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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatcattagcaacaccatccattctgttatgtttgcttgtagtagcagactaagaaagaaatattagactaaacatatggtatgggtgcatgcagGTGGGTACGGTGGGAGGTGGCACCCAACTGGCATCTCAGTCAGCTTGCCTGAACCTACTAGGTGTAAAGGGTGCAAGCAAAGAGTCTCCAGGGTCAAACT

Basic information

species Vitis vinifera
transcript Vv04s0044g01740.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0044g01740.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA01G36080.1 (Glycine max), 3'ss of exon 3
gtaaatcattagcaacaccatccattctgttatgtttgcttg-tagtagcagactaagaaagaaatattagactaaacatatggtatgggtgcat---gcagGTGGGTACGGTGGGAGGTGGCACCCAACTGGCATCTCAGTCAGCTTGCCTGAACCTACTAGGTGTAAAGGGTGCAAGCAAAGAGTCTCCAGGGTCAAACT
   ||  |||        | |  ||| || |   |  |  |  || ||   |      |    |   ||  | |  | ||| |  | || |  ||   |||||||||||| || ||||| ||||| |||||||| ||||| ||||| ||||| ||  ||||||| ||||||||||| ||||||||||| |||||  |||| |
--caaaaattgcttgtgtctttgattatgatccctgagaataataataatggcaatgcatgccacctttcaatttgatatacgtcacggtttaatggtgcagGTGGGTACAGTTGGAGGGGGCACACAACTGGCGTCTCAATCAGCATGCCTTAATTTACTAGGAGTAAAGGGTGCGAGCAAAGAGTCCCCAGGTGCAAATT

upper sequence: Vv04s0044g01740.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA11G09330.1 (Glycine max), 3'ss of exon 3
gtaaatcattagcaacaccatccattctgttatgtttgcttgtagtagca--gactaagaaagaaatattagacta-aacatatggtatgggtgcat---gcagGTGGGTACGGTGGGAGGTGGCACCCAACTGGCATCTCAGTCAGCTTGCCTGAACCTACTAGGTGTAAAGGGTGCAAGCAAAGAGTCTCCAGGGTCAAACT
   | |||  | |     | |  | |  |||||| |  ||   | ||  |  | | | | | |  |  ||  | |   | ||| |  |||| |  ||   |||||||||||| || ||||| ||||| ||||| || ||||||||||| ||||| ||  || |||| ||||||||||| ||||||||||| |||||  |||| |
---agtcaagaactg-gtcgtgtactaggttatgatccctgagaataataatgccaatgcatgccacctttcaatgtgatatacgtcatggtttaatggtgcagGTGGGTACAGTTGGAGGGGGCACACAACTTGCGTCTCAGTCAGCATGCCTTAATTTATTAGGAGTAAAGGGTGCGAGCAAAGAGTCCCCAGGTGCAAATT

upper sequence: Vv04s0044g01740.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA09G32850.1 (Glycine max), 3'ss of exon 7
---gtaaatcattagcaacaccatccat-tctgttatgt-ttgcttgtagtagcagactaagaaagaaatattagactaaacatatggtatgggtgcatgcagGTGGGTACGGTGGGAGGTGGCACCCAACTGGCATCTCAGTCAGCTTGCCTGAACCTACTAGGTGTAAAGGGTGCAAGCAAAGAGTCTCCAGGGTCAAACT
   || | | |||    |   ||| | | ||    |||| ||| |  |  |    || | |     |  ||      |  |    |  |||   | |   ||||| ||||| || ||||||||||| ||||| |||||||||||||| || || ||  |||| ||||| |||||||| | |||||| ||||| ||  |||| |
gcagtgagt-attgtacatggcatacttatccaccatgtgttgatatttctttgggaatgaattcaacctaacctgttttattcttaatataatttct--cagGTTGGTACTGTTGGAGGTGGCACACAACTCGCATCTCAGTCAGCATGTCTTAATTTACTTGGTGTCAAGGGTGCCAACAAAGAATCTCCGGGTGCAAATT

upper sequence: Vv04s0044g01740.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA16G21620.1 (Glycine max), 3'ss of exon 4
--gtaaatcattagcaacaccatccattctgttatgtttgcttgtagtagcagactaagaaagaaatattagactaaacatatggtatgggtg-catgcagGTGGGTACGGTGGGAGGTGGCACCCAACTGGCATCTCAGTCAGCTTGCCTGAACCTACTAGGTGTAAAGGGTGCAAGCAAAGAGTCTCCAGGGTCAAACT
   |   | |||   |     || | |||  || | ||   ||| |     |  |  |   ||    |  | | | |  | ||  |    |||     ||||| ||||| || ||||| ||||| ||||| |||||||||||||| || || ||  |||| ||||| |||||||| |  ||||| ||||| ||  |||| |
acctgttttattcttactttaattccttccttttt-ttcaattgcacccataagcataactagcttcaggataatgataacatcctccttgtggttctcagGTTGGTACTGTTGGAGGCGGCACACAACTCGCATCTCAGTCAGCATGTCTTAATTTACTTGGTGTCAAGGGTGCCAATAAAGAATCTCCCGGTGCAAATT

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|34548984|gb|CF517216.1|CF517216
EST:     TGAATGATGGGAAGGACCTTCATATCTCAGTCACCATGCCTTCCATTGAG                         GTGGGTACGGTGGGAGGTGGCACCCAACTGGCATCTCAGTCAGCTTGCCTG
genomic: TGAATGATGGGAAGGACCTTCATATCTCAGTCACCATGCCTTCCATTGAGgtaaatcatt ... gtgcatgcagGTGGGTACGGTGGGAGGTGGCACCCAACTGGCATCTCAGTCAGCTTGCCTG
EST: gi|34549509|gb|CF517741.1|CF517741
EST:     TGAATGATGGGAAGGACCTTCATATCTCAGTCACCATGCCTTCCATTGAG                         GTGGGTACGGTGGGAGGTGGCACCCAACTGGCATCTCAGTCAGCTTGCCTG
genomic: TGAATGATGGGAAGGACCTTCATATCTCAGTCACCATGCCTTCCATTGAGgtaaatcatt ... gtgcatgcagGTGGGTACGGTGGGAGGTGGCACCCAACTGGCATCTCAGTCAGCTTGCCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtagcagactaagaaagaaatattagactaaacatatggtatgggtgcatgcagGTGGGTACGGTGGGAGGTGGCACCCAACTGGCATCTCAGTCAGCTTGCCTGAACCTACTAGGTGTAAAGGGTGCAAGCAAAGAGTCTCCAGGGTCAAACT
                          gactaaa  putative branch site (score: 2)
          taagaaagaaatatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatcattagcaacaccatccattctgttatgtttgcttgtagtagcagactaagaaagaaatattagactaaacatatggtatgggtgcatgcagGTGGGTACGGTGGGAGGTGGCACCCAACTGGCATCTCAGTCAGCTTGCCTGAACCTACTAGGTGTAAAGGGTGCAAGCAAAGAGTCTCCAGGGTCAAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG