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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attacctgtatttttctggcgttttcaccatccctgcaatcttgccttcattttgcctcccagtttcactagcacttaaagctatttgcgtttattccagCTCACAGGAGATTTAAACAAGATGGTTGCACTGCAGAGGTTATTGGAGCCCTATGGGATTTGTGAG

Basic information

species Vitis vinifera
transcript Vv00s0220g00110.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0220g00110.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G407044_T01 (Zea mays), 3'ss of exon 10
-attacctgtat--ttttctggcgttttcaccatccctgcaatcttgccttcattttgcctcccagtttcactagcacttaaagctatttgcgtttattccagCTCACAGGAGATTTAAACAAGATGGTTGCACTGCAGAGGTTATTGGAGCCCTATGGGATTTGTGAG
   | || |||   ||||||   | | |    |||       ||    ||      ||   |  |  |     |  |  |  ||  ||    | | ||| ||||| || |||||| |  |||||||||||||||| || |||||||||||||| ||||| || ||||||
tgatgccggtaccattttctcatgctgtt-ttatctaactgctccaagctattagctgttgcaaaactcttgcataa--tggagggatcattgatgattgcagCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAG
















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|351035256|gb|FQ458613.1|FQ458613
EST:     TTTTCCGGGCCAAAGCTGTTGATGTGTCTGATCACACAATTACCCTAGAG                         CTCACAGGAGATTTAAACAAGATGGTTGCACTGCAGAGGTTATTGG
genomic: TTTTCCGGGCCAAAGCTGTTGATGTGTCTGATCACACAATTACCCTAGAGgtgaaaatgg ... tttattccagCTCACAGGAGATTTAAACAAGATGGTTGCACTGCAGAGGTTATTGG
EST: gi|351012893|gb|FQ430456.1|FQ430456
EST:     TTTTCCGGGCCAAAGCTGTTGATGTGTCTGATCACACAATTACCCTAGAG                         CTCACAGGAGATTTAAACAAGATGGTTGCACTGCAGAG
genomic: TTTTCCGGGCCAAAGCTGTTGATGTGTCTGATCACACAATTACCCTAGAGgtgaaaatgg ... tttattccagCTCACAGGAGATTTAAACAAGATGGTTGCACTGCAGAG
EST: gi|351046895|gb|FQ454505.1|FQ454505
EST:     TTTTCCGGGC-AAAGCTGTTGATGTGTCTGATCACACAATTACCCTAGAG                         CTCACAGGAGATTTAAACAAGATGG
genomic: TTTTCCGGGCCAAAGCTGTTGATGTGTCTGATCACACAATTACCCTAGAGgtgaaaatgg ... tttattccagCTCACAGGAGATTTAAACAAGATGG
EST: gi|351043332|gb|FQ451384.1|FQ451384
EST:     TTTTTCGGGCCAAAGCTGTTGATGTGTCTGATCACACAATTACCCTAGAG                         CTCACAGGAGATTTAAACA
genomic: TTTTCCGGGCCAAAGCTGTTGATGTGTCTGATCACACAATTACCCTAGAGgtgaaaatgg ... tttattccagCTCACAGGAGATTTAAACA
EST: gi|351044506|gb|FQ443037.1|FQ443037
EST:     TTTTCCGGGCCAAAGCTGTTGATGTGTCTGATCACACAATTACCCTAGAG                         CTCACAGGAGATT-AAACCAGATGGTTGCACTGCAGAGGTTAT
genomic: TTTTCCGGGCCAAAGCTGTTGATGTGTCTGATCACACAATTACCCTAGAGgtgaaaatgg ... tttattccagCTCACAGGAGATTTAAACAAGATGGTTGCACTGCAGAGGTTAT
EST: gi|352795642|gb|FQ480230.1|FQ480230
EST:     TTTTCCGGGCCAAAGCTGTTGATGTGTCTGATCACACAATTACCCTAGAG                         CTCACAGGAGATTTAAACAAGATGGTTGCACTGCAAAGGTTATTGGAGCCC
genomic: TTTTCCGGGCCAAAGCTGTTGATGTGTCTGATCACACAATTACCCTAGAGgtgaaaatgg ... tttattccagCTCACAGGAGATTTAAACAAGATGGTTGCACTGCAGAGGTTATTGGAGCCC
EST: gi|351017801|gb|FQ436154.1|FQ436154
EST:     TTTTCCGGGCCAAAGCTGTTGATGTGTCTGATCACACAATTACCCTAGAG                         CTCACAGGAGATT-AAACAAGATG
genomic: TTTTCCGGGCCAAAGCTGTTGATGTGTCTGATCACACAATTACCCTAGAGgtgaaaatgg ... tttattccagCTCACAGGAGATTTAAACAAGATG
EST: gi|351032123|gb|FQ460380.1|FQ460380
EST:     TTT-CCGGGGCAAAGCTGTTGATGTGTCTGATCACACAATTACCCTAGAG                         CTCACAGGAGATTTAAACAAGATGGTTGC
genomic: TTTTCCGGGCCAAAGCTGTTGATGTGTCTGATCACACAATTACCCTAGAGgtgaaaatgg ... tttattccagCTCACAGGAGATTTAAACAAGATGGTTGC
EST: gi|351039410|gb|FQ461277.1|FQ461277
EST:     TTTTCCGGGCCAAAGCTGTTGATGTGGCTGATCACACAATTACCCTAGAG                         CTCACAGGAGATTTAAACCAGATGG
genomic: TTTTCCGGGCCAAAGCTGTTGATGTGTCTGATCACACAATTACCCTAGAGgtgaaaatgg ... tttattccagCTCACAGGAGATTTAAACAAGATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcattttgcctcccagtttcactagcacttaaagctatttgcgtttattccagCTCACAGGAGATTTAAACAAGATGGTTGCACTGCAGAGGTTATTGGAGCCCTATGGGATTTGTGAG
                                             tttattcc  CT-rich tract
                                             tttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attacctgtatttttctggcgttttcaccatccctgcaatcttgccttcattttgcctcccagtttcactagcacttaaagctatttgcgtttattccagCTCACAGGAGATTTAAACAAGATGGTTGCACTGCAGAGGTTATTGGAGCCCTATGGGATTTGTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- tacctgt
- - - - - - tttctgg
- - - - - - - - - - - - - -ccatccc