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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCATCTGTGAAAGATGTCTGTGGGAAGCCTCCAACTGAGCGCCTCTTCCTTGATAAGTACGGAAAGATATGCTTATGTCTGGACGAAATTGTTTGGAAGgtgaggggatgcatcaaattttttgcaacctataaaggcttttgtctctctactatcagtactataagaatcacacataactctgttcagcaaagaaata...

Basic information

species Vitis vinifera
transcript Vv09s0002g06730.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g06730.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G138053_T03 (Zea mays), 5'ss of exon 5
CTCATCTGTGAAAGATGTCTGTGGGAAGCCTCCAACTGAGCGCCTCTTCCTTGATAAGTACGGAAAGATATGCTTATGTCTGGACGAAATTGTTTGGAAGgtgaggggatgcatcaaattttttgcaacctataaaggcttttgtctctctactatcagtactataagaatcacacataactctgttcagcaaagaaata-
 ||| | || || ||||| ||||  || ||||| || ||||||||||||||||| || ||||| | ||| ||||| || || || || ||||||||||||||           ||   ||| | ||  | |  | |    |||||  || || | |  |||   ||  |  |  ||  |  || | |         |||  
ATCAGCAGTCAAGGATGTTTGTGCAAAACCTCCTACCGAGCGCCTCTTCCTTGACAAATACGGGAGGATCTGCTTGTGCCTTGATGAGATTGTTTGGAAGgtacatctccaactcgtttttctggcctcgtggatatttctttgtgcctgtaatctgggtatggtataatgcttac-catatcagctggatgttccaatgt

upper sequence: Vv09s0002g06730.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G138053_T02 (Zea mays), 5'ss of exon 4
CTCATCTGTGAAAGATGTCTGTGGGAAGCCTCCAACTGAGCGCCTCTTCCTTGATAAGTACGGAAAGATATGCTTATGTCTGGACGAAATTGTTTGGAAGgtgaggggatgcatcaaattttttgcaacctataaaggcttttgtctctctactatcagtactataagaatcacacataactctgttcagcaaagaaata-
        | || ||||| ||||  || ||||| || ||||||||||||||||| || ||||| | ||| ||||| || || || || ||||||||||||||           ||   ||| | ||  | |  | |    |||||  || || | |  |||   ||  |  |  ||  |  || | |         |||  
--------TCAAGGATGTTTGTGCAAAACCTCCTACCGAGCGCCTCTTCCTTGACAAATACGGGAGGATCTGCTTGTGCCTTGATGAGATTGTTTGGAAGgtacatctccaactcgtttttctggcctcgtggatatttctttgtgcctgtaatctgggtatggtataatgcttac-catatcagctggatgttccaatgt

upper sequence: Vv09s0002g06730.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA08G22580.2 (Glycine max), 5'ss of exon 3
CTCATCTGTGAAAGATGTCTGTGGGAAGCCTCCAACTGAGCGCCTCTTCCTTGATAAGTACGGAAAGATATGCTTATGTCTGGACGAAATTGTTTGGAAGgtgagggg--atgcatcaaattttttgcaacctataaaggcttttgtctctctactatcagtactataagaatcacacataactctgttcagcaaagaaata
|||| ||||||| ||||| ||||||||||| |||| ||||||||| |||||||| ||||| ||||  || ||  | |||||||| |||||||| ||| |||| ||| |  || ||  | | |||| |  |   | ||   |      |    || | |   |   ||   | ||| |  |   |   ||  | ||   |  |
CTCAGCTGTGAAGGATGTATGTGGGAAGCCCCCAAGTGAGCGCCTTTTCCTTGACAAGTATGGAAGAATTTGTCTGTGTCTGGATGAAATTGTATGGCAGgtaaggaggcatacagaacagttttagttatgcaaaataacaagaaccagattattttttttgtcattttactca-atctgcttgcctttgg-aactcatca

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|37190396|gb|CF609745.1|CF609745
EST:     TTGATAAGTACGGAAAGATATGCTTATGTCTGGACGAAATTGTTTGGAAG                         GGAATGCTGGAGAATGCTGACAAAGACAGAATCAGGAGACTGACAAGGTTG
genomic: TTGATAAGTACGGAAAGATATGCTTATGTCTGGACGAAATTGTTTGGAAGgtgaggggat ... ttttctgaagGGAATGCTGGAGAATGCTGACAAAGACAGAATCAGGAGACTGACAAGGTTG
EST: gi|352777162|gb|FQ474469.1|FQ474469
EST:     TTGATAAGTACGGAAAGATATGCTTATGTCTGGACGAAATTGTTTGGAAG                         GGAATGCTGGAGAATGCTGACAAAGACAGAATCAGGAGACTGACAAGGTTG
genomic: TTGATAAGTACGGAAAGATATGCTTATGTCTGGACGAAATTGTTTGGAAGgtgaggggat ... ttttctgaagGGAATGCTGGAGAATGCTGACAAAGACAGAATCAGGAGACTGACAAGGTTG
EST: gi|37190163|gb|CF609512.1|CF609512
EST:     TTGATAAGTACGGAAAGATATGCTTATGTCTGGACGAAATTGTTTGGAAG                         GGAATGCTGGATAATGCTGACAAAGACAGAATCAGGAGACTGACAAGGTTG
genomic: TTGATAAGTACGGAAAGATATGCTTATGTCTGGACGAAATTGTTTGGAAGgtgaggggat ... ttttctgaagGGAATGCTGGAGAATGCTGACAAAGACAGAATCAGGAGACTGACAAGGTTG

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCATCTGTGAAAGATGTCTGTGGGAAGCCTCCAACTGAGCGCCTCTTCCTTGATAAGTACGGAAAGATATGCTTATGTCTGGACGAAATTGTTTGGAAGgtgaggggatgcatcaaattttttgcaacctataaaggcttttgtctctctactatcagtactataagaatcacacataactctgttcagcaaagaaata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctctac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ataagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaagaaa