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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgctcggaaaactaatttattgggaagaaatgttctccacataaatagagcctcataaaaaagaagctaatcttgtcatggtttggcattcctgcacagATGGATCGCATACTTGCTGCATATCGGAAGTCCTCAAAACAGTGGTCATCCACATTGAATAAGCTAGCTCAAG

Basic information

species Vitis vinifera
transcript Vv07s0151g00550.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0151g00550.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA17G04930.1 (Glycine max), 3'ss of exon 5
atgctcggaaaactaatttattgggaagaaatgttctccacataaatagagcctcataaaaaagaagctaatc--ttgtcatggtttggcatt--------cctgcacagATGGATCGCATACTTGCTGCATATCGGAAGTCCTCAAAACAGTGGTCATCCACATTGAATAAGCTAGCTCAAG
       |||  || |||  |    || |  || | || || || | | ||  | || || ||| |   |||    || |||  |||   |||         ||| |||||||||||  ||||||||||||||  ||||||| ||||| |||||||||||||||||||| ||||| || ||||
------tgaagccttattcttctataata--tgctttctacttagacaaag--ttatgaacaagtaatcaattggctgacattttttaatattggattttgtctggacagATGGATCAGATACTTGCTGCATACAGGAAGTCATCAAAGCAGTGGTCATCCACATTGAACAAGCTGGCACAAG

upper sequence: Vv07s0151g00550.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA18G06300.1 (Glycine max), 3'ss of exon 5
atgctcggaaaactaatttattgggaagaaatgttc--tccacataaatagagcctcataaaaaagaagctaatc--ttgtcatggtttggcatt---------cctgcacagATGGATCGCATACTTGCTGCATATCGGAAGTCCTCAAAACAGTGGTCATCCACATTGAATAAGCTAGCTCAAG
            || |||  |    || |    |||     | | ||| | |   || | || ||| | | |||    || |||  |||   |||          ||| |||||||||||  ||||||||||||||  ||||||| ||||| || ||||||||||||||||| || || || ||| 
-----------ccttattcttctataatatgctttcaacttagacaaacaaaagttc-tgaataagtaaccaattgactgacattttttaatattggatttttgtctggacaGATGGATCAGATACTTGCTGCATACAGGAAGTCATCAAAGCAATGGTCATCCACATTGAACAAACTTGCACAA-

upper sequence: Vv07s0151g00550.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA02G34690.1 (Glycine max), 3'ss of exon 5
--atgctcggaaaactaatttattgggaagaaatgttctccacataaatagagcctcataaaaaagaagctaatcttgtcatggtttggcattcctgcacagATGGATCGCATACTTGCTGCATATCGGAAGTCCTCAAAACAGTGGTCATCCACATTGAATAAGCTAGCTCAAG
   |       |  ||   |  || |  | | |||||      || || ||    |||  |  |||   |  ||  | |    ||||    |  |||  |||||||||   |||||||||||||| || ||||| ||||| ||||| |||||||||||||| || ||||| ||||
tcttctataatatgctttctgctttgacaaacatgtt------atgaacaggtaatca--attaagtgacatataatatttgagtttt---tatctgggcagatggattagATACTTGCTGCATACCGCAAGTCATCAAAGCAGTGCTCATCCACATTGAACAAACTAGCACAAG

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|26265932|gb|CA816995.1|CA816995
EST:     ATGTACTTGAGCGGGCCTTGCTATCAATGCATTCTTCATGTGGGAATGTG                         ATGGATCGCATACTTGCTGCATATCGGAAGTCCTCAAAACAGTGGTCATCC
genomic: ATGTACTTGAGCGGGCCTTGCTATCAATGCATTCTTCATGTGGGAATGTGgtaagtgaag ... tcctgcacagATGGATCGCATACTTGCTGCATATCGGAAGTCCTCAAAACAGTGGTCATCC
EST: gi|110727233|gb|EE103760.1|EE103760
EST:     TGTACTTGAGCGGGCCTTGCTATCAATGCATTCTTCATGGTGGGAATGTG                         ATGGATCGCATACCTGCTGCATATCGGAAGTC-TCCAAACAGTGGGCATCC
genomic: TGTACTTGAGCGGGCCTTGCTATCAATGCATTCTTCATG-TGGGAATGTGgtaagtgaag ... tcctgcacagATGGATCGCATACTTGCTGCATATCGGAAGTCCTCAAAACAGTGGTCATCC
EST: gi|37188657|gb|CF608006.1|CF608006
EST:     ATGTACTTGAGCGGGCCTTGCTATCAATGCATTCTTCATGTGGGAATGTG                         ATGGATCGCATACTTGCTGCATATCGGAAGTCCTCAAAACAGTGGTCATCC
genomic: ATGTACTTGAGCGGGCCTTGCTATCAATGCATTCTTCATGTGGGAATGTGgtaagtgaag ... tcctgcacagATGGATCGCATACTTGCTGCATATCGGAAGTCCTCAAAACAGTGGTCATCC
EST: gi|28958875|gb|CB339437.1|CB339437
EST:     ATGTACTTGAGCGGGCCTTGCTATCAATGCATTCTTCATGTGGGAATGTG                         ATGGATCGCATACTTGCTGCATATCGGAAGTCCTCAAAACAGTGGTCATCC
genomic: ATGTACTTGAGCGGGCCTTGCTATCAATGCATTCTTCATGTGGGAATGTGgtaagtgaag ... tcctgcacagATGGATCGCATACTTGCTGCATATCGGAAGTCCTCAAAACAGTGGTCATCC
EST: gi|27581764|gb|CB004459.1|CB004459
EST:     ATGTACTTGAGCGGGCCTTGCTATCAATGCATTCTTCATGTGGGAATGTG                         ATGGATCGCATACTTGCTGCATATCGGAAGTC
genomic: ATGTACTTGAGCGGGCCTTGCTATCAATGCATTCTTCATGTGGGAATGTGgtaagtgaag ... tcctgcacagATGGATCGCATACTTGCTGCATATCGGAAGTC
EST: gi|28959679|gb|CB339840.1|CB339840
EST:     ATGTACTTGAGCGGGCCTTGCTATCAATGCATTCTTCATGNNGGAATGTG                         ATGGATCGCATACTTGCTGCATATNNNAAGTCCTCAAAACAGTGGTCATCC
genomic: ATGTACTTGAGCGGGCCTTGCTATCAATGCATTCTTCATGTGGGAATGTGgtaagtgaag ... tcctgcacagATGGATCGCATACTTGCTGCATATCGGAAGTCCTCAAAACAGTGGTCATCC
EST: gi|26257835|gb|CA808898.1|CA808898
EST:     ATGTACTTGAGCGGGCCTTGCTATCAATGCATTCTTCATGTGGGAATGTG                         ATGGATCGCATACTTGCTGCATATCGGAAGTCCTCAAAACAGTGGTCATCC
genomic: ATGTACTTGAGCGGGCCTTGCTATCAATGCATTCTTCATGTGGGAATGTGgtaagtgaag ... tcctgcacagATGGATCGCATACTTGCTGCATATCGGAAGTCCTCAAAACAGTGGTCATCC
EST: gi|26258595|gb|CA809658.1|CA809658
EST:     ATGTACTTGAGCGGGCCTTGCTATCAATGCATTCTTCATGTGGGAATGTG                         ATGGATCGCATACTTGCTGCATATCGGAAGTCCTCAAAACAGTGGTCATCC
genomic: ATGTACTTGAGCGGGCCTTGCTATCAATGCATTCTTCATGTGGGAATGTGgtaagtgaag ... tcctgcacagATGGATCGCATACTTGCTGCATATCGGAAGTCCTCAAAACAGTGGTCATCC
EST: gi|30126284|gb|CB911623.1|CB911623
EST:     ATGTACTTGAGCGGGCCTTGCTATCAATGCATTCTTCATGTGGGAATGTG                         ATGGATCGCATACTTGCTGCATATCGGAAGTCCTCCGAACAGTGGTCATCC
genomic: ATGTACTTGAGCGGGCCTTGCTATCAATGCATTCTTCATGTGGGAATGTGgtaagtgaag ... tcctgcacagATGGATCGCATACTTGCTGCATATCGGAAGTCCTCAAAACAGTGGTCATCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagagcctcataaaaaagaagctaatcttgtcatggtttggcattcctgcacagATGGATCGCATACTTGCTGCATATCGGAAGTCCTCAAAACAGTGGTCATCCACATTGAATAAGCTAGCTCAAG
                    agctaat  putative branch site (score: 3)
                                          cattcct  putative PPT
          ataaaaaagaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgctcggaaaactaatttattgggaagaaatgttctccacataaatagagcctcataaaaaagaagctaatcttgtcatggtttggcattcctgcacagATGGATCGCATACTTGCTGCATATCGGAAGTCCTCAAAACAGTGGTCATCCACATTGAATAAGCTAGCTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - -aaactaa
- - - - - - - - - - - -ggaagaa
- - - - - - - - - - - - - - - - - -ctccaca
- - - - - - - - - - - - - - - - - - - - - - - - -agcctca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - taaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtttgg