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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctacaagcacactaagtcttccacagagggtttcttctctgatcggcctctggctattacatccgtaagtttgatctttcttaatgttctttattgcagGCAGCTCGAATGCGTTATGTATTTGAAAATGAACCATATTGCCTGAATCTAATTGATACTCCAGGGCATGTGGACTTCTCCTATGAG

Basic information

species Vitis vinifera
transcript Vv07s0031g03050.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0031g03050.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G003157_T01 (Zea mays), 3'ss of exon 2
--cctacaagcacactaagtcttccacagagggtttcttctctgatcggcctctggctattacatccgtaagtttg-atctttcttaatgttctttattgcagGCAGCTCGAATGCGTTATGTATTTGAAAATGAACCATATTGCCTGAATCTAATTGATACTCCAGGGCATGTGGACTTCTCCTATGAG
  | |        ||  || || | || |  | | ||   |   ||    |  |   |  |  ||   || ||||  |  | |  ||||  | | | ||  |||||||||| ||||| || ||  |  | ||||| || || ||||||||| |||||||||| ||||||||||| || ||||| || |||
gtcatttgcttgtacatag-ctcctactggagttctcccattgtattattcattt-ttgatgtatg-atatgtttacacatgttctaataatttgttttatagGCAGCTCGGATGCGCTACGTCATGAATAATGAGCCTTACTGCCTGAATTTAATTGATACACCAGGGCATGTTGATTTCTCGTACGAG

upper sequence: Vv07s0031g03050.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA04G38360.1 (Glycine max), 3'ss of exon 2
---------------------------------------cctacaagcacacta-agtcttccacagagggtttcttctctgatcggcctctggctattacatccgtaagtttgatctttcttaatgttctttattgcagGCAGCTCGAATGCGTTATGTATTTGAAAATGAACCATATTGCCTGAATCTAATTGATACTCCAGGGCATGTGGACTTCTCCTATGAG
                                       | ||    |  || | ||  |   | | | | |||      || |           ||  | ||  || |   |    ||   |||| ||  | || |||||||||| ||||||||||||| |||||||||||||| |||||| |||||||||| |||||||| |||||||| |||||||| ||||||
gttcccatcttttcctaattccttattagcttatattatcttaatttcgtacgagagattgggaaatatgattttgaaaatgcttttttcgatattaagatatttgtgaaagta--tttgactaattttgatcatggcagGCAGCTAGAATGCGTTATGTGTTTGAAAATGAACCTTATTGCTTGAATCTAATAGATACTCCGGGGCATGTTGACTTCTCGTATGAG

upper sequence: Vv07s0031g03050.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA06G16700.1 (Glycine max), 3'ss of exon 2
----cctacaagcacactaagtcttccacagagggtttcttctctgatcggcctctggctattacatccgtaagtttgatctttcttaatgttctttattgcagGCAGCTCGAATGCGTTATGTATTTGAAAATGAACCATATTGCCTGAATCTAATTGATACTCCAGGGCATGTGGACTTCTCCTATGAG
      ||     |   | ||||||  | | |      ||| | || |     | ||  |     ||  || |   |    ||   |||| ||  | || |||||||||  ||||||||||||| |||||||||||||| |||||| |||||||||| || |||||||||||||| |||||||| ||||||
tagatttatttatat-ttgagtcttagatacaaaacaacttttttgctta-tatatgagttcagtatttgtgaaagta--tttgactaattttaatcatggcagGCAGCCAGAATGCGTTATGTGTTTGAAAATGAACCTTATTGCTTGAATCTAATAGACACTCCAGGGCATGTTGACTTCTCGTATGAG

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|46917805|gb|CN547134.1|CN547134
EST:     TTGATAACATGGATCTAGAGCGTGAAAGAGGAATCACAATCATACTACAG                         GCAGCTCGAATGCGTTATGTATTTGAAAATGAACCATATTGCCTGAATCTA
genomic: TTGATAACATGGATCTAGAGCGTGAAAGAGGAATCACAATCAAACTACAGgttcatattt ... tttattgcagGCAGCTCGAATGCGTTATGTATTTGAAAATGAACCATATTGCCTGAATCTA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcctctggctattacatccgtaagtttgatctttcttaatgttctttattgcagGCAGCTCGAATGCGTTATGTATTTGAAAATGAACCATATTGCCTGAATCTAATTGATACTCCAGGGCATGTGGACTTCTCCTATGAG
                                  tcttaat  putative branch site (score: 3)
                                          ttctttatt  CT-rich tract
                                    ttaatgttctttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cctacaagcacactaagtcttccacagagggtttcttctctgatcggcctctggctattacatccgtaagtttgatctttcttaatgttctttattgcagGCAGCTCGAATGCGTTATGTATTTGAAAATGAACCATATTGCCTGAATCTAATTGATACTCCAGGGCATGTGGACTTCTCCTATGAG

- -acaagca
- - - - - - - - - cttccac
- - - - - - - - - - - - - - - - - - - - - - cggcctc
- - - - - - - - - - - - - - - - - - - - - - - - - -tggctat