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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgtttgcttttgggtttttgtttttgtttttttttttttggtttttgggggttttgagttttgttttatctatgtagtgttgatttccaattgatctcaaattcctattcgttttgatgcagCAATTGGGTTTAATGTGGAAACAGTTCAGTATAACAACATCAAGTTTCAAGTCTGGGATCTGG

Basic information

species Vitis vinifera
transcript Vv04s0008g07360.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g07360.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os08g15040.2 (Oryza sativa), 3'ss of exon 2
gtatgtgtttgcttttgggtttttgtttttgtttttttttttttggtttttgggggttttgagttttgttttatctatgtagtgttgatttccaattgatctcaaattcctattcgttttgatgcagCAATTGGGTTTAATGTGGAAACAGTTCAGTATAACAACATCAAGTTTCAAGTCTGGGATCTGG
              | || |    | |   | ||   |  ||||  || ||        |  | |||| |       | | |||  | | |    ||| | |           | |  ||| |||||| |||||||| || ||||| || || ||||| |||||||||||||| |||||||||||||| |
-------------gtgggttccccgctcccgattccctcattttttttctt-----ccattcggtttgctccgcgggtttggtgacg-tgtgtgcttgttgttg---------ttgcgttgctgcagCGATTGGGTTCAACGTGGAGACGGTGCAGTACAACAACATCAAGTTCCAAGTCTGGGATCTCG

upper sequence: Vv04s0008g07360.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G147726_T01 (Zea mays), 3'ss of exon 2
gtatgtgtttgcttttgggtttttgtttttgtttttttttttttggtttttgggggttttgagttttgttttatctatgtagtgttgatttccaattgatctcaaattcctattcgttttgatgcagCAATTGGGTTTAATGTGGAAACAGTTCAGTATAACAACATCAAGTTTCAAGTCTGGGATCTGG
                                    |   || || |||   | | |  | | |  ||||    ||   |   ||||  ||  | ||||| |      ||    ||| | | |||||||||||| || || || || || || ||||| |||||||||||||| ||||| |||||||| |
-----------------------------------gtgagttctgatttaccgag-tcgtcattcctgttg---ctggttgaagttg--ttggatttgatgtggtgccccg---cgtgt-gttgcagCAATTGGATTCAACGTTGAGACGGTGCAGTACAACAACATCAAGTTCCAAGTATGGGATCTTG
















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|30137308|gb|CB922646.1|CB922646
EST:     ATCGGCTTCAAATGGGTGAGGTGGTCTCCACGATTCCAA                         CAATTGGGTTTAATGTGGAAACAGTTCAGTATAACAACATCAAGTTTCAAG
genomic: ATCGGCTTCAAATGGGTGAGGTGGTCTCCACGATTCCAAgtatgtgttt ... tttgatgcagCAATTGGGTTTAATGTGGAAACAGTTCAGTATAACAACATCAAGTTTCAAG
EST: gi|33406636|gb|CF212263.1|CF212263
EST:     ATCGGCTTCAAATGGGTGAGGTGGTCTCCACGATTCCAA                         CAATTGGGTTTAATGTGGAAACAGTTCAGTATAACAACATCAAGTTTCAAG
genomic: ATCGGCTTCAAATGGGTGAGGTGGTCTCCACGATTCCAAgtatgtgttt ... tttgatgcagCAATTGGGTTTAATGTGGAAACAGTTCAGTATAACAACATCAAGTTTCAAG
EST: gi|30126854|gb|CB912193.1|CB912193
EST:     ATCGGCTTCAAATGGGTGAGGTGGTCTCCACGATTCCAA                         CAATTGGGTTTAATGTGGAAACAGTTCAGTATAACAACATCAAGTTTCAAG
genomic: ATCGGCTTCAAATGGGTGAGGTGGTCTCCACGATTCCAAgtatgtgttt ... tttgatgcagCAATTGGGTTTAATGTGGAAACAGTTCAGTATAACAACATCAAGTTTCAAG
EST: gi|33408309|gb|CF213936.1|CF213936
EST:     ATCGGCTTCAAATGGGTGAGGTGGTCTCCACGATTCCAA                         CAATTGGGTTTAATGTGGAAACAGTTCAGTATAACAACATCAAGTTTCAAG
genomic: ATCGGCTTCAAATGGGTGAGGTGGTCTCCACGATTCCAAgtatgtgttt ... tttgatgcagCAATTGGGTTTAATGTGGAAACAGTTCAGTATAACAACATCAAGTTTCAAG
EST: gi|33408221|gb|CF213848.1|CF213848
EST:     ATCGGCTTCAAATGGGTGAGGTGGTCTCCACGATTCCAA                         CAATTGGGTTTAATGTGGAAACAGTTCAGTATAACAACATCAAGTTTCAAG
genomic: ATCGGCTTCAAATGGGTGAGGTGGTCTCCACGATTCCAAgtatgtgttt ... tttgatgcagCAATTGGGTTTAATGTGGAAACAGTTCAGTATAACAACATCAAGTTTCAAG
EST: gi|110406223|gb|EC971789.1|EC971789
EST:     ATCGGCTTCAAATGGGTGAGGTGGTCTCCACGATTCCAA                         CAATTGGGTTTAATGTGGAAACAGTTCAGTATAACAACATCAAGTTTCAAG
genomic: ATCGGCTTCAAATGGGTGAGGTGGTCTCCACGATTCCAAgtatgtgttt ... tttgatgcagCAATTGGGTTTAATGTGGAAACAGTTCAGTATAACAACATCAAGTTTCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctatgtagtgttgatttccaattgatctcaaattcctattcgttttgatgcagCAATTGGGTTTAATGTGGAAACAGTTCAGTATAACAACATCAAGTTTCAAGTCTGGGATCTGG
                                            ttttgat  putative branch site (score: 4)
                                  ttcctattcgtttt  CT-rich tract
            ttgattt  TA-rich tract