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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatatcatgtttgatatttgattattggccctcctattctatgtggttatgcttgtctcttagatttatgtaaattttgtagGATGCGGCAGCATGGCTTGAGTACTTCGAGTCCAAGGCTCTGGAGCAGCAAGAAGCTGCCCGCAATGGCACTCCAAAGCCAGATGCCTCTATCTCCAGCA

Basic information

species Vitis vinifera
transcript Vv11s0037g00850.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0037g00850.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os02g15660.1 (Oryza sativa), 3'ss of exon 3
-------------------------gtaatatcatgtttgatat-ttgatta--ttggccctcctattctatgtggttatgct-tgtctcttagattta-----tgtaaattttgtagGATGCGGCAGCATGGCTTGAGTACTTCGAGTCCAAGGCTCTGGAGCAGCAAGAAGCTGCCCGCAATGGCACTCCAAAGCCAGATGCCTCTATCTCCAGCA
                         || || |  | ||  |  |    || |  ||    ||    || | |    || | ||    |    | || ||     | |   ||    ||||||| || || |||||||| || || ||||||||||| || |||||||| ||||| || || ||||| ||||||||||| ||||| || ||  | ||||
gtaagccgacaaaaattgcttcctggtgatgtgttcttccacttaccaatcaatttcattctttagttattttccattctactgcagcaaggaaatctaataactatgttttccacagGATGCTGCTGCTTGGCTTGAATATTTTGAGTCCAAGGCACTAGAGCAGCAGGAAGCAGCACGTAATGGTACTCCAAAGCCTGATGCTTCAATAGCAAGCA

upper sequence: Vv11s0037g00850.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G318635_T01 (Zea mays), 3'ss of exon 20
-----------------------------gtaatatcatgt-----ttgatatttgattat-tggccctcctattctatgtggttatgcttgtctcttagatttatgtaaattttgtagGATGCGGCAGCATGGCTTGAGTACTTCGAGTCCAAGGCTCTGGAGCAGCAAGAAGCTGCCCGCAATGGCACTCCAAAGCCAGATGCCTCTATCTCCAGCA
                             |||||  ||  |        || ||   |||  ||  |  ||| |  | |      | |    |||  |||   ||| |    |    |||||||  | || ||||| || ||||| || |||||||| || |||||||| ||||| || || ||||| ||||||||||| ||||| || ||  | ||||
gtaagctgaaaaggctggcttggttatgtgtaattccacttagccaccaattttcagttaaatgatctacctttcttgttgcaccaaggaaatctaatagccatattt----tccacagGATGCTTCTGCTTGGCTGGAATACTTTGAATCCAAGGCACTAGAGCAGCAGGAAGCAGCACGAAATGGTACTCCAAAGCCTGATGCTTCAATAGCAAGCA

upper sequence: Vv11s0037g00850.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA06G30000.1 (Glycine max), 3'ss of exon 18
gtaatatcatgtttgatatttgattattggccctcctattctatgtggttatgcttgtctcttag--atttatgtaaattt--tgtagGATGCGGCAGCATGGCTTGAGTACTTCGAGTCCAAGGCTCTGGAGCAGCAAGAAGCTGCCCGCAATGGCACTCCAAAGCCAGATGCCTCTATCTCCAGCA
    ||  |  |||| | ||| || || |       ||| | |  | || ||||||||  |||||  |  ||| | |||||  |  ||||||| || |||||||| || ||||| ||||| |||||||||||||| || || ||||| || ||||| || || || ||||||||||| ||||||||||
---gtagtacctttgcttttttatgatagattaaaatatacaa-atagtaatgcttgttccttaggcacatatatgaatttattacagGATGCTGCTGCATGGCTAGAATACTTTGAGTCAAAGGCTCTGGAGCAACAGGAGGCTGCACGGAATGGTACACCTAAACCAGATGCCTCAATCTCCAGCA

upper sequence: Vv11s0037g00850.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA04G24430.1 (Glycine max), 3'ss of exon 20
gtaatatcatgtttgatatttgattattggccctcctattctatgtggttatgcttgtctcttag----atttatgtaaattttgtagGATGCGGCAGCATGGCTTGAGTACTTCGAGTCCAAGGCTCTGGAGCAGCAAGAAGCTGCCCGCAATGGCACTCCAAAGCCAGATGCCTCTATCTCCAGCA
||| | | |  |||| | |||   |  | |           ||  | || ||||||||  ||||     || |||| |  | ||  ||||||| || |||||||| || ||||| || || |||||||||||||| || || ||||| || ||||| || || ||||| |||||||| ||||||||||
gtagtcttacctttggtttttctatgatagattaaaatacataaatagtaatgcttgttccttatgcacatatatgaatgtattacagGATGCAGCTGCATGGCTAGAATACTTTGAATCAAAGGCTCTGGAGCAACAGGAGGCTGCACGGAATGGTACACCTAAGCCGGATGCCTCAATCTCCAGCA

upper sequence: Vv11s0037g00850.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT4G28080.1 (Arabidopsis thaliana), 3'ss of exon 20
gtaatatcatgtttgatatttgattattggccctcctattctatgtggttatgcttgtctcttagatttatgtaaattttgtagGATGCGGCAGCATGGCTTGAGTACTTCGAGTCCAAGGCTCTGGAGCAGCAAGAAGCTGCCCGCAATGGCACTCCAAAGCCAGATGCCTCTATCTCCAGCA
         || || ||   | || |||  |       |||  |    | |    ||| |||||  ||  |  || | |  ||||||||||| || |||||||| || ||||||||||| |||||||| |||||||||||||| || ||||| ||||| |||||||| |||||||| |||||||
--------gtgcttaattagttatgatttacagggagtttcagt----taaaatgtgtttcttacgttc-taaaactatgttagGATGCGGCTGCGTGGCTTGAATATTTCGAGTCCAAAGCTCTGGAACAGCAAGAAGCTGCACGAAATGGTACTCCCAAGCCAGACGCCTCTATTTCCAGCA

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|352768570|gb|FQ467526.1|FQ467526
EST:     CTCTACAGATACTGCAGGCCAAGCTTGGACCAGATGATTTGCGTACACAG                         GATGCGGCAGCATGGCTTGAGTACTTCGAGTCCAAGGCTCTGGAGCAGCAA
genomic: CTCTACAGATACTGCAGGCCAAGCTTGGACCAGATGATTTGCGTACACAGgtaatatcat ... aattttgtagGATGCGGCAGCATGGCTTGAGTACTTCGAGTCCAAGGCTCTGGAGCAGCAA
EST: gi|352773143|gb|FQ470758.1|FQ470758
EST:     CTCTACAGATACTGCAGGCCAAGCTTGGACCAGATGATTTGCGTACACAG                         GATGCGGCAGCATGGCTTGAGTACTTCGAGTCCAAGGCTCTGGAGCAGCAA
genomic: CTCTACAGATACTGCAGGCCAAGCTTGGACCAGATGATTTGCGTACACAGgtaatatcat ... aattttgtagGATGCGGCAGCATGGCTTGAGTACTTCGAGTCCAAGGCTCTGGAGCAGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccctcctattctatgtggttatgcttgtctcttagatttatgtaaattttgtagGATGCGGCAGCATGGCTTGAGTACTTCGAGTCCAAGGCTCTGGAGCAGCAAGAAGCTGCCCGCAATGGCACTCCAAAGCCAGATGCCTCTATCTCCAGCA
                                ttagatttatgtaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatatcatgtttgatatttgattattggccctcctattctatgtggttatgcttgtctcttagatttatgtaaattttgtagGATGCGGCAGCATGGCTTGAGTACTTCGAGTCCAAGGCTCTGGAGCAGCAAGAAGCTGCCCGCAATGGCACTCCAAAGCCAGATGCCTCTATCTCCAGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG