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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgcttttggcttttaaagttcatcaagttgtgaaaaaaacatttgttatctgtgaaagttcctgatatgaattggcgtatccatgcagTTGGTGGAGTGATGGCTTTTCTTACCTTGCATGAAATGCTGCCATTGGCATTTGACTATGCTGGGCCGAAGCAAGCTGTCAAGGCAGTCTTCTTTGGAAT

Basic information

species Vitis vinifera
transcript Vv06s0004g01860.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g01860.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os02g10230.1 (Oryza sativa), 3'ss of exon 10
gtttgcttttggcttttaaagttcatcaagttgtgaaaaaaacatttgttatctgt-----gaaagttcctgatatgaattggcgtatccatgcagTTGGTGGAGTGATGGCTTTTCTTACCTTGCATGAAATGCTGCCATTGGCATTTGACTATGCTGGGCCGAAGCAAGCTGTCAAGGCAGTCTTCTTTGGAAT
                    ||   ||   |  | |||| || |  || |||| ||     | |  ||  |||  |    ||  |  |   |||||||||||| || ||||| || || || |||||||||||| | ||  | ||||||||||||||||| |  || || |||||||| ||||||||  |||| ||
--------------------gtcagtctgttaataaaaagaaaaactggtatcagtattctgcattttgttgacctcccatg-tgcctttctgcagTTGGTGGGGTTATGGCCTTCCTCACTTTGCATGAAATGTTACCTCTAGCATTTGACTATGCTGGTCAAAAACAGGCTGTCAAAGCAGTCTTTGTTGGCAT

upper sequence: Vv06s0004g01860.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G050484_T01 (Zea mays), 3'ss of exon 10
gtttgcttttggcttttaaagttcatcaagttgtgaaaaaaacatttgttatctgtgaa------agttcctgatatgaattggcgtatccatgcagTTGGTGGAGTGATGGCTTTTCTTACCTTGCATGAAATGCTGCCATTGGCATTTGACTATGCTGGGCCGAAGCAAGCTGTCAAGGCAGTCTTCTTTGGAAT
                   ||| | | | |   |  || |   ||||||||| | |  |      ||| |    |     |  | |  |   |||||| ||||| || |||||||| || || |||||||||||||||||  | ||||||||||||  ||| | ||||||||||||||| || |||||  | || ||
----------------gtcagtccgttaggaaattgaatag-tatttgttatgtttccatacctgagtactctgttgacttctgtgcctttgtgcagTGGGTGGTGTCATGGCTTTCCTCACTTTGCATGAAATGCTGCCTCTTGCATTTGACTATTGTGGCCAGAAGCAAGCTGTCAAAGCTGTCTTTGTGGGCAT

upper sequence: Vv06s0004g01860.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA15G03820.2 (Glycine max), 3'ss of exon 10
gtttgcttttggcttttaaagttcatcaagttgtgaaaaaaacatttgttatctgtgaaagt-tcctgatatgaattggcgtatcca--tgcagTTGGTGGAGTGATGGCTTTTCTTACCTTGCATGAAATGCTGCCATTGGCATTTGACTATGCTGGGCCGAAGCAAGCTGTCAAGGCAGTCTTCTTTGGAAT
      |||    |  || ||    |  |  |   ||   ||  ||||  || | |   | | | | ||| |||  |    |    |  | ||||||||||||| ||||||||||| ||| | |||||||||||||||||||| ||||| ||||| || | ||||||| |||| ||||| ||||| || || ||
-----gtttgcaatgatacagcatgtagatgtcacaatggaatttttggcatttattttattatgcagatttgacctatgatgattaattacagTTGGTGGAGTTATGGCTTTTCTGACCCTTCATGAAATGCTGCCATTGGCTTTTGATTATGCGGGACAGAAGCAATCTGTTAAGGCTGTCTTTTTGGGGAT

upper sequence: Vv06s0004g01860.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA13G41580.1 (Glycine max), 3'ss of exon 10
gtttgcttttggcttttaaagttcatcaagttgtgaaaaaaacatttgttatctgtgaaagt-tcctgatatgaattggcgtatcca--tgcagTTGGTGGAGTGATGGCTTTTCTTACCTTGCATGAAATGCTGCCATTGGCATTTGACTATGCTGGGCCGAAGCAAGCTGTCAAGGCAGTCTTCTTTGGAAT
        || ||  | | |   |||| || ||| |    ||  ||||  || | ||    | | | ||| |||  |    |    |  | ||||||||||||| ||||||||||| ||| | ||||||||||| |||||||| ||||| ||||| || | ||||||| |||| ||||| ||||| || || ||
-------gtttgcaatgatacagcatctagatgtcactggaatctttggcatttatgtttttatgcagatttgatctatgatgattaattacagTTGGTGGAGTTATGGCTTTTCTGACCCTTCATGAAATGCTTCCATTGGCTTTTGATTATGCGGGACAGAAGCAATCTGTGAAGGCTGTCTTTTTGGGGAT

upper sequence: Vv06s0004g01860.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA11G14090.1 (Glycine max), 3'ss of exon 8
gtttgcttttggcttttaaagttcat-caagttgtgaaaaaaacatttgttatctgtgaaagttcctgatatgaattggcgtatccatgcagTTGGTGGAGTGATGGCTTTTCTTACCTTGCATGAAATGCTGCCATTGGCATTTGACTATGCTGGGCCGAAGCAAGCTGTCAAGGCAGTCTTCTTTGGAAT
               |||    | || ||| || |       ||||||  | | || | |  ||  | |    | || |  ||     |||||||||||||| ||||||||||| ||| | ||||| ||||||||| | || ||||| ||||| || |  || ||| |||| ||||| ||||| | ||||||
--------------gttagtactaatacaatttctagttgtcacattttgtttttgggcactttattaagtatattttgatta-----gcagTTGGTGGAGTTATGGCTTTTCTAACCCTTCATGAGATGCTGCCACTTGCTTTTGAGTATGCGGGACAAAAACAATCTGTTAAGGCCGTCTTTTGTGGAAT

upper sequence: Vv06s0004g01860.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT3G20870.1 (Arabidopsis thaliana), 3'ss of exon 10
gtttgcttttggcttttaaagttcatcaagttgtgaaaaaaacatttgttatctgtgaaagttcctgatatgaa-ttggcgtatcca---tgcagTTGGTGGAGTGATGGCTTTTCTTACCTTGCATGAAATGCTGCCATTGGCATTTGACTATGCTGGGCCGAAGCAAGCTGTCAAGGCAGTCTTCTTTGGAAT
   |   |  |  || |  ||   ||| |    | |||  || ||   ||   ||  |||     ||||   ||  ||  || |  |   ||||||||||||| | |||||||| || || ||||| |||||||| || ||||||||||| ||||| || | ||| |||||||| || || || || ||||| ||
--gtaagtaggaattctgcagcaaatcgatactttaaactaaaatc-attggatggaaaacgaattgatgcaaaactgttgtttgtatgatgcagTTGGTGGAATCATGGCTTTCCTAACATTGCACGAAATGCTTCCTTTGGCATTTGATTATGCGGGACAGAAACAAGCTGTGAAAGCTGTGTTTTTTGGCAT

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|30251805|gb|CB969538.1|CB969538
EST:     GTTCCCAAGCAGCTTGAATCCAGAAATTCTTGAGGGCCTGTTAGGATCAG                         TTGGTGGAGTGATGGCTTTTCTTACCTTGCATGAAATGCTGCCATTGGCAT
genomic: GTTCCCAAGCAGCTTGAATCCAGAAATTCTTGAGGGCCTGTTAGGATCAGgtttgctttt ... atccatgcagTTGGTGGAGTGATGGCTTTTCTTACCTTGCATGAAATGCTGCCATTGGCAT
EST: gi|110693658|gb|EE070084.1|EE070084
EST:     GTTCCCAAGCAGCTTGAATCCAGAAATTCTTGAGGGCCTGTTAGGATCAG                         TTGGTGGAGTGATGGCTTTTCTTACCTTGCATGAAATGCTGCCATTGGCAT
genomic: GTTCCCAAGCAGCTTGAATCCAGAAATTCTTGAGGGCCTGTTAGGATCAGgtttgctttt ... atccatgcagTTGGTGGAGTGATGGCTTTTCTTACCTTGCATGAAATGCTGCCATTGGCAT
EST: gi|30251808|gb|CB969541.1|CB969541
EST:     GTTCCCAAGCAGCTTGAATCCAGAAATTCTTGAGGGCCTGTTAGGATCAG                         TTGGTGGAGTGATGGCTTTTCTTACCTTGCATGAAATGCTGCCATTGGCAT
genomic: GTTCCCAAGCAGCTTGAATCCAGAAATTCTTGAGGGCCTGTTAGGATCAGgtttgctttt ... atccatgcagTTGGTGGAGTGATGGCTTTTCTTACCTTGCATGAAATGCTGCCATTGGCAT
EST: gi|110382518|gb|EC946816.1|EC946816
EST:     GTTCCCAAGCAGCTTGAATCCAGAAATTCTTGAGGGCCTGTTAGGATCAG                         TTGGTGGAGTGATGGCTTTTCTTACCTTGCATGAAATGCTGCCATTGGCAT
genomic: GTTCCCAAGCAGCTTGAATCCAGAAATTCTTGAGGGCCTGTTAGGATCAGgtttgctttt ... atccatgcagTTGGTGGAGTGATGGCTTTTCTTACCTTGCATGAAATGCTGCCATTGGCAT
EST: gi|110693804|gb|EE070356.1|EE070356
EST:     GTTCCCAAGCAGCTTGAATCCAGAAATTCTTGANGGCCTGTTAGGATCAG                         TTGGTGGAGTGATGGCTTTTCTTACCTTGCATNGAA-TGCTGCCATTGGCA
genomic: GTTCCCAAGCAGCTTGAATCCAGAAATTCTTGAGGGCCTGTTAGGATCAGgtttgctttt ... atccatgcagTTGGTGGAGTGATGGCTTTTCTTACCTTGCAT-GAAATGCTGCCATTGGCA
EST: gi|110689440|gb|EE065664.1|EE065664
EST:     TTCCCAAGCAGCTTGAATCCANAAATTCTTGGAGGGC-TGTTANGATCAN                         TTGGTGGAGTGATGGCTTTTCTTACCTTGCATG
genomic: TTCCCAAGCAGCTTGAATCCAGAAATTCTTG-AGGGCCTGTTAGGATCAGgtttgctttt ... atccatgcagTTGGTGGAGTGATGGCTTTTCTTACCTTGCATG
EST: gi|110698572|gb|EE076222.1|EE076222
EST:     GTTCCCAAGCAGCTTGAATCCGGAAATTCTTGAGGGCCTGTTAAGATCAG                         TTGGTGGAGTGATGGCTTTTCTTACCTTGCATGAA-TGGCTGCC-TTGGCA
genomic: GTTCCCAAGCAGCTTGAATCCAGAAATTCTTGAGGGCCTGTTAGGATCAGgtttgctttt ... atccatgcagTTGGTGGAGTGATGGCTTTTCTTACCTTGCATGAAATG-CTGCCATTGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaaacatttgttatctgtgaaagttcctgatatgaattggcgtatccatgcagTTGGTGGAGTGATGGCTTTTCTTACCTTGCATGAAATGCTGCCATTGGCATTTGACTATGCTGGGCCGAAGCAAGCTGTCAAGGCAGTCTTCTTTGGAAT
                          tcctgat  putative branch site (score: 3)
       atttgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgcttttggcttttaaagttcatcaagttgtgaaaaaaacatttgttatctgtgaaagttcctgatatgaattggcgtatccatgcagTTGGTGGAGTGATGGCTTTTCTTACCTTGCATGAAATGCTGCCATTGGCATTTGACTATGCTGGGCCGAAGCAAGCTGTCAAGGCAGTCTTCTTTGGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG