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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcataatttgcttgcatttacaaataattcctgagccctgcatttctcactgtgaaggcaataatggtgatggtattatctctattccttttaaatgcagGCAACTCCAGAGTTGGAGTATGGCCGGATGAACATTGGAAGTCGTCCATCAAAACGAAAGCCAAGTGGGGGCATTGAGTCACTCCGCGCAATCCCCTGGA

Basic information

species Vitis vinifera
transcript Vv12s0028g02180.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0028g02180.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os01g55350.1 (Oryza sativa), 3'ss of exon 10
--tcataatttgcttgcatttacaaata-attcctgagccctgcatttctcactgtgaaggcaataatggtgatggtattatctctattccttttaaatgcagGCAACTCCAGAGTTGGAGTATGGCCGGATGAACATTGGAAGTCGTCCATCAAAACGAAAGCCAAGTGGGGGCATTGAGTCACTCCGCGCAATCCCCTGGA
  |||   | |  |  | || | ||||   ||  |  ||     |||  ||     |   | |  |||  |     | ||   ||| || || | ||||  ||||||| ||||||||||| |||||  ||||||| ||||||||| | ||||||||||||||||| ||||| |||||||| ||||| || ||||| || ||||
cttcactctgtagtcaccttcataaatttgttattttgctaatgattattctaatggtctgtataaataatctcaattttgcttct-ttgctgtcaaat--agGCAACACCAGAGTTGGAATATGGTAGGATGAATATTGGAAGTAGGCCATCAAAACGAAAGCCTAGTGGAGGCATTGAATCACTTCGTGCAATTCCTTGGA

upper sequence: Vv12s0028g02180.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os08g27840.1 (Oryza sativa), 3'ss of exon 8
--------------------------tcataatttg---cttgcattta---caaataattc-ctgagccctgcatttctcactgtgaaggcaataatggtga--tggtattatctctattccttttaaatgcagGCAACTCCAGAGTTGGAGTATGGCCGGATGAACATTGGAAGTCGTCCATCAAAACGAAAGCCAAGTGGGGGCATTGAGTCACTCCGCGCAATCCCCTGGA
                          ||| | || |    || ||| ||   ||  |||  | || |||    ||||  ||| |        ||   | || |  |  | || | |  |||  |  | ||  |||||||| |||||| ||||||||||  ||||||| || |||||  | ||||| ||  ||||||| ||||| ||||| ||||||||||| || ||||| ||||
gtgagtgttttgtttcttcataatcatcagacttggaacatttcatataatgcatttaaggcacttagctaaacattgttcatttcaggcaaaacctttgtaaattaattttctttacatttttcatgaaatcagGCAACACCAGAGATGGAGTATGGAAGGATGAATATAGGAAGCAGGCCATCCAAGAGAAAGCCGAGTGGTGGCATCGAGTCACTCCGTGCCATCCCATGGA

upper sequence: Vv12s0028g02180.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G110714_T01 (Zea mays), 3'ss of exon 8
tcataatttgcttgcatttacaaataattcctgagccctgcatttctcactgtgaagg----caataatggtgatggtattatctctattccttttaaatgcagGCAACTCCAGAGTTGGAGTATGGCCGGATGAACATTGGAAGTCGTCCATCAAAACGAAAGCCAAGTGGGGGCATTGAGTCACTCCGCGCAATCCCCTGGA
     | |   ||| | |  |   |||    |    | ||  ||  |    |   |      |        | ||  |   ||   | |   | ||  |  |||||||| |||||| ||||||||||| |||||||||| |||||  | ||||| ||| ||||||| |||| |||||| ||||| || ||||||||||| ||||
----tactcctttgtagtaccctgtaaaattttcatcttgttttggtagtgggtcaaattttctgcgtaactaatcctggcattcgtgtctttatttgaaacagGCAACGCCAGAGATGGAGTATGGCAGGATGAACATCGGAAGCAGGCCATCGAAAAGAAAGCCGAGTGCGGGCATCGAGTCGCTGCGCGCAATCCCTTGGA

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|110690611|gb|EE067864.1|EE067864
EST:     ATCGTTCCATTGTCTTCCAGGAACCCCGCTTTGTTGAATATTTCCGCCTG                         GCAACTCCAGAGTTGGAGTATGGCCGGATGAACATTGGAAGTCGTCCATCA
genomic: ATCGTTCCATTGTCTTCCAGGAACCCCGCTTTGTTGAATATTTCCGCCTGgtaagtttga ... ttaaatgcagGCAACTCCAGAGTTGGAGTATGGCCGGATGAACATTGGAAGTCGTCCATCA
EST: gi|110378389|gb|EC943519.1|EC943519
EST:     TATTTCCGCCTG                         GCAACTCCAGAGTTGGAGTATGGCCGGATGAACATTGGAAGTCGTCCATCA
genomic: TATTTCCGCCTGgtaagtttga ... ttaaatgcagGCAACTCCAGAGTTGGAGTATGGCCGGATGAACATTGGAAGTCGTCCATCA
EST: gi|110366969|gb|EC930889.1|EC930889
EST:     ATCGTTCCATTGTCTTCCAGGAACCCCGCTTTGTTGAATATTTCCGCCTG                         GCAACTCCAGAGTTGGAGTATGGCCGGATGAACATTGGAAGTCGTCCATCA
genomic: ATCGTTCCATTGTCTTCCAGGAACCCCGCTTTGTTGAATATTTCCGCCTGgtaagtttga ... ttaaatgcagGCAACTCCAGAGTTGGAGTATGGCCGGATGAACATTGGAAGTCGTCCATCA
EST: gi|110419647|gb|EC985893.1|EC985893
EST:     TATTTCCGCCTG                         GCAACTCCAGAGTTGGAGTATGGCCGGATGAACATTGGAAGTCGTCCATCA
genomic: TATTTCCGCCTGgtaagtttga ... ttaaatgcagGCAACTCCAGAGTTGGAGTATGGCCGGATGAACATTGGAAGTCGTCCATCA
EST: gi|352765184|gb|FQ465881.1|FQ465881
EST:     ATCGTTCCATTGTCTTCCAGGAACCTCGCTTTGTTGAATATTTCCGCCTG                         GCAACTCCAGAATTGGAGTATGGCCGGATGAACATTGGA
genomic: ATCGTTCCATTGTCTTCCAGGAACCCCGCTTTGTTGAATATTTCCGCCTGgtaagtttga ... ttaaatgcagGCAACTCCAGAGTTGGAGTATGGCCGGATGAACATTGGA
EST: gi|22009484|gb|BQ794518.1|BQ794518
EST:     ATCG-TCCATTGTC-TCCAGGAA-CCCGC-TTGTTGAATA-TTCCGCCTG                         GCAACTCCAGAGTTGGAGTATGGCCGGATGAACATTGGAAGTCGTCCATCA
genomic: ATCGTTCCATTGTCTTCCAGGAACCCCGCTTTGTTGAATATTTCCGCCTGgtaagtttga ... ttaaatgcagGCAACTCCAGAGTTGGAGTATGGCCGGATGAACATTGGAAGTCGTCCATCA
EST: gi|352772670|gb|FQ472145.1|FQ472145
EST:     ATCGTTCCATTGTCTTCCAGGAACCCCGCTTTGTTGAATATTTCCGCCTG                         GCAACTCCAGAGTTGGAGTATGGCCGGATGAACATTGGAAGTCGTCCATCA
genomic: ATCGTTCCATTGTCTTCCAGGAACCCCGCTTTGTTGAATATTTCCGCCTGgtaagtttga ... ttaaatgcagGCAACTCCAGAGTTGGAGTATGGCCGGATGAACATTGGAAGTCGTCCATCA
EST: gi|110417555|gb|EC983621.1|EC983621
EST:     ATCGTTCCATTGTCTTCCAGGAACCCCGCTTTGTTGAATATTTCCGCCTG                         GCAACTCCAGAGTTGGAGTATGGCCGGATGAACATTGGAAGTCGTCCATCA
genomic: ATCGTTCCATTGTCTTCCAGGAACCCCGCTTTGTTGAATATTTCCGCCTGgtaagtttga ... ttaaatgcagGCAACTCCAGAGTTGGAGTATGGCCGGATGAACATTGGAAGTCGTCCATCA
EST: gi|110731837|gb|EE106600.1|EE106600
EST:     TGAATATTTCCGCCTG                         GCAACTCCAGAGTTGGAGTATGGCCGGATGAACATTGGAAGTCGTCCATCA
genomic: TGAATATTTCCGCCTGgtaagtttga ... ttaaatgcagGCAACTCCAGAGTTGGAGTATGGCCGGATGAACATTGGAAGTCGTCCATCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcactgtgaaggcaataatggtgatggtattatctctattccttttaaatgcagGCAACTCCAGAGTTGGAGTATGGCCGGATGAACATTGGAAGTCGTCCATCAAAACGAAAGCCAAGTGGGGGCATTGAGTCACTCCGCGCAATCCCCTGGA
 ttctcac  putative branch site (score: 2)
                              ttatctctattccttt  putative PPT
                                     tattccttttaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcataatttgcttgcatttacaaataattcctgagccctgcatttctcactgtgaaggcaataatggtgatggtattatctctattccttttaaatgcagGCAACTCCAGAGTTGGAGTATGGCCGGATGAACATTGGAAGTCGTCCATCAAAACGAAAGCCAAGTGGGGGCATTGAGTCACTCCGCGCAATCCCCTGGA

- - - - -gcttgca
- - - - - - - - - - caaataa
- - - - - - - - - - - - - -ttcctga
- - - - - - - - - - - - - - - - - -ccctgca
- - - - - - - - - - - - - - - - - - - - - - -ctcactg
- - - - - - - - - - - - - - - - - - - - - - - - - - -gaaggca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgatgg