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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cccacacgtccttggtatttatgtttccaggcctctgtatgtttgcaaggagtacagttgtgatacttcttctaatgtaaatgtttttgcatgtatacagAAGCAAGGGATGGTGAAGGAAGGAGAAGAGGTGGCTCTTGTTCAGAGTGGCAGGCAGCCGATCTGGCGGTTCCAATCCACACACAATATCCAGGTCAGGA

Basic information

species Vitis vinifera
transcript Vv16s0050g02180.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0050g02180.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os01g47080.1 (Oryza sativa), 3'ss of exon 11
--cccacacgtccttgg-tatttatgtttccaggcctctgtatgtttgcaaggagtacagttgtgatact--tcttctaatgtaaatgtttttgcatgtatacagAAGCAAGGGATGGTGAAGGAAGGAGAAGAGGTGGCTCTTGTTCAGAGTGGCAGGCAGCCGATCTGGCGGTTCCAATCCACACACAATATCCAGGTCAGGA
      |      | |  |  | |  |  ||| ||| |   || |   | |    | ||  |  ||||||   | | | || | |   | | |  || |  |||||| || || |||||||||||||| || ||||| || |||||||| ||||||||||| || ||||||||||  || ||||| || ||||| ||||||||||
ttgttgctgaaaatagactgataaaatagccatgccccaa-atatccactat---tccacatacgatactcaccatttgatatgatgctatatatat-tccacagAAACATGGTATGGTGAAGGAAGGCGAGGAGGTTGCACTTGTTCAAAGTGGCAGGCAACCTATCTGGCGGTCGCAGTCCACCCATAATATTCAGGTCAGGA

upper sequence: Vv16s0050g02180.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA09G23150.1 (Glycine max), 3'ss of exon 11
cccacacgtccttggtatttatgtttccag-gcctctgtatgtttgcaaggagtacagttgtgatacttcttctaatgtaaatgtttttgcatg-------tatacagAAGCAAGGGATGGTGAAGGAAGGAGAAGAGGTGGCTCTTGTTCAGAGTGGCAGGCAGCCGATCTGGCGGTTCCAATCCACACACAATATCCAGGTCAGGA
      |     |  || |      |  || | ||   ||     |      || || ||||  || |  ||||  | | |   | ||||||||       |  |||||||||||| |||||||||||||||||||| || || ||||| || ||||| ||||| || || ||| ||||||||||||| |||||||||||||| ||||
------caaaaatactactctcaccttaagtgactgcttaaaccag-ggcttgtgcaattgttttattgtttctt-tatgatgatatttgcatggttttcgtgcacagAAGCAAGGAATGGTGAAGGAAGGAGAAGAAGTAGCACTTGTACAAAGTGGTAGGCAACCCATATGGAGGTTCCAATCCACGCACAATATCCAGGTTAGGA

upper sequence: Vv16s0050g02180.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA16G28980.2 (Glycine max), 3'ss of exon 9
cccacacgtcct-tggtatttatgtttccaggcctctgtatgtttgca-aggagtacagttgtgatacttcttctaatgtaaatgtttttgca-----tgtatacagAAGCAAGGGATGGTGAAGGAAGGAGAAGAGGTGGCTCTTGTTCAGAGTGGCAGGCAGCCGATCTGGCGGTTCCAATCCACACACAATATCCAGGTCAGGA
       ||||| |  | ||  | ||||      ||| ||||       |    | |  || |  |  ||  | || ||   || |||          ||| | ||||||||||  |||||||||||||||||||| || || ||||| || ||||| ||||| || || ||| ||||||||||||| |||||||||||||| ||||
------tgtcctgtcattttcctatttctttttttctttatgaagatggatccatgcgatttttgttgtttcttta-tgatcatatttgcatggtttctgtgtgcagAAGCAAGCAATGGTGAAGGAAGGAGAAGAAGTAGCACTTGTACAAAGTGGTAGGCAACCCATATGGAGGTTCCAATCCACGCACAATATCCAGGTTAGGA

upper sequence: Vv16s0050g02180.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA10G37210.1 (Glycine max), 3'ss of exon 11
cccacacgtccttggtatttatgtttccaggcctctgtatgtttgcaaggagtacagttgtgatacttcttctaatg--taaatgtttttgcatgtatacagAAGCAAGGGATGGTGAAGGAAGGAGAAGAGGTGGCTCTTGTTCAGAGTGGCAGGCAGCCGATCTGGCGGTTCCAATCCACACACAATATCCAGGTCAGGA
                  | ||||||  |||       || | | ||   | |  ||||    || || || |||||   |  ||| ||       || ||||||||||| ||||||||   ||||||||| || || || || || ||||||||||| || || ||| ||||||||||||| ||||||||||||||| | |
-----------------gtaatgtttggagg-------atatcttcagtaaatttagtttatttagttgttttaatgatcatttgtgttgttcgaaatgcagAAGCAAGGAATGGTGAAATCAGGAGAAGAAGTAGCACTAGTACAAAGTGGCAGGCAACCCATATGGAGGTTCCAATCCACTCACAATATCCAGGTCCGAA

upper sequence: Vv16s0050g02180.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA20G30430.1 (Glycine max), 3'ss of exon 11
-cccacacgtccttggtatttatgtttccaggcctctgtatgtttgcaaggagtacagttgtgatacttcttctaatg-taaatgtttttgcatgtat-acagAAGCAAGGGATGGTGAAGGAAGGAGAAGAGGTGGCTCTTGTTCAGAGTGGCAGGCAGCCGATCTGGCGGTTCCAATCCACACACAATATCCAGGTCAGGA
 |  |        ||   |  |    | || |   ||  ||  |  |      |  |||| |  |  || || ||||| | | | || |||  |  || |||||||||||| ||||||||   ||||||||| || || || || || ||||||| ||| || || ||| ||||||||||||| ||||||||||||||| | |
gcatattatgttatgtcctaaacacattcacgtgacta-atagtccctttttatttagttttagt--tttttttaatgatcatttttgttgtttccattacagAAGCAAGGAATGGTGAAATCAGGAGAAGAAGTAGCACTAGTACAAAGTGGCACGCAACCCATATGGAGGTTCCAATCCACTCACAATATCCAGGTCCGAA

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|110361781|gb|EC925279.1|EC925279
EST:     TCTCAGACGATGCCGAAGAAACCTTTGCAAATGCCTTGACTTTGTTGCAG                         AAGCAAGGGATGGTGAAGGAAGGAGAAGAGGTGGCTCTTGTTCAGAGTGGC
genomic: TCTCAGACGATGCCGAAGAAACCTTTGCAAATGCCTTGACTTTGTTGCAGgtaaggtttt ... atgtatacagAAGCAAGGGATGGTGAAGGAAGGAGAAGAGGTGGCTCTTGTTCAGAGTGGC
EST: gi|30134905|gb|CB920243.1|CB920243
EST:     TCTCAGACGATGCTGAAGAAACCTTTGCAAATGCCTTGTCTTTGTTGCAG                         AAGCAAGGGATGGTGAAGGAAGGAGAAGAGGTGGCTCTTGTTCAGAGTGGC
genomic: TCTCAGACGATGCCGAAGAAACCTTTGCAAATGCCTTGACTTTGTTGCAGgtaaggtttt ... atgtatacagAAGCAAGGGATGGTGAAGGAAGGAGAAGAGGTGGCTCTTGTTCAGAGTGGC
EST: gi|30321651|gb|CD004913.1|CD004913
EST:     TCTCAGACGATGCTGAAGAAACCTTTGCAAATGCCTTGTCTNTGTTGCAG                         AAGCAAGNGATGGTGAAGGAAGGAGAAGAGGT
genomic: TCTCAGACGATGCCGAAGAAACCTTTGCAAATGCCTTGACTTTGTTGCAGgtaaggtttt ... atgtatacagAAGCAAGGGATGGTGAAGGAAGGAGAAGAGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaggagtacagttgtgatacttcttctaatgtaaatgtttttgcatgtatacagAAGCAAGGGATGGTGAAGGAAGGAGAAGAGGTGGCTCTTGTTCAGAGTGGCAGGCAGCCGATCTGGCGGTTCCAATCCACACACAATATCCAGGTCAGGA
                        ttctaat  putative branch site (score: 2)
                           taatgtaaatgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cccacacgtccttggtatttatgtttccaggcctctgtatgtttgcaaggagtacagttgtgatacttcttctaatgtaaatgtttttgcatgtatacagAAGCAAGGGATGGTGAAGGAAGGAGAAGAGGTGGCTCTTGTTCAGAGTGGCAGGCAGCCGATCTGGCGGTTCCAATCCACACACAATATCCAGGTCAGGA

-ccacacg
- - - - tccttgg
- - - - - - - - - - - - - ccaggcc
- - - - - - - - - - - - - - - - - ctgtatg
- - - - - - - - - - - - - - - - - - - - - - gcaagga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgtaaa