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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcagaaagttatctttcctgaacttgttatagtcttatttgaattgaaattttgttcaaaatttaagtgttgtttttgtattattttattttccatgcagGTTATACTAGTACAGCAATTACTGATGGTCCTGGATGTTTGATGTTGCGCTGTCCTGATCCAACCTGTGGTGCTGCTGTTGGTCAGGACATGATAAATTT

Basic information

species Vitis vinifera
transcript Vv00s0207g00090.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0207g00090.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM5G876621_T02 (Zea mays), 3'ss of exon 4
tcagaaagttatctttcctgaacttgttatagtctta-tttgaattgaaattttgttcaaaatttaagtgt-tgtttttgtattattttattt-tccat--gcagGTTATACTAGTACAGCAATTACTGATGGTCCTGGATGTTTGATGTTGCGCTGTCCTGATCCAACCTGTGGTGCTGCTGTTGGTCAGGACATGATAAATTT
       ||  | || | | | | | | || |    |  ||   || ||    | | |  ||||| | | | |   |  |||  |||||| |  |  ||  |||||||| | ||| || || || | ||||||||| ||||||||||||||| | |||||||||||| | |||| |||||||||||| || || |||||||||| 
-----ttgtcttgttacttcatcatttcatggaagcaactttctttaaagggctctaccgaattttactatgtcactaagtaacattttaataatgtattggcagGTTACATTAGCACTGCTATAAGTGATGGTCCAGGATGTTTGATGTTGAGGTGTCCTGATCCATCTTGTGCTGCTGCTGTTGGACAAGATATGATAAATTC

upper sequence: Vv00s0207g00090.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G431691_T01 (Zea mays), 3'ss of exon 3
----------------------------------------------tcagaaagttatctttcctg-----aacttgttatagtcttatttgaattgaaattttgttcaaaatttaagtgttgtttttgtattattttattttccatgcagGTTATACTAGTACAGCAATTACTGATGGTCCTGGATGTTTGATGTTGCGCTGTCCTGATCCAACCTGTGGTGCTGCTGTTGGTCAGGACATGATAAATTT
                                              |  ||    ||| |||| ||     |||||| | ||     || |   ||  ||||||  |       | |||    |||| ||| | | ||          ||||||| | ||| || || || | ||||||||| ||||| |||||| || | |||||||||||  |||||| |||||||||||| || || |||||||||| 
gtttgtcaattggggcttgaaatatttatctgcatacaaaggaaccttggattcctatttttcgtggaagcaacttgctctaaaga-atctacctttgaattttactatgtcactgagtaacattttagtaatgtattg--------acagGTTACATTAGCACTGCTATAAGTGATGGTCCGGGATGCTTGATGCTGAGGTGTCCTGATCCGTCCTGTGCTGCTGCTGTTGGACAAGATATGATAAATTC

upper sequence: Vv00s0207g00090.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G006428_T01 (Zea mays), 3'ss of exon 4
tcagaaagttatctttcctgaacttgttatagtcttatttgaattgaaattttgttcaaaatttaagtgt-tgtttttgtattattttattt-tccat--gcagGTTATACTAGTACAGCAATTACTGATGGTCCTGGATGTTTGATGTTGCGCTGTCCTGATCCAACCTGTGGTGCTGCTGTTGGTCAGGACATGATAAATTT
       ||||  |   |    | ||  |    |||  |  ||    |||     |   ||||| | | | |   |  |||  |||||| |  |  ||   ||||||| | ||| || || || | ||||||||| ||||| |||||| || | |||||||||||  |||||| |||||||||||| || || |||||||||| 
--gtgttgttacttcatcatttcatggaagcaacttgctctaa--agaatcaacctttgaattttactatgtcactgagtaacattttagtaatgtattgacagGTTACATTAGCACTGCTATAAGTGATGGTCCGGGATGCTTGATGCTGAGGTGTCCTGATCCGTCCTGTGCTGCTGCTGTTGGACAAGATATGATAAATTC

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|28961323|gb|CB340672.1|CB340672
EST:     GATAAGTTCTGCTGCTTGTGGTCACCCTTTCTGTGGTACATGCTGGGCAG                         GTTATACTAGTACAGCAATTACTGATGGTCCTGGATGTTTGATGTTGCGCT
genomic: GATAAGTTCTGCTGCTTGTGGTCACCCTTTCTGTGGTACATGCTGGGCAGgtttgtgtta ... ttccatgcagGTTATACTAGTACAGCAATTACTGATGGTCCTGGATGTTTGATGTTGCGCT
EST: gi|110378373|gb|EC943503.1|EC943503
EST:     GATAAGTTCTGCTGCTTGTGGTCACCCTTTCTGTGGTACATGCTGGGCAG                         GTTATACTAGTACAGCAATTACTGATGGTCCTGGATGTTTGATGTTGCGCT
genomic: GATAAGTTCTGCTGCTTGTGGTCACCCTTTCTGTGGTACATGCTGGGCAGgtttgtgtta ... ttccatgcagGTTATACTAGTACAGCAATTACTGATGGTCCTGGATGTTTGATGTTGCGCT
EST: gi|294965747|gb|GW839202.1|GW839202
EST:     GATAAGTTCTGCTGCTTGTGGTCACCCTTTCTGTGGTACATGCTGGGCGG                         GTTATACTAGTACAGCAATTACTGATGGTCCTGGATGTTTGATGTTGCGCT
genomic: GATAAGTTCTGCTGCTTGTGGTCACCCTTTCTGTGGTACATGCTGGGCAGgtttgtgtta ... ttccatgcagGTTATACTAGTACAGCAATTACTGATGGTCCTGGATGTTTGATGTTGCGCT
EST: gi|110383372|gb|EC947743.1|EC947743
EST:     GATAAGTTCTGCTGCTTGTGGTCACCCTTTCTGTGGTACATGCTGGGCAG                         GTTATACTAGTACAGCAATTACTGATGGTCCTGGATGTTTGATGTTGCGCT
genomic: GATAAGTTCTGCTGCTTGTGGTCACCCTTTCTGTGGTACATGCTGGGCAGgtttgtgtta ... ttccatgcagGTTATACTAGTACAGCAATTACTGATGGTCCTGGATGTTTGATGTTGCGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaattttgttcaaaatttaagtgttgtttttgtattattttattttccatgcagGTTATACTAGTACAGCAATTACTGATGGTCCTGGATGTTTGATGTTGCGCTGTCCTGATCCAACCTGTGGTGCTGCTGTTGGTCAGGACATGATAAATTT
                                   ttattttattttcc  CT-rich tract
         ttcaaaatttaagtgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcagaaagttatctttcctgaacttgttatagtcttatttgaattgaaattttgttcaaaatttaagtgttgtttttgtattattttattttccatgcagGTTATACTAGTACAGCAATTACTGATGGTCCTGGATGTTTGATGTTGCGCTGTCCTGATCCAACCTGTGGTGCTGCTGTTGGTCAGGACATGATAAATTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
-cagaaag
- - - - - - - ttcctga
- - - - - - - - - - - - - - - - - - - - -aattgaa