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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtattaatcaccatgtaacaaatgaaagggtgcactatattcatgcagcattgtaatcattatgtaaatggatgagtgtttgatactctgaacttgcagAAATCATGGACTTTGGTTATCCACAAAATCTTTCTCCAGAAATTTTGAAGCTCTACATCACCCAAGAAGGAGTTCGGTCTCCATTCTCATCCAAG

Basic information

species Vitis vinifera
transcript Vv02s0012g00910.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0012g00910.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G331032_T01 (Zea mays), 3'ss of exon 3
tgtattaatcaccatgtaacaaatgaaagggtgcactatattcatgcagcattgtaatcatta-tgtaaatggatg-agtgtttgatactctgaacttgcagAAATCATGGACTTTGGTTATCCACAAAATCTTTCTCCAGAAATTTTGAAGCTCTACATCACCCAAGAAGGAGTTCGGTCTCCATTCTCATCCAAG
               ||||  ||  |     | |  |   | |||   |||   | |  |||  |||  ||  ||  ||   | |||| |       | |||| |||||||| ||||||||||| ||||| || || || |||||||||||| | || || || |||||||| |||||||| ||||| || || |||
---------------gtaattaagcatcctattctttgcctgcataatgcaacatgagtatttctgttcattcatccagacatcgataattg-----tacagAGATCATGGATTTTGGTTATCCTCAAAACCTGTCACCTGAAATTTTGAAGTTGTATATAACTCAAGAAGGTGTTCGGTCACCATTTTCCTCAAAG

upper sequence: Vv02s0012g00910.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA01G40700.1 (Glycine max), 3'ss of exon 3
tgtattaatcaccatgtaacaaatgaaagggt--gcactatattcatg-cagcattgtaatcattatgtaaat--ggatgagtgtttgatactctgaacttgcagAAATCATGGACTTTGGTTATCCACAAAATCTTTCTCCAGAAATTTTGAAGCTCTACATCACCCAAGAAGGAGTTCGGTCTCCATTCTCATCCAAG
    | || |      ||| || | ||||       | | |  |||||  || |   || | || || | |||  | ||| || | |||||   |  | || ||||||||||||||||||||||||| ||||||||||| || ||||| || ||||| || ||||| || |||||||| || || ||||| |||||||||
---ttcaaactttgcataataa-taaaagacccaatagtgttctcatgatagaaaaatatttatcatttgaatttgaatgtgtttatgataaa-tatatttacagAAATCATGGACTTTGGTTATCCTCAAAATCTTTCACCGGAAATCTTAAAGCTTTATATCACTCAGGAAGGAGTGCGTTCCCCATTTTCATCCAAG

upper sequence: Vv02s0012g00910.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA11G04600.1 (Glycine max), 3'ss of exon 3
tgtattaatcaccatgtaacaa-atgaaagggtgcactatattcatg-cagcattgtaatcattatgtaaatggatgagtgtttgatactc---tgaacttgcagAAATCATGGACTTTGGTTATCCACAAAATCTTTCTCCAGAAATTTTGAAGCTCTACATCACCCAAGAAGGAGTTCGGTCTCCATTCTCATCCAAG
      || |      ||| || |  | |      | | |  ||||| ||| |   || | || || | ||||| |   || |  ||| |       | |||||||||||||||||||||||||||| ||||||||||| || ||||| || ||||| || ||||| || |||||||| || || ||||| || ||||||
-----caaactttgcttaataataaaagaccaaatagtgttctcatgacagaaaaatatttatcatttgaatgggtttatgataaatatttacacatatttgcagAAATCATGGACTTTGGTTATCCTCAAAATCTTTCACCGGAAATCTTAAAGCTTTATATCACTCAGGAAGGAGTGCGTTCCCCATTTTCTTCCAAG

upper sequence: Vv02s0012g00910.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT5G46630.2 (Arabidopsis thaliana), 3'ss of exon 3
----------------------tgtattaatcaccatgt-aacaaatgaaagggtgcacta-tattcatgcagcattgtaatcattatgtaaatggatgagtgtttgatactctgaacttgcagAAATCATGGACTTTGGTTATCCACAAAATCTTTCTCCAGAAATTTTGAAGCTCTACATCACCCAAGAAGGAGTTCGGTCTCCATTCTCATCCAAG
                      ||    ||||||  | | | ||  || || | |||| || |  | ||     ||| || |   |    | |   |||| || |   |  | |  | ||||||| || ||||||||||| |||||||||||||| || || |||||||| || || || ||||| || ||||| || ||||| ||||| ||||| |||
gtaagtaagcctgatagggtcatgatcaaatcactttcttatcacttgtaaagttgcattagtcgttatatgttattctattttgtggtaacaccaatgaatgatattttgtattgaattgcagAGATTATGGACTTTGGCTATCCACAAAATCTCTCACCTGAAATTTTAAAACTTTATATCACTCAGGAAGGTGTACGGTCACCATTTTCATCGAAG

upper sequence: Vv02s0012g00910.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S197_28V6.1 (Physcomitrella patens), 3'ss of exon 3
tgtattaatcaccatgtaacaaatgaaagggtgcactatattcatg--cagcattgtaatcattatgtaaatggatgagtgtt--tgatact----ctgaacttgcagAAATCATGGACTTTGGTTATCCACAAAATCTTTCTCCAGAAATTTTGAAGCTCTACATCACCCAAGAAGGAGTTCGGTCTCCATTCTCATCCAAG
       || | | | || |   | |  | |  ||| |  ||||||  | |  || || |  || |  |  |       ||||  ||| |        |  |||||||||||||||||||| || ||||| |||||  | |||||||| ||||||||||| ||||| || ||||| || ||||| ||||||||||||||||||
------gatgagctt-tatctcgtcatggtgaccac-aggttcatgatcggacttttatttcttgttgacgtattcatatgttactgacatcaatgtcgttcttgcagAAATCATGGACTTCGGGTATCCTCAAAACTTGTCTCCAGAGATTTTGAAGCTTTACATTACTCAAGAGGGTGTTCGTTCTCCATTCTCATCCAAG

upper sequence: Vv02s0012g00910.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ22278 (Selaginella moellendorffii), 3'ss of exon 3
tgtattaatcaccatgtaacaaatgaaagggtgcactatattcatgcagcattgtaatcattatgtaaatggatgagtgtttgatactctgaacttgcagAAATCATGGACTTTGGTTATCCACAAAATCTTTCTCCAGAAATTTTGAAGCTCTACATCACCCAAGAAGGAGTTCGGTCTCCATTCTCATCCAAG
                                                | ||| |  |  ||   |  |||||  | |  |      | ||||  |||||| |||||||||||||| || || |||||||||||||| || |||||||||||||| || || || || || ||||| || ||||||||    |||
------------------------------------------------gtattttcgt--ttggtttcatggaaaattcatcacgcttttgaatgtgcagAGATCATGGACTTTGGATACCCGCAAAATCTTTCTCCTGAGATTTTGAAGCTCTATATAACTCAGGAGGGTGTTCGTTCGCCATTCTCG---AAG

upper sequence: Vv02s0012g00910.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ25669 (Selaginella moellendorffii), 3'ss of exon 3
tgtattaatcaccatgtaacaaatgaaagggtgcactatattcatgcagcattgtaatcattatgtaaatggatgagtgtttgatactct--gaacttgcagAAATCATGGACTTTGGTTATCCACAAAATCTTTCTCCAGAAATTTTGAAGCTCTACATCACCCAAGAAGGAGTTCGGTCTCCATTCTCATCCAAG
                                                    | |  || ||  ||   | |   | |   | | ||| |   ||  |||||| |||||||||||||| || || |||||||||||||| || |||||||||||||| || || || || || ||||| || ||||||||    |||
---------------------------------------------------gtattttcgtttggtttctcggaaaattcatcacacttttgaaatgtgcagAGATCATGGACTTTGGATACCCGCAAAATCTTTCTCCTGAGATTTTGAAGCTCTATATAACTCAGGAGGGTGTTCGTTCGCCATTCTCG---AAG

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|71860461|gb|DT009516.1|DT009516
EST:     TGAAGATGCTATTCGTAACAACTTTGTTCTGATTTATGAGCTATTGGATG                         AAATCATGGACTTTGGTTATCCACAAAATCTTTCTCCAGAAATT
genomic: TGAAGATGCTATTCGTAACAACTTTGTTCTGATTTATGAGCTATTGGATGgtatgcaatt ... gaacttgcagAAATCATGGACTTTGGTTATCCACAAAATCTTTCTCCAGAAATT
EST: gi|71864801|gb|DT013856.1|DT013856
EST:     TGAAGATGCTATTCGTAACAACTTTGTTCTGATTTATGAGCTATTGGATG                         AAATCATGGACTTTGGTTATCCACAAAATCTTTC
genomic: TGAAGATGCTATTCGTAACAACTTTGTTCTGATTTATGAGCTATTGGATGgtatgcaatt ... gaacttgcagAAATCATGGACTTTGGTTATCCACAAAATCTTTC
EST: gi|71863379|gb|DT012434.1|DT012434
EST:     TGAAGATGCTATTCGTAACAACTTTGTTCTGATTTATGAGCTATTGGATG                         AAATCATGGACTTTGGTTATCCACAAAATCTTTCTCCAGAAATTTTGAAGC
genomic: TGAAGATGCTATTCGTAACAACTTTGTTCTGATTTATGAGCTATTGGATGgtatgcaatt ... gaacttgcagAAATCATGGACTTTGGTTATCCACAAAATCTTTCTCCAGAAATTTTGAAGC
EST: gi|161712815|gb|FC062338.1|FC062338
EST:     TGAAGATGCTATTCGTAACAACTTTGTTCTGATTTATGAGCTATTGGATG                         AAATCATGGACTTTGGTTATCCACAAAATCTTTCTCCAGAAATTTTGAAGC
genomic: TGAAGATGCTATTCGTAACAACTTTGTTCTGATTTATGAGCTATTGGATGgtatgcaatt ... gaacttgcagAAATCATGGACTTTGGTTATCCACAAAATCTTTCTCCAGAAATTTTGAAGC
EST: gi|71863591|gb|DT012646.1|DT012646
EST:     TGAAGATGCTATTCGTAACAACTTTGTTCTGATTTATGAGCTATTGGATG                         AAATCATGGACTTTGGTTATCCACAAAATCTTTCTCC
genomic: TGAAGATGCTATTCGTAACAACTTTGTTCTGATTTATGAGCTATTGGATGgtatgcaatt ... gaacttgcagAAATCATGGACTTTGGTTATCCACAAAATCTTTCTCC
EST: gi|71857060|gb|DT006115.1|DT006115
EST:     TGAAGATGCTATTCGTAACAACTTTGTTCTGATTTATGAGCTATTGGATG                         AAATCATGGACTTTGGTTATCCACAAAATCTTTCTCCAGAAATTTTGAAGC
genomic: TGAAGATGCTATTCGTAACAACTTTGTTCTGATTTATGAGCTATTGGATGgtatgcaatt ... gaacttgcagAAATCATGGACTTTGGTTATCCACAAAATCTTTCTCCAGAAATTTTGAAGC
EST: gi|352777816|gb|FQ466869.1|FQ466869
EST:     TGAAGATGCTATTCGTAACAACTTTGTTCTGATTTATGAGCTATTGGATG                         AAATCATGGACTTTGGTTATCCACAAAATCTTTCTCCAGAAATTTTGAAGC
genomic: TGAAGATGCTATTCGTAACAACTTTGTTCTGATTTATGAGCTATTGGATGgtatgcaatt ... gaacttgcagAAATCATGGACTTTGGTTATCCACAAAATCTTTCTCCAGAAATTTTGAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcagcattgtaatcattatgtaaatggatgagtgtttgatactctgaacttgcagAAATCATGGACTTTGGTTATCCACAAAATCTTTCTCCAGAAATTTTGAAGCTCTACATCACCCAAGAAGGAGTTCGGTCTCCATTCTCATCCAAG
                                 gtttgat  putative branch site (score: 5)
         taatcattatgtaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtattaatcaccatgtaacaaatgaaagggtgcactatattcatgcagcattgtaatcattatgtaaatggatgagtgtttgatactctgaacttgcagAAATCATGGACTTTGGTTATCCACAAAATCTTTCTCCAGAAATTTTGAAGCTCTACATCACCCAAGAAGGAGTTCGGTCTCCATTCTCATCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - -ccatgta
- - - - - - - - - - aaatgaa
- - - - - - - - - - - - - - - - - - - - -tcatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaatgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgagtgt