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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttttattgttgatattgctaactgtttattcttttaataggattttatctaaaaaaatttcaaagattatatttttatttattatcttgtctctacagATCCAACATACATGATCCGAGCTATTCCAAGTAATGCATCAGACAATATCTACTGCACCCTCCTTGCACATAGTGCTGTACATGGGGCCATGGCAGGGTA

Basic information

species Vitis vinifera
transcript Vv16s0013g01140.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0013g01140.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA10G33820.1 (Glycine max), 3'ss of exon 12
--gtttttattgttgatattgctaactgtttattcttttaataggattttatctaaaaaaatttcaaagattatatttttatttattatcttgtctctacagATCCAACATACATGATCCGAGCTATTCCAAGTAATGCATCAGACAATATCTACTGCACCCTCCTTGCACATAGTGCTGTACATGGGGCCATGGCAGGGTA
     |  | |  ||||   |  |  |||| | |  | || |   || ||   |       ||| |    ||||  |   | || ||   ||   |  | |||||||||||||||||| || ||||||||||||||||| || ||||| || |||||||| || ||||||||| ||||||| ||||| || ||||| || ||
taaaatcaactaatgatgggggcagttgtt-acttctctattcaaatcttgaattttgttgttttattt-ttattataaaacttgtttgtttactttcatagATCCAACATACATGATTCGGGCTATTCCAAGTAATGCCTCGGACAACATTTACTGCACTCTTCTTGCACATGGTGCTGTTCATGGAGCTATGGCTGGATA

upper sequence: Vv16s0013g01140.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: PP1S81_165V6.1 (Physcomitrella patens), 3'ss of exon 13
----------------------------gtttttattgttgata-ttgctaactgt-ttattcttttaataggattttatctaaaaaaatttcaaagattatatttttatttattatcttgtctctacagATCCAACATACATGATCCGAGCTATTCCAAGTAATGCATCAGACAATATCTACTGCACCCTCCTTGCACATAGTGCTGTACATGGGGCCATGGCAGGGTA
                            | |||| |  ||| |  ||| |    ||  |  | | || ||   |||   | ||      |||        ||||   || | |  | | ||  ||| |||||||||| |||||||| |||||| ||||||| ||||| || |||||  | ||||||||  | ||||| ||||| ||  | ||||| || |||||||||||
gtggccatatgcccagttgaaaacttttggttttttctttgctgcttggttctcgtgcttctatattcatgaaattccttttagtcgtttttaggcttgaatatgagtactcacca-catgattctgcagATCCAACGTACATGATTCGAGCTGTTCCAAGCAATGCTTCTGACAACGTGTACTGCACTTTGCTTGCTCATAGCGCCATCCATGGAGCTATGGCAGGGTA

upper sequence: Vv16s0013g01140.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: PP1S282_45V6.1 (Physcomitrella patens), 3'ss of exon 12
------------------------------------------------------gtttttat-tgttgatattgctaactgttta----ttcttttaataggattttatctaaaaaaatttcaaagattatatttttatttattatcttgt--ctctacagATCCAACATACATGATCCGAGCTATTCCAAGTAATGCATCAGACAATATCTACTGCACCCTCCTTGCACATAGTGCTGTACATGGGGCCATGGCAGGGTA
                                                      || |  || ||| ||| ||    |||||       | |||  | |  |      || |     || |   |    |||    |  | |||||    |   ||| ||||||| || || ||||| ||||| |||||||| ||||| || |||||| ||||||||||  | || || ||||| ||  | |||||||| |||||||||||
gtacagtagccgtcaactgttctaactgttgagtgatggtgatccgtcttcctggtctacatctgtcgattttttacactgtggggaattgcttacattctggccacgtccatggtgatcttgcattcgataagactgctcattatgccatagttctgcagATCCGACGTATATGATTCGAGCAATTCCAAGCAATGCTTCGGACAATGTCTACTGCACATTGCTGGCTCATAGCGCCATCCATGGGGCTATGGCAGGGTA

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|110409783|gb|EC975454.1|EC975454
EST:     GATCATTTCACAAAGGTACAGAAGATGGCAGTAAATATGAAATATATAG                         ATCCAACATACATGATCCGAGCTATTCCAAGTAATGCATCAGACAATATCT
genomic: GATCATTTCACAAAGGTACAGAAGATGGCAGTAAATATGAAATATATAGgtatttctca ... gtctctacagATCCAACATACATGATCCGAGCTATTCCAAGTAATGCATCAGACAATATCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatctaaaaaaatttcaaagattatatttttatttattatcttgtctctacagATCCAACATACATGATCCGAGCTATTCCAAGTAATGCATCAGACAATATCTACTGCACCCTCCTTGCACATAGTGCTGTACATGGGGCCATGGCAGGGTA
   atctaaa  putative branch site (score: 3)
                                         tcttgtctct  putative PPT
      taaaaaaatttcaaag  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttttattgttgatattgctaactgtttattcttttaataggattttatctaaaaaaatttcaaagattatatttttatttattatcttgtctctacagATCCAACATACATGATCCGAGCTATTCCAAGTAATGCATCAGACAATATCTACTGCACCCTCCTTGCACATAGTGCTGTACATGGGGCCATGGCAGGGTA

- - - - - - - - -tgctaac
- - - - - - - - - - - - - - - - - - -aatagga
- - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa