||||| | ||||||||||| ||||| ||||||||||| |||||||||
gtagtattttttatttcattagattgtagttcatgattcttgatctctttatctgtctcctgtcaccgattcgatagtaaattaggattcatcggtattccactgtggagaataaatgttagaaacttttcatttcagATAATGAGAGATCCCGATACTGGAAACTCACGAGGTTTTGGTTTCATCAGCTATGACTCCTTTGAAGCATCTGATGCTGCTATTGAG

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|71877269|gb|DT026324.1|DT026324
EST:     TTCTGTATGATACTTTCAGTGCATTTGGAGTCATTGTCACAAATCCTAAG                         ATAATGAGAGATCCTGATACAGGAAATTCTCGTGGTTTTGGTTTCGTTAGC
genomic: TTCTGTATGATACTTTCAGTGCATTTGGAGTCATTGTCACAAATCCCAAGgtgacgcctc ... tccttgtcagATAATGAGAGATCCTGATACAGGAAATTCTCGTGGTTTTGGTTTCGTTAGC
EST: gi|110729959|gb|EE106491.1|EE106491
EST:     TTCTGTATGATACTTTCAGTGCATTTGGAGTCATTGTCACAAATCCCAAG                         ATAATGAGAGATCCTGATACAGGAAATTCTCGTGGTTTTGGTTTCGTTAGC
genomic: TTCTGTATGATACTTTCAGTGCATTTGGAGTCATTGTCACAAATCCCAAGgtgacgcctc ... tccttgtcagATAATGAGAGATCCTGATACAGGAAATTCTCGTGGTTTTGGTTTCGTTAGC
EST: gi|294965569|gb|GW837168.1|GW837168
EST:     TCTGTATGATACTTTCAGTGCATTTGGAGTCAATTGTCACAAATCCTAAG                         ATAATGAGAGATCCTGATACAGGAAATTCTCGTGGT
genomic: TCTGTATGATACTTTCAGTGCATTTGGAGTCA-TTGTCACAAATCCCAAGgtgacgcctc ... tccttgtcagATAATGAGAGATCCTGATACAGGAAATTCTCGTGGT
EST: gi|161719366|gb|FC068974.1|FC068974
EST:     TTCTGTATGATACTTTCAGTGCATTTGGAGTCATTGTCACAAATCCTAAG                         ATAATGAGAGATCCTGATACAGGAAATTCTCGTGGTTTTGGTTTCGTTAGC
genomic: TTCTGTATGATACTTTCAGTGCATTTGGAGTCATTGTCACAAATCCCAAGgtgacgcctc ... tccttgtcagATAATGAGAGATCCTGATACAGGAAATTCTCGTGGTTTTGGTTTCGTTAGC
EST: gi|110387686|gb|EC952373.1|EC952373
EST:     TTCTGTATGATACTTTCAGTGCATTTGGAGTCATTGTCACAAATCCTAAG                         ATAATGAGAGATCCTGATACAGGAAATTCTCGTGGTTTTGGTTTCGTTAGC
genomic: TTCTGTATGATACTTTCAGTGCATTTGGAGTCATTGTCACAAATCCCAAGgtgacgcctc ... tccttgtcagATAATGAGAGATCCTGATACAGGAAATTCTCGTGGTTTTGGTTTCGTTAGC
EST: gi|37186306|gb|CF605659.1|CF605659
EST:     TTCTGTATGATACTTTCAGTGCATTTGGAGTCATTGTCACAAATCCTAAG                         ATAATGAGAGATCCTGATACAGGAAATTCTCGTGGTTTTGGTTTCGTTAGC
genomic: TTCTGTATGATACTTTCAGTGCATTTGGAGTCATTGTCACAAATCCCAAGgtgacgcctc ... tccttgtcagATAATGAGAGATCCTGATACAGGAAATTCTCGTGGTTTTGGTTTCGTTAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatgatgatgcttctttgcaattgaatatgacgtttggcacttctccttgtcagATAATGAGAGATCCTGATACAGGAAATTCTCGTGGTTTTGGTTTCGTTAGCTATGACTCTTTTGAGGCATCTGATGCAGCTATTGAG
 gactaaa  putative branch site (score: 2)
                                       cacttctccttgtc  putative PPT
                    aattgaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaaaaatgcacagggacaatttcatttgtgttctgtgctgactaaaatgatgatgcttctttgcaattgaatatgacgtttggcacttctccttgtcagATAATGAGAGATCCTGATACAGGAAATTCTCGTGGTTTTGGTTTCGTTAGCTATGACTCTTTTGAGGCATCTGATGCAGCTATTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
-taaaaat
- - - - - - agggacaa
- - - - - - - - - - - - - -tgtgttc
- - - - - - - - - - - - - - - - - - tgctgac
- - - - - - - - - - - - - - - - - - - - - - aaaatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aattgaa