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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgatagagcctactgtcaagaggggatacagttaattttcctgaattgaatgaaaattattgtcattgttaggactttgctaattagccttgtttgcagGGCATAATGTCTCCTCAGCTATCATCTTTGCTGTTTCTTGTGGTGGGAATTTCTATGGCCCTGACCCCATGGTTAGCTGCTGGAGGACAATTAATTGCGT

Basic information

species Vitis vinifera
transcript Vv15s0046g03390.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G093643_T01 (Zea mays), 3'ss of exon 13
ttgatagagcctactgt--caagaggggatacagttaattttcctgaattgaatgaaaattattgtcattgttaggactttgctaattagccttgtttgcagGGCATAATGTCTCCTCAGCTATCATCTTTGCTGTTTCTTGTGGTGGGAATTTCTATGGCCCTGACCCCATGGTTAGCTGCTGGAGGACAATTAATTGCGT
   | |      | |||   | |    ||  ||  | ||| |  ||   || ||  |  |||| |     |   |||   |  | |  |  ||  ||| |||||  |  | || |||||  || |||| ||||| ||| | || || || ||||| ||||| ||||| |||||||||||||||||||| || ||  | || |
-gaacatctataattgttgtatgtcacgaatcatatgattgttgtgctatggatagatgttataga-gcagaggggaaactaatgaacacactattttacagGGTCTTCTATCACCTCAATTAACATCGTTGCTATTTTTAGTCGTTGGCATTTCAATGGCTCTGACACCATGGTTAGCTGCTGGAGGGCAGTTTCTGGCAT

upper sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA18G46420.1 (Glycine max), 3'ss of exon 20
-ttgatagagcctactgtcaagaggggatacagt-taattttcctgaattgaatgaaaattattgtcattgttaggactttgctaattagccttgtttgcagGGCATAATGTCTCCTCAGCTATCATCTTTGCTGTTTCTTGTGGTGGGAATTTCTATGGCCCTGACCCCATGGTTAGCTGCTGGAGGACAATTAATTGCGT-
     |||| | |  |      |   | || | | |  ||||| | |||    || |||| |     | | ||    |    |||||| ||  | | ||||||||||||||||| | ||||| |||||||||||||||||||| ||||| ||||| |||||| | || |||||| ||||||| ||||| || || ||||| | 
aaatgtagatcattgtactggtaactgctaaattgttgttttctttaataatttgcaaataaa-actactattttc-ccccactaattggcact-tctgcaggGCATAATGTCTTCCCAGCTGTCATCTTTGCTGTTTCTTGTTGTGGGCATTTCAATGGCCATCACACCATGGCTAGCTGCAGGAGGCCAGTTGATTGCTTC

upper sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA09G39770.1 (Glycine max), 3'ss of exon 16
ttgatagagcctactgtcaagaggggatacagttaattttcc---tgaattgaatga---aaattattg-tcattgttaggactttgctaattagccttgtttgcagGGCATAATGTCTCCTCAGCTATCATCTTTGCTGTTTCTTGTGGTGGGAATTTCTATGGCCCTGACCCCATGGTTAGCTGCTGGAGGACAATTAATTGCGT
     |     || | ||   |    | |   || || ||||   | | |||||  |   |||  || | |||||||    |||  |||||  |   ||||||  |||||||||||||| | ||||| |||||||||||||||||||| ||||| ||||| |||||| | || |||||| ||||||| ||||| ||  | ||||| |
----aattttgtattatctttactttaaatgattgatcttccccgtaagttgaaaaatacaaaacatagatcattgtagtaact--gctaaaaattgttgttt-tagGGCATAATGTCTTCCCAGCTGTCATCTTTGCTGTTTCTTGTTGTGGGCATTTCAATGGCCATCACACCATGGCTAGCTGCAGGAGGCCAGCTGATTGCTT

upper sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA07G08030.1 (Glycine max), 3'ss of exon 12
ttgatagagcctactgtcaagaggggatacagttaattttcctgaattgaatgaaaattattgtcattgttaggactttgctaattagc------cttgtttgcagGGCATAATGTCTCCTCAGCTATCATCTTTGCTGTTTCTTGTGGTGGGAATTTCTATGGCCCTGACCCCATGGTTAGCTGCTGGAGGACAATTAATTGCGT
         || |   || |  |||  |  |     ||||||| | |   ||   | || || | |    ||    ||||||| ||           | | ||||||||||||||||| | ||  | || ||||| ||||||||||| ||||||||||| |||||||| || |||||| ||||||  ||||| ||  |  |||| |
-----tttcccaaacatccatggggcctttaacct-ttttcctcattgtcattttatttgttataaaaactaacgttttgctatttgataattaatatttgtgcagGGCATAATGTCTTCCCAAATGTCCTCTTTACTGTTTCTTGTCGTGGGAATTTCAATGGCCCTCACTCCATGGCTAGCTGAAGGAGGTCAGCTCCTTGCTT

upper sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA03G01600.1 (Glycine max), 3'ss of exon 5
ttgatagagcctac-tgtcaagaggggatacagttaattttcctgaattgaatgaaaattattgtcattgttaggact-ttgctaattagccttgtttgcagGGCATAATGTCTCCTCAGCTATCATCTTTGCTGTTTCTTGTGGTGGGAATTTCTATGGCCCTGACCCCATGGTTAGCTGCTGGAGGACAATTAATTGCGT
||   |  ||| |    || |  |||  |  |   | ||||||| | |  ||   || ||  | | |  | ||  | | |||||| |      | | ||||||||||||||||| | ||| | || ||||| ||||||||||| ||||||||||| ||||| || || |||||| ||||||  ||||| ||  |  |||| |
tttgcattgcccagacatccatggggcctttaac-atttttcctcattgaaacttaattttctataaaagctaacattattgctattcgatact-tatgcagGGCATAATGTCTTCCCAGTTGTCCTCTTTACTGTTTCTTGTTGTGGGAATTTCAATGGCTCTCACTCCATGGCTAGCTGAAGGAGGTCAGCTCCTTGCTT

upper sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT4G00630.2 (Arabidopsis thaliana), 3'ss of exon 12
ttgatagagcctactgtcaag-----aggggat-acagttaattttcctgaattgaatgaaaattattgtcattgttaggactttgctaattagccttgtttgcagGGCATAATGTCTCCTCAGCTATCATCTTTGCTGTTTCTTGTGGTGGGAATTTCTATGGCCCTGACCCCATGGTTAGCTGCTGGAGGACAATTAATTGCGT
 |   | |   || ||||| |      ||  || |||| | |  || | |   |   | |     || ||      || | |||     ||| |  ||  || ||||| |||||| |||| |||||||| || || |||||||| || |||||||| || ||||| || || || |||||||||||||| || |||||||||||||
-tagaaaacgatattgtcatgttttatggatatgacagctgaggtttcagttctactttattcccat-gtttcctctaaggctt----gattggtatttcttccagGGTATAATGACTCCGCAGCTATCTTCATTACTGTTTCTCGTCGTGGGAATATCAATGGCTCTTACTCCTTGGTTAGCTGCTGGCGGCCAATTAATTGCGT

upper sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT1G01790.1 (Arabidopsis thaliana), 3'ss of exon 13
------------------------------------ttgatagagcctactgtcaagaggg--gatacagttaattttcctga-attgaatgaaaattattgtca-ttgttaggactttg-----ctaattagccttgtttgcagGGCATAATGTCTCCTCAGCTATCATCTTTGCTGTTTCTTGTGGTGGGAATTTCTATGGCCCTGACCCCATGGTTAGCTGCTGGAGGACAATTAATTGCGT
                                       ||   |  ||   |||  |  |  | |  | |   ||  ||| | |    |   | |||  |||||  ||||    | | |     |||||  |   |  || ||||| ||||||||||||||| |||| || ||||| || ||||| |||||||| || |||||  | || || |||||||||||||| || || |||||||| |
gtttgttatcaacatggcgtatttttttgcttttttccaatgaggtatataatcagcaatgttgttttaatggtttacccttacacattacatatatttctgtcaactgtttttccctagaaggcctaatctgtggttcttccagGGTATAATGTCTCCTCAGTTATCTTCGTTGCTATTCCTTGTCGTGGGAATCTCAATGGCTATCACACCCTGGTTAGCTGCTGGTGGCCAGTTAATTGCAT

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|110389557|gb|EC954408.1|EC954408
EST:     CTCCGGGGGGAGAATTTGCTTTTGTGGCTTTTGGTGAAGCTGTTAATCAG                         GGCATAATGTCTCCTCAGCTATCATCTTTGCTGTTTCTTGTGGTGGGAATT
genomic: CTCCGGGGGGAGAATTTGCTTTTGTGGCTTTTGGTGAAGCCGTTAATCAGgttttccttt ... ttgtttgcagGGCATAATGTCTCCTCAGCTATCATCTTTGCTGTTTCTTGTGGTGGGAATT
EST: gi|34546770|gb|CF515002.1|CF515002
EST:     CTCCGGGGGGAGAATTTGCTTTTGTGGCTTTTGGTGAAGCCGTTAATCAG                         GGCATAATGTCTCCTCAGCTATCATCTTTGCTGTTTCTTGTGGTGGGAATT
genomic: CTCCGGGGGGAGAATTTGCTTTTGTGGCTTTTGGTGAAGCCGTTAATCAGgttttccttt ... ttgtttgcagGGCATAATGTCTCCTCAGCTATCATCTTTGCTGTTTCTTGTGGTGGGAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgaatgaaaattattgtcattgttaggactttgctaattagccttgtttgcagGGCATAATGTCTCCTCAGCTATCATCTTTGCTGTTTCTTGTGGTGGGAATTTCTATGGCCCTGACCCCATGGTTAGCTGCTGGAGGACAATTAATTGCGT
                                 tgctaat  putative branch site (score: 2)
                                           ccttgttt  putative PPT
        aaaattattgtcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgatagagcctactgtcaagaggggatacagttaattttcctgaattgaatgaaaattattgtcattgttaggactttgctaattagccttgtttgcagGGCATAATGTCTCCTCAGCTATCATCTTTGCTGTTTCTTGTGGTGGGAATTTCTATGGCCCTGACCCCATGGTTAGCTGCTGGAGGACAATTAATTGCGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - -cctactg
- - - - - - - - - - -aggggata
- - - - - - - - - - - - - - - - - - - ttcctga
- - - - - - - - - - - - - - - - - - - - - - - - - - -aaaatta