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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgattaacaaactcatttggcattcttgttcgataaataggacttccgcatcgtttctctggagaaaaaacaaagctactttttagttttaatggtttgagctactgttatcgtatgttgacacctgtgttttccagATCTGGTAAACGTGTTTGAGGTGTTCCTTCCGCAACTTCTTTTGTATCCCAACCCATCAGATCCATTAAATGGAGAGGCTGCAGCTCTAATGATGCGTGA

Basic information

species Vitis vinifera
transcript Vv15s0046g02280.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0046g02280.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os10g31000.1 (Oryza sativa), 3'ss of exon 4
gtaatgattaacaaactcatttggcattcttgttcgataaataggacttccgcatcgtttctctggagaaaaaacaaagctactttttagttttaatggtttgagctactgtta-tcgtatgttgacacctgtgttttccagATCTGGTAAACGTGTTTGAGGTGTTCCTTCCGCAACTTCTTTTGTATCCCAACCCATCAGATCCATTAAATGGAGAGGCTGCAGCTCTAATGATGCGTGA
                                         |  ||   |    ||||   | |  |  |  |  |  | |||||  |  || |  | | ||     ||  |   | | || ||  ||    | |||  ||||||| || || ||||| || || |||||||| |||||||| ||||| || || || || || |||||||||||||||||||| || || |||||||||||
----------------------------------------gtgagataactc--tcgtccttgtc-attattagtacgggtacttgctgtttattctagcttctataaccctgggttgaatatttccatgaatttttggcagATCTAGTTAATGTGTTCGAAGTCTTCCTTCCACAACTTCTATTGTACCCAAATCCTTCTGACCCATTAAATGGAGAGGCTGCTGCACTGATGATGCGTGA

upper sequence: Vv15s0046g02280.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G150867_T02 (Zea mays), 3'ss of exon 4
gtaatgattaacaaactcatttggcattcttgttcgataaataggacttccgcatcgtttctctggagaaaaaacaaagctactttttagttttaatggtttgagctactgttatcgtatgttgacacctg-tgttttccagATCTGGTAAACGTGTTTGAGGTGTTCCTTCCGCAACTTCTTTTGTATCCCAACCCATCAGATCCATTAAATGGAGAGGCTGCAGCTCTAATGATGCGTGA
|||| |||| |      |||||     |   | |||| ||  ||  | | | |   ||  ||     | | |   |||||| | | ||  || || |   ||     |  |||| | |           || | |||| ||||||| || || ||||| ||||| |||||||| |||||||| || ||||| || || || ||||||||||||||||| || || ||  | |||||||||||
gtaa-gattgatctttgcatttcattattaggatcgacaaccagttcattctctctgtgccttatctgtacagttaaagcttcatgtt--ttgtactctgttataacagggttaacttgaacctgtgtgtgatattttgcagATCTTGTTAATGTGTTCGAGGTCTTCCTTCCACAACTTCTGTTATATCCTAATCCTTCTGATCCATTAAATGGAGATGCAGCTGCGTTGATGATGCGTGA

upper sequence: Vv15s0046g02280.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AC149818.2_FGT006 (Zea mays), 3'ss of exon 4
gtaatgattaacaaactcatttggcattcttgttcgataaataggacttccgcatcgtttctctggagaaaaaacaaagc-tactttttagttt-taatggtttgagctactgttatcgtatgttgacacctgtgttttccagATCTGGTAAACGTGTTTGAGGTGTTCCTTCCGCAACTTCTTTTGTATCCCAACCCATCAGATCCATTAAATGGAGAGGCTGCAGCTCTAATGATGCGTGA
                    |||   ||    |   || | |||||  |||||  | | ||| |  | ||  | |    | |  ||| || | | | ||     |    ||| | | | |||||         | |||| ||||||| || || ||||| ||||| |||||||| |||||||| || ||||| || || || ||||||||||||||||| || || ||  | |||||||||||
--------------gtaagattgatctttacatctcattattaggatctccgcgccttatctgtatacaattagcgctccatgttttgtactctgttataacagggttaactttgaacctatgtgtg-----atattttgcagATCTTGTCAATGTGTTCGAGGTCTTCCTTCCACAACTTCTGTTATATCCTAATCCTTCTGATCCATTAAATGGAGATGCAGCTGCGTTGATGATGCGTGA

upper sequence: Vv15s0046g02280.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G053764_T06 (Zea mays), 3'ss of exon 3
gtaatgattaacaaactcatttggcattcttgttcgataaataggacttccgcatcgtttctctggagaaaaaacaaagctactttttagttttaatggtttgagctactgttatcgtatgttgacacctgtgttttccagATCTGGTAAACGTGTTTGAGGTGTTCCTTCCGCAACTTCTTTTGTATCCCAACCCATCAGATCCATTAAATGGAGAGGCTGCAGCTCTAATGATGCGTGA
                                         |  ||    | | |   |||| | ||    |        ||  || ||   |  ||  | |||||||     ||| | | |  |||    | |||| ||||||| ||||| || ||||| || |||||||| || ||  |  | ||||| || || || |||||||||||||| ||||||||||| || |||||||||||
----------------------------------------gtgagatactctcttgccttctattgatgctatgagctcttatcttatataatctataatctgagctag----atctttt-tccacattcctcttttgcagATCTAGTAAATGTTTTTGAAGTATTCCTTCCACAGCTGTTACTATATCCAAATCCTTCTGATCCATTAAATGGGGAGGCTGCAGCACTGATGATGCGTGA

upper sequence: Vv15s0046g02280.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G053764_T03 (Zea mays), 3'ss of exon 4
gtaatgattaacaaactcatttggcattcttgttcgataaataggacttccgcatcgtttctctggagaaaaaacaaagctactttttagttttaatggtttgagctactgttatcgtatgttgacacctgtgttttccagATCTGGTAAACGTGTTTGAGGTGTTCCTTCCGCAACTTCTTTTGTATCCCAACCCATCAGATCCATTAAATGGAGAGGCTGCAGCTCTAATGATGCGTGA
                                         |  ||    | | ||  |||  | ||    |        ||  || ||   |  ||  | |||||||     ||| | | |  |||    | |||| ||||||| ||||| || ||||| || |||||||| || ||  |  | ||||| || || || |||||||||||||| ||||||||||| || |||||||||||
----------------------------------------gtgagatactctcttctcttccattgatgctatgagctcttatcttatataatctataatctgagctag----atctttt-tccacattcctcttttgcagATCTAGTAAATGTTTTTGAAGTATTCCTTCCACAGCTGTTACTATATCCAAATCCTTCTGATCCATTAAATGGGGAGGCTGCAGCACTGATGATGCGTGA

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|161706781|gb|FC055498.1|FC055498
EST:     CGGATCAGTGTGTTTAGATGTTATCAACCAAACCTGGAGCCCTATGTTCG                         ATCTGGTAAACGTGTTTGAGGTGTTCCTTCCGCAACTTCTTTTGTATCCCA
genomic: CGGATCAGTGTGTTTAGATGTTATCAACCAAACCTGGAGCCCTATGTTCGgtaatgatta ... tgttttccagATCTGGTAAACGTGTTTGAGGTGTTCCTTCCGCAACTTCTTTTGTATCCCA
EST: gi|351029514|gb|FQ436908.1|FQ436908
EST:     CGGATCAGTGTGTTTAGATGTTATCAACCAAACCTGGAGCCCTATGTTCG                         ATCTGGTAAACGTGTTTGAGGTGTTCCTTCCGCAACTTCTTTTGTATCCCA
genomic: CGGATCAGTGTGTTTAGATGTTATCAACCAAACCTGGAGCCCTATGTTCGgtaatgatta ... tgttttccagATCTGGTAAACGTGTTTGAGGTGTTCCTTCCGCAACTTCTTTTGTATCCCA
EST: gi|46918632|gb|CN547961.1|CN547961
EST:     CGGATCAGTGTGTTTAGATGTTATCAACCAAACCTGGAGCCCTATGTTCG                         ATCTGGTAAACGTGTTTGAGGTGTTCCTTCCGCAACTTCTTTTGTATCCCA
genomic: CGGATCAGTGTGTTTAGATGTTATCAACCAAACCTGGAGCCCTATGTTCGgtaatgatta ... tgttttccagATCTGGTAAACGTGTTTGAGGTGTTCCTTCCGCAACTTCTTTTGTATCCCA
EST: gi|110420607|gb|EC986882.1|EC986882
EST:     CGGATCAGTGTGTTTAGATGTTATCAACCAAACCTGGAGCCCTATGTTCG                         ATCTGGTAAACGTGTTTGAGGTGTTCCTTCCGCAACTTCTTTTGTATCCCA
genomic: CGGATCAGTGTGTTTAGATGTTATCAACCAAACCTGGAGCCCTATGTTCGgtaatgatta ... tgttttccagATCTGGTAAACGTGTTTGAGGTGTTCCTTCCGCAACTTCTTTTGTATCCCA
EST: gi|34550367|gb|CF518585.1|CF518585
EST:     CGGATCAGTGTGTTTAGATGTTATCAACCAAACCTGGAGCCCTATGTTCG                         ATCTGGTAAACGTGTTTGAGGTGTTCCTTCCGCAACTTCTTTTGTATCCCA
genomic: CGGATCAGTGTGTTTAGATGTTATCAACCAAACCTGGAGCCCTATGTTCGgtaatgatta ... tgttttccagATCTGGTAAACGTGTTTGAGGTGTTCCTTCCGCAACTTCTTTTGTATCCCA
EST: gi|83274683|gb|DV938779.1|DV938779
EST:     CGGATCAGTGTGTTTAGATGTTATCAACCAAACCTGGAGCCCTATGTTCG                         ATCTGGTAAACGTGTTTGAGGTGTTCCTTCCGCAACTTCTTTTGTATCCCA
genomic: CGGATCAGTGTGTTTAGATGTTATCAACCAAACCTGGAGCCCTATGTTCGgtaatgatta ... tgttttccagATCTGGTAAACGTGTTTGAGGTGTTCCTTCCGCAACTTCTTTTGTATCCCA
EST: gi|351037950|gb|FQ465188.1|FQ465188
EST:     CGGATCAGTGTGTTTAGATGTTATCAACCAAACCTGGAGCCCTATGTTCG                         ATCTGGTAAACGTGTTTGAGGTGTTCCTTCCGCAACTTCTTTTGTATCCCA
genomic: CGGATCAGTGTGTTTAGATGTTATCAACCAAACCTGGAGCCCTATGTTCGgtaatgatta ... tgttttccagATCTGGTAAACGTGTTTGAGGTGTTCCTTCCGCAACTTCTTTTGTATCCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagttttaatggtttgagctactgttatcgtatgttgacacctgtgttttccagATCTGGTAAACGTGTTTGAGGTGTTCCTTCCGCAACTTCTTTTGTATCCCAACCCATCAGATCCATTAAATGGAGAGGCTGCAGCTCTAATGATGCGTGA
                                 tgttgac  putative branch site (score: 3)
                                             tgttttcc  putative PPT
     tttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgattaacaaactcatttggcattcttgttcgataaataggacttccgcatcgtttctctggagaaaaaacaaagctactttttagttttaatggtttgagctactgttatcgtatgttgacacctgtgttttccagATCTGGTAAACGTGTTTGAGGTGTTCCTTCCGCAACTTCTTTTGTATCCCAACCCATCAGATCCATTAAATGGAGAGGCTGCAGCTCTAATGATGCGTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC