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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattatgttcatttctacctgtgctctatatacaatttgagttcttatttgagtcctagcgtgttaatgggttgatttttcaattatatttttatggcagATAAGTTTGGAGCTGCTATGGCACTTGTAAAATCTGATATTGGTGGTAATATCTCG

Basic information

species Vitis vinifera
transcript Vv05s0049g01330.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0049g01330.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os02g40890.2 (Oryza sativa), 3'ss of exon 2
cattatgttcatttctacctgtgctctatatacaatttgagttcttatt--tgagtcctagcgtgttaatgggttgatttttcaattatatttttatggcagATAAGTTTGGAGCTGCTATGGCACTTGTAAAATCTGATATTGGTGGTAATATCTCG
  ||   || | |  |   |  | | ||  | ||        ||| | |  || | |  || ||     ||  |   || |||  | |  ||| |||  ||||||| ||||||||||||||||||||||| ||   ||| ||||||||||||||| ||
acttcaattaaatcgtttgttagttttaagt-cagggcatactctaactattgtggctaagtgttcctttgtctcctttgttctctgac-tttgtattccagATAAATTTGGAGCTGCTATGGCACTTGTGAAGAGTGACATTGGTGGTAATATCACG

upper sequence: Vv05s0049g01330.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G060870_T03 (Zea mays), 3'ss of exon 2
-------------cattatgttcatttctacctgtgctctatatacaatttgagttcttatttgagtcctagcgtgttaatgggttgatttttcaattatatttttatggcagATAAGTTTGGAGCTGCTATGGCACTTGTAAAATCTGATATTGGTGGTAATATCTCG
             | ||||||| |  | ||| |||| |   || |||||      | || ||  |    ||   |         |   ||| ||   |  |||| |    ||||||| |||||||||||||||||| |||||||   ||||||  | || |||||| | 
cagttctctgtttctttatgttgagctgtacttgtgttgcttaaacaataaaccatttttttcaa----taattt---------tccctttatcccctgcatttatgcaccagATAAATTTGGAGCTGCTATGGCAATTGTAAAGAATGATATCAGCGGCAATATCACA

upper sequence: Vv05s0049g01330.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G00690.1 (Glycine max), 3'ss of exon 2
----cattatgttcatttctacctgtgctctatatacaatttgagttcttatttgagtcctagcgtgttaatgggttgatttttcaattatatttttatggcagATAAGTTTGGAGCTGCTATGGCACTTGTAAAATCTGATATTGGTGGTAATATCTCG
     | | ||  | | |  |||   | |   |      ||  |    |||   || | || | |   |  | |        |  ||   | || ||||||||||||||||||||||||||||||| ||||| |||||||| || |||||||| || |||
aattgactgtgaacctatgcacccaagtttagtgcttgctt--aagcattaaaggaatacttgtgccatggttgaaaagagct--aacacttttcttatggcagATAAGTTTGGAGCTGCTATGGCCCTTGTTAAATCTGACATAGGTGGTAACATATCG

upper sequence: Vv05s0049g01330.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA02G00670.1 (Glycine max), 3'ss of exon 2
----cattatgttcatttctacctgtgctctatatacaatttgagttcttatttgagtcctagcgtgttaatgggttgatttttcaattatatttttatggcagATAAGTTTGGAGCTGCTATGGCACTTGTAAAATCTGATATTGGTGGTAATATCTCG
     ||| ||  | | |  |||   | |   |      |   |    |||  ||| |  | | |   |  |          |  ||   | ||  |||||||||||||||||||||||||||||| ||||| |||||||| || |||||||| || |||
aatagattgtgaacctatgcacccaagtttagtgcttgctc--aagcattaaatgaatatttgtgccatggttaaaaagagct--aacacttttcatatggcagATAAGTTTGGAGCTGCTATGGCCCTTGTTAAATCTGACATAGGTGGTAACATATCG

upper sequence: Vv05s0049g01330.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G32590.3 (Glycine max), 3'ss of exon 2
cattatgttcatttctacctgtgctctatatacaatttgagttcttatttgagtcctagcgtgt-taatgggttgatttttcaattatatttttatggcagATAAGTTTGGAGCTGCTATGGCACTTGTAAAATCTGATATTGGTGGTAATATCTCG
  ||    |  |||   |  ||| |   |    ||          |||   | |  ||     |  | |    ||||     |||  | || || || ||||||||||||||||||||||||| ||||| |||||||| ||||||||||| || |||
-gttgacctttttttgtcgggtgatgcttggttaagccttaaatgtatgacaatattaatacttacagttatctgatggactaatacttttcttttgacagATAAGTTTGGAGCTGCTATGGCCCTTGTTAAATCTGACATTGGTGGTAACATATCG

upper sequence: Vv05s0049g01330.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA20G34980.1 (Glycine max), 3'ss of exon 3
--cattatgttcatttctacctgtgctc---tatatacaatttgagttcttatttgagtcctagcgtgttaatgggttgatttttcaattatatttttatggcagATAAGTTTGGAGCTGCTATGGCACTTGTAAAATCTGATATTGGTGGTAATATCTCG
       | ||  | || |    ||||    ||     ||  ||  |    || ||| | ||  | | ||| | | | || |    |||  | || |||||||||| |||||||||||||||||||| ||||| |||||||| || |||||||| || |||
gttgaccttttgttgtcgagtgatgcttggttaagcctaaaatgtatgacaatatgaatacttac-tattatttgatggact----aatacttttcttatggcagACAAGTTTGGAGCTGCTATGGCCCTTGTTAAATCTGACATCGGTGGTAACATATCG

upper sequence: Vv05s0049g01330.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT2G33470.2 (Arabidopsis thaliana), 3'ss of exon 2
------cattatgttcatttctacctgtgctctatatacaatttgagttcttatttgagtcctagcgtgttaatgggttgatttttcaattat-atttttatggcagATAAGTTTGGAGCTGCTATGGCACTTGTAAAATCTGATATTGGTGGTAATATCTCG
      | |   | |  |   |     |  |   |||  ||    | |  |   ||   ||||| | ||   |||  || |||||||  |  | || | | |  ||||||| ||||||||||||||| | || || |||||||| |||||||| || ||  ||
agttcacgtatagcttgtgattgttcatttttcctatgtaacacaaatgttgtgtt---tccta-catg---atgacttcatttttctgtggttatctattttccagATAAATTTGGAGCTGCTATGACTCTCGTGAAATCTGACATTGGTGGCAACATAACG

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|30306238|gb|CB983032.1|CB983032
EST:     GCTGACTAAGCCTTTCTTGGATGTGTGCAAACTCATATTACCTGTTATAG                         ATAAGTTTGGAGCTGCTATGGCACTTGTAAAATCTGATATTGGTGGTAATA
genomic: GCTGACTAAGCCTTTCTTGGATGTGTGCAAACTCATATTACCTGTTATAGgtgtgttttc ... tttatggcagATAAGTTTGGAGCTGCTATGGCACTTGTAAAATCTGATATTGGTGGTAATA
EST: gi|71883183|gb|DT032238.1|DT032238
EST:     GCTGACTAAGCCTTTCTTGGATGTATGCAAACTCATATTACCTGTTATAG                         ATAAGTTTGGAGCTGCTATGGCACTTGTAAAATCTGATATTGGTGGTAATA
genomic: GCTGACTAAGCCTTTCTTGGATGTGTGCAAACTCATATTACCTGTTATAGgtgtgttttc ... tttatggcagATAAGTTTGGAGCTGCTATGGCACTTGTAAAATCTGATATTGGTGGTAATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttgagtcctagcgtgttaatgggttgatttttcaattatatttttatggcagATAAGTTTGGAGCTGCTATGGCACTTGTAAAATCTGATATTGGTGGTAATATCTCG
                                         tattttt  CT-rich tract
                          ttgatttttcaattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cattatgttcatttctacctgtgctctatatacaatttgagttcttatttgagtcctagcgtgttaatgggttgatttttcaattatatttttatggcagATAAGTTTGGAGCTGCTATGGCACTTGTAAAATCTGATATTGGTGGTAATATCTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - -tacctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - -tcctagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gggttga