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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggcattatataaggggaattgtcatatgacaatagttccaaaattataggggacacaatgctgcattcttaattaattttaaaatttttgttggtgcagTAACTGATGCGATCTCAATATTGGGGGAATACTTGGAGGATGAGCCTTGGTTGAAGCTTTTGTGTGACCATCTAAA

Basic information

species Vitis vinifera
transcript Vv04s0008g03180.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g03180.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA06G08230.3 (Glycine max), 3'ss of exon 8
aggcattatataaggggaattgtcatatgacaatagttccaaaattataggggacacaatgctgcattcttaattaattttaaaatttttgt-----tggtgcagTAACTGATGCGATCTCAATATTGGGGGAATACTTGGAGGATGAGCCTTGGTTGAAGCTTTTGTGTGACCATCTAAA
    | |||  | |  ||    ||   | | | | |      |  | | ||        |    || | ||  |     ||||  |  ||||     || |||||| | ||||||  |||| ||||| || || || ||| ||||  ||||||||||| ||||||||||||||||||| ||
----aatattaatgtagatgcttctcttaatacttgaaatgcacctct-ggtctttttctatcacagttttgctgtgcattaacgtacttgtgttactgatgcagTGATTGATGCAGTCTCCATATTAGGAGAGTATTTGAAGGAAAAGCCTTGGTTGCAGCTTTTGTGTGACCATCTTAA

upper sequence: Vv04s0008g03180.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA04G08160.1 (Glycine max), 3'ss of exon 4
----aggcattatataaggggaattgtcatatgacaatagttccaaaattataggggacacaatgctgcattcttaattaattttaaaatttttgttggtgcagTAACTGATGCGATCTCAATATTGGGGGAATACTTGGAGGATGAGCCTTGGTTGAAGCTTTTGTGTGACCATCTAAA
    |   || | ||   |    || || ||  ||   |  | |     | |  |   |||| |  |||  | |  |||||  | |    | ||  || |||||| | ||||||  |||| ||||| || || || ||| |||| |||||||||||| ||||||||||| ||||||| ||
tagtaaatatca-atgttgatgtttctcttaatacttgaaatgctggtctttttgtttcacagttttgc--tgtgcattaacgt-acttgtgttactgatgcagTGATTGATGCAGTCTCTATATTAGGAGAGTATTTGAAGGAAGAGCCTTGGTTGCAGCTTTTGTGTAACCATCTTAA
















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|30322576|gb|CD005838.1|CD005838
EST:     TCTACCCACATTGGACAAAAACTATGCTGCTCGTGATAAGAAGGATACAT                         TAACTGATGCGATCTCAATATTGGGGGAATACTTGGAGGATGAGCCTTGGT
genomic: TCTACCCACATTGGACAAAAACTATGCTGCTCGTGATAAGAAGGATACATgtatggtttt ... gttggtgcagTAACTGATGCGATCTCAATATTGGGGGAATACTTGGAGGATGAGCCTTGGT
EST: gi|71856752|gb|DT005807.1|DT005807
EST:     TCTACCCACATTGGACAAAAACTATGCTGCTCGTGATAAGAAGGATACAT                         TAACTGATGCGAT
genomic: TCTACCCACATTGGACAAAAACTATGCTGCTCGTGATAAGAAGGATACATgtatggtttt ... gttggtgcagTAACTGATGCGAT
EST: gi|32267964|gb|CD717123.1|CD717123
EST:     TCTACCCACATTGGACAAAAACTATGCTGCTCGTGATAAGAAGGATACAT                         TAACTGATGCGATCTCAATATTGGGGGAATACTTGGAGGATGAGCCTTGGT
genomic: TCTACCCACATTGGACAAAAACTATGCTGCTCGTGATAAGAAGGATACATgtatggtttt ... gttggtgcagTAACTGATGCGATCTCAATATTGGGGGAATACTTGGAGGATGAGCCTTGGT
EST: gi|34417073|gb|CF415827.1|CF415827
EST:     TCTACCCACATTGGACAAAAACTATGCTGCTCGTGATAAGAAGGATACAT                         TAACTGATGCGATCTCAATATTGGGGGAATACTTGGAGGATGAGCCTTGGT
genomic: TCTACCCACATTGGACAAAAACTATGCTGCTCGTGATAAGAAGGATACATgtatggtttt ... gttggtgcagTAACTGATGCGATCTCAATATTGGGGGAATACTTGGAGGATGAGCCTTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tataggggacacaatgctgcattcttaattaattttaaaatttttgttggtgcagTAACTGATGCGATCTCAATATTGGGGGAATACTTGGAGGATGAGCCTTGGTTGAAGCTTTTGTGTGACCATCTAAA
                          aattaat  putative branch site (score: 3)
                                        tttttgtt  putative PPT
                 tgcattcttaattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggcattatataaggggaattgtcatatgacaatagttccaaaattataggggacacaatgctgcattcttaattaattttaaaatttttgttggtgcagTAACTGATGCGATCTCAATATTGGGGGAATACTTGGAGGATGAGCCTTGGTTGAAGCTTTTGTGTGACCATCTAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
-ggcatta
- - - - - - aggggaat
- - - - - - - - - - - - - - - - - - - - aaaatta
- - - - - - - - - - - - - - - - - - - - - - - - aggggaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - caatgct