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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgagaatctaggcaactgatttttttcagaatgcctccttaactttatgatacacttatcctgaccttttccaaactttttcctattgcagCTAAGCAATGTTGCGAGTTTGTGGTTTTTATCCCTTTTTATCTGTATTTTTGCGACTAGCATCCTGGAAATGAGATGGAGTGGTGTTGGAATTGATGATT

Basic information

species Vitis vinifera
transcript Vv03s0038g04250.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g04250.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os07g24190.2 (Oryza sativa), 3'ss of exon 9
gtatgagaatctaggcaactgatttttttcagaatgcctccttaactttatgatacacttatcctgaccttttccaaactttttcctattgcagCTAAGCAATGTTGCGAGTTTGTGGTTTTTATCCCTTTTTATCTGTATTTTTGCGACTAGCATCCTGGAAATGAGATGGAGTGGTGTTGGAATTGATGATT
    |  |||||    |    | |||        | ||   |  | ||  ||  |   | | ||| || ||| ||   || ||   |  ||||||| |  |||||||| ||| | |||||  | || ||||||||||| |||||||| ||| ||||||||||||||||||||||||||||||| ||||||||||
----gtaaatct---tattcaactttcagttctgttccgtatgcagttgctgtgat-ttgagccttacatttcccttcctgttctgttgtgcagCTTACGAATGTTGCCAGTCTCTGGTTCATGTCACTTTTTATCTGCATTTTTGCTACTGGCATCCTGGAAATGAGATGGAGTGGTGTTGGCATTGATGATT

upper sequence: Vv03s0038g04250.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os07g14850.1 (Oryza sativa), 3'ss of exon 12
gtatgagaatctaggcaactgatttttttcagaatgcctccttaactttatgatacacttatcctgaccttttccaaacttt--ttcctattgcagCTAAGCAATGTTGCGAGTTTGTGGTTTTTATCCCTTTTTATCTGTATTTTTGCGACTAGCATCCTGGAAATGAGATGGAGTGGTGTTGGAATTGATGATT
              | ||    | || | |   ||   |   | |  || |||      | ||   | |||     |  |||  |||  | ||||||| | ||||||||| ||| | |||||  | || ||||| |||||||||||||  ||| ||||||| |||||||||||||||||||| |  || ||||| |
--------------gtaagcattattgtgctacataattttgtgatcttctga-gtttctgtctgaatcttacatcatttttatttcaaactgcagCTCACCAATGTTGCTAGTCTATGGTTCATGTCGCTTTTCATCTGTATTTTTGTCACTGGCATCCTTGAAATGAGATGGAGTGGTGTGGCCATCGATGACT

upper sequence: Vv03s0038g04250.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os03g62090.1 (Oryza sativa), 3'ss of exon 13
gtatgagaatctaggcaactgatttttttcagaatgcctccttaactttatgatacacttatcctgaccttttccaaactttttcc-tattgcagCTAAGCAATGTTGCGAGTTTGTGGTTTTTATCCCTTTTTATCTGTATTTTTGCGACTAGCATCCTGGAAATGAGATGGAGTGGTGTTGGAATTGATGATT
|||        |  ||   | ||| | |   |  ||      ||        ||   || | ||| || ||| |     || |||| |  ||||||| |  ||| | || ||  | |||||  | || || |||||||| |||||||| ||  |||| ||||||||||||||||||||||| || || |||||||
gtaacgcttattctgctcgtaattctgtgtggtgtgaaattgtagaagaccaatgacctgaaccttacttttcctccttttgttccattctgcagCTTACTAATATCGCCAGCCTTTGGTTCATGTCACTATTTATCTGCATTTTTGCTACGGGCATTCTGGAAATGAGATGGAGTGGTGTAGGCATCGATGATT

upper sequence: Vv03s0038g04250.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G028353_T01 (Zea mays), 3'ss of exon 13
-----gtatgagaatctaggcaactgatttttttcagaatgcct--ccttaactttat--gatacact-tatcctgaccttttccaaactttttc--ctattgcagCTAAGCAATGTTGCGAGTTTGTGGTTTTTATCCCTTTTTATCTGTATTTTTGCGACTAGCATCCTGGAAATGAGATGGAGTGGTGTTGGAATTGATGATT
     |  | |  | |||      || | |||   | ||  |    |  ||  ||| |  | |      | ||   ||||| |    ||| ||||  ||  ||||||| | ||||||||| ||  |||||||  | || ||||||||||| |||||||| || |||||||| ||||||||||||||||||||||| ||||||||||
gtaaagcttaatcaactatagttttgttgtttgagaaaaaacaaaactatagttttgtttgttgtggaatgtctgaaccttatgttcactgtttcatctgctgcagCTGAACAATGTTGCCAGCCTGTGGTTCATGTCACTTTTTATCTGCATTTTTGCTACAAGCATCCTAGAAATGAGATGGAGTGGTGTTGGGATTGATGATT

upper sequence: Vv03s0038g04250.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G025231_T01 (Zea mays), 3'ss of exon 13
gtatgagaatctaggcaactga----tttttttcagaatgcctccttaacttt--atgatacact-tatcctgaccttttccaaactttttc--ctattgcagCTAAGCAATGTTGCGAGTTTGTGGTTTTTATCCCTTTTTATCTGTATTTTTGCGACTAGCATCCTGGAAATGAGATGGAGTGGTGTTGGAATTGATGATT
     | |   || ||||||      | || |||   |        ||  |||  ||  |   |  | ||   | ||| |    ||| ||||  ||  ||||||| |  |||||||| ||  |||||||  | || ||||||||||| |||||||| || |||||||| |||||||||||||||||||||||||||||||| |
---gtaaagcttaagcaactatagtttgttgttcgagaaaaaaaactagttttgtatattgtgcaatgtctgaagcttatgttcactgtttcatctgctgcagCTGAATAATGTTGCCAGCCTGTGGTTCATGTCACTTTTTATCTGCATTTTTGCTACGAGCATCCTAGAAATGAGATGGAGTGGTGTTGGAATTGATGACT

upper sequence: Vv03s0038g04250.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G113137_T01 (Zea mays), 3'ss of exon 13
gtatgagaatctaggcaactgat--ttttttcagaatgcctccttaactttatgatacact--tatcctgaccttttccaaactttttcctat--tgcagCTAAGCAATGTTGCGAGTTTGTGGTTTTTATCCCTTTTTATCTGTATTTTTGCGACTAGCATCCTGGAAATGAGATGGAGTGGTGTTGGAATTGATGATT
   |    || ||  ||     |  ||   |   | ||     || |     ||  | | |   |  |    |  || | | | || || |||  ||||||| | ||||||||| ||  |||||||  | || ||||| ||||| |||||||| || ||||||||||||||||||||||||||||| || || ||||| |
--gtacccatttattcagtctctaattccgttgtattgtggtgttgaaccggtggaagattatgacaccttacgattactatcattctcttatcgtgcagCTTAACAATGTTGCCAGCCTGTGGTTCATGTCACTTTTCATCTGCATTTTTGCTACGAGCATCCTGGAAATGAGATGGAGTGGTGTAGGCATCGATGACT

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|34544368|gb|CF512600.1|CF512600
EST:     GTACCTTACCTGCTGTTTGCTTGCTCACAGGCAAATTCATCACTCCAGAG                         CTAAGCAATGTTGCGAGTTTGTGGTTTTTATCCCTTTTTATCTGTATTTTT
genomic: GTACCTTACCTGCTGTTTGCTTGCTCACAGGCAAATTCATCACTCCAGAGgtatgagaat ... cctattgcagCTAAGCAATGTTGCGAGTTTGTGGTTTTTATCCCTTTTTATCTGTATTTTT
EST: gi|161714301|gb|FC064180.1|FC064180
EST:     GTACCTTACCTGCTGTTTGCTTGCTCACAGGCAAATTCATCACTCCAGAG                         CTAAGCAATGTTGCGAGTTTGTGGTTTTTATCCCTTTTTATCTGTATTTTT
genomic: GTACCTTACCTGCTGTTTGCTTGCTCACAGGCAAATTCATCACTCCAGAGgtatgagaat ... cctattgcagCTAAGCAATGTTGCGAGTTTGTGGTTTTTATCCCTTTTTATCTGTATTTTT
EST: gi|30304878|gb|CB981672.1|CB981672
EST:     GTACCTTACCTGCTGTTTGCTTGCTCACAGGCAAATTCATCACTCCAGAG                         CTAAGCAATGTTGCGAGTTTGTGGTTTTTATCCCTTTTTATCTGTATTTTT
genomic: GTACCTTACCTGCTGTTTGCTTGCTCACAGGCAAATTCATCACTCCAGAGgtatgagaat ... cctattgcagCTAAGCAATGTTGCGAGTTTGTGGTTTTTATCCCTTTTTATCTGTATTTTT
EST: gi|110695242|gb|EE073035.1|EE073035
EST:     TTGCTTGCTCACAGGCAAATTCATCACTCCAGAG                         CTAAGCAATGTTGCGAGTTTGTGGTTTTTATCCCTTTTTATCTGTATTTTT
genomic: TTGCTTGCTCACAGGCAAATTCATCACTCCAGAGgtatgagaat ... cctattgcagCTAAGCAATGTTGCGAGTTTGTGGTTTTTATCCCTTTTTATCTGTATTTTT
EST: gi|71860009|gb|DT009064.1|DT009064
EST:     GTACCTTACCTGCTGTT-GCTTGCTCACAGGCAAATTCATCACTCCAGAG                         CTAAGCAATGTTGCGAGTTTGTGGTTTTTATCCCTTTTTATCTGTATTTTT
genomic: GTACCTTACCTGCTGTTTGCTTGCTCACAGGCAAATTCATCACTCCAGAGgtatgagaat ... cctattgcagCTAAGCAATGTTGCGAGTTTGTGGTTTTTATCCCTTTTTATCTGTATTTTT
EST: gi|110727924|gb|EE105243.1|EE105243
EST:     GTACCTTACCTGCTGTTTGCTTGCTCACAGGCAAATTCATCACTCCAGAG                         CTAAGCAATGTTGCGAGTTTGTGGTTTTTATCCCTTTTTATCTGTATTTTT
genomic: GTACCTTACCTGCTGTTTGCTTGCTCACAGGCAAATTCATCACTCCAGAGgtatgagaat ... cctattgcagCTAAGCAATGTTGCGAGTTTGTGGTTTTTATCCCTTTTTATCTGTATTTTT
EST: gi|33407928|gb|CF213555.1|CF213555
EST:     GTACCTTACCTGCTGTTTGCTTGCTCACAGGCAAATTCATCACTCCAGAG                         CTAAGCAATGTTGCGAGTTTGTGGTTTTTATCCCTTTTTATCTGTATTTTT
genomic: GTACCTTACCTGCTGTTTGCTTGCTCACAGGCAAATTCATCACTCCAGAGgtatgagaat ... cctattgcagCTAAGCAATGTTGCGAGTTTGTGGTTTTTATCCCTTTTTATCTGTATTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttaactttatgatacacttatcctgaccttttccaaactttttcctattgcagCTAAGCAATGTTGCGAGTTTGTGGTTTTTATCCCTTTTTATCTGTATTTTTGCGACTAGCATCCTGGAAATGAGATGGAGTGGTGTTGGAATTGATGATT
                      tcctgac  putative branch site (score: 2)
                                       ctttttcctattgc  putative PPT
       tttatgata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgagaatctaggcaactgatttttttcagaatgcctccttaactttatgatacacttatcctgaccttttccaaactttttcctattgcagCTAAGCAATGTTGCGAGTTTGTGGTTTTTATCCCTTTTTATCTGTATTTTTGCGACTAGCATCCTGGAAATGAGATGGAGTGGTGTTGGAATTGATGATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA