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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgaatactataatagatgatactgtactactattctataagcttatcatattgctaagatcactccctgattctgctctctagAAATGGTATTTAAATATCCTGGAGGCTGATAAAGTACAACCGCCAAAGAAAACAGAAGATGGAAAGCTATATACACCAGCTGCTGTTGACTTATTTAGGA

Basic information

species Vitis vinifera
transcript Vv03s0097g00670.t01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0097g00670.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GRMZM2G070045_T01 (Zea mays), 3'ss of exon 9
gtaatgaatactataatagatgatactgtactactattctataagcttatcatattgctaagatcactccctgattctgctctctagAAATGGTATTTAAATATCCTGGAGGCTGATAAAGTACAACCGCCAAAGAAAACAGAAGATGGAAAGCTATATACACCAGCTGCTGTTGACTTATTTAGGA
||| |   | ||| |   | |||   |  |  |   ||  | | |   ||||| |       ||   |  ||  || |  ||| |||||||||||    || ||  |||||||||| |||  |||||| |||||||  ||||| |||||||| ||||||||||| || || || ||  |||| || |
gtacttctttctagatctgttgaatgtagatgaac-ttaaacatgagaatcatgt-------atttttttcttgttttcttctgtagAAATGGTACAGCAACATTTTGGAGGCTGACAAAACACAACCACCAAAGAGTACAGAGGATGGAAAACTATATACACCTGCAGCAGTGGATCTATTCAGAA

upper sequence: Vv03s0097g00670.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA03G03120.1 (Glycine max), 3'ss of exon 15
gtaatgaatactataatagatgatactgtactactattctataagcttatcatattgctaagatcactccctgattctgctctctagAAATGGTATTTAAATATCCTGGAGGCTGATAAAGTACAACCGCCAAAGAAAACAGAAGATGGAAAGCTATATACACCAGCTGCTGTTGACTTATTTAGGA
|||||    | |||  |   || |  |       |    | |  |     ||||   ||||| |   | | | ||  |    | |||||||||||  | |||||  |||||||||||| |  ||| || || |||||||| |||||||| ||||||||||| ||||||||||||||  | || ||||
gtaatcctaaatatcttg--tggtgtttcttgggtgacttctttgtcatacataagactaagctttattcttaatgtt----tatagAAATGGTACCTGAATATTTTGGAGGCTGATAGAACACAGCCCCCTAAGAAAACTGAAGATGGGAAGCTATATACCCCAGCTGCTGTTGATCTCTTCAGGA

upper sequence: Vv03s0097g00670.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: EFJ12004 (Selaginella moellendorffii), 3'ss of exon 13
gtaatgaatactataatagatgatactgtactactattctataagcttatcatattgc-taagatcactccctgattctgctctcta---gAAATGGTATTTAAATATCCTGGAGGCTGATAAAGTACAACCGCCAAAGAAAACAGAAGATGGAAAGCTATATACACCAGCTGCTGTTGACTTATTTAGGA
                                        | || | || ||  |||| |    |   | | || ||  |  || ||   |||||||||    || || |||||||| |||||||| || ||||| |||||||||||  | ||||||||||  || ||||||||||| || || || ||||
-------------------------------------gtaagaaacgtaccaccttgcgtgctcttgtttcatgcttgcgtgctgtatcagAAATGGTACACCAACATTCTGGAGGCGGATAAAGTGCAGCCGCCGAAGAAAACAGATCAAGGAAAGCTATGGACCCCAGCTGCTGTGGATTTGTTCAGGA

upper sequence: Vv03s0097g00670.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: EFJ08885 (Selaginella moellendorffii), 3'ss of exon 13
gtaatgaatactataatagatgatactgtactactattctataagcttatcatattgc-taagatcactccctgattctgctctcta---gAAATGGTATTTAAATATCCTGGAGGCTGATAAAGTACAACCGCCAAAGAAAACAGAAGATGGAAAGCTATATACACCAGCTGCTGTTGACTTATTTAGGA
                                        | ||   || ||  |||| |    |   | | || ||  |  || ||   |||||||||    || ||||||||||| |||||||| || ||||| |||||||||||  | ||||||||||  || ||||||||||| || || || ||||
-------------------------------------gtaagaaatgtaccaccttgcgtgctcttgtttcatgcttacgtgctgtatcagAAATGGTACACCAACATCCTGGAGGCGGATAAAGTGCAGCCGCCGAAGAAAACAGATCAAGGAAAGCTATGGACCCCAGCTGCTGTGGATTTGTTCAGGA

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|71861663|gb|DT010718.1|DT010718
EST:     TGGATCCTCTCATGAATTCATATGTTGAAAGGATGCAAGCCACGACAAAG                         AAATGGTATTTAAATATCCTGGAGGCTGATAAAGTACAACCACCAAAGAAA
genomic: TGGATCCTCTCATGAATTCATATGTTGAAAGAATGCAAGCCACAACAAAGgtaatgaata ... tgctctctagAAATGGTATTTAAATATCCTGGAGGCTGATAAAGTACAACCGCCAAAGAAA
EST: gi|30136345|gb|CB921683.1|CB921683
EST:     TGGATCCTCTCATGAATTCATATGTTGAAAGGATGCAAGCCACAACAAAG                         AAATGGTATTTAAATATCCTGGAGGCTGATAAAGTACAACCACCAAAGAAA
genomic: TGGATCCTCTCATGAATTCATATGTTGAAAGAATGCAAGCCACAACAAAGgtaatgaata ... tgctctctagAAATGGTATTTAAATATCCTGGAGGCTGATAAAGTACAACCGCCAAAGAAA
EST: gi|161712685|gb|FC062257.1|FC062257
EST:     TGGATCCTCTCATGAATTCATATGTTGAAAGAATGCAAGCCACAACAAAG                         AAATGGTATTTAAATATCCTGGAGGCTGATAAAGTACAACCGCCAAAGAAA
genomic: TGGATCCTCTCATGAATTCATATGTTGAAAGAATGCAAGCCACAACAAAGgtaatgaata ... tgctctctagAAATGGTATTTAAATATCCTGGAGGCTGATAAAGTACAACCGCCAAAGAAA
EST: gi|161708434|gb|FC056140.1|FC056140
EST:     TGGATCCTCTCATGAATTCATATGTTGAAAGAATGCAAGCCACAACAAAG                         AAATGGTATTTAAATATCCT
genomic: TGGATCCTCTCATGAATTCATATGTTGAAAGAATGCAAGCCACAACAAAGgtaatgaata ... tgctctctagAAATGGTATTTAAATATCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actattctataagcttatcatattgctaagatcactccctgattctgctctctagAAATGGTATTTAAATATCCTGGAGGCTGATAAAGTACAACCGCCAAAGAAAACAGAAGATGGAAAGCTATATACACCAGCTGCTGTTGACTTATTTAGGA
                                    ccctgat  putative branch site (score: 4)
                                          ttctgctctct  CT-rich tract
              ttatcatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgaatactataatagatgatactgtactactattctataagcttatcatattgctaagatcactccctgattctgctctctagAAATGGTATTTAAATATCCTGGAGGCTGATAAAGTACAACCGCCAAAGAAAACAGAAGATGGAAAGCTATATACACCAGCTGCTGTTGACTTATTTAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT