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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttttgcattaaagttgattgctgttcaagattcctattccataaatgaagaggccaaccttcttttttcattctttgctttttttaattgcacagGTCCAACACCTTCTTGGTCAGTGTGCCCAACATCTTGAAAAGGGTGAAACCCACCAAGGCCCAGCTGTACTTGGAATTGCAATGGTGGCAATGGCTGAAG

Basic information

species Vitis vinifera
transcript Vv12s0028g03130.t01
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0028g03130.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: LOC_Os06g48640.3 (Oryza sativa), 3'ss of exon 18
---gttttgcattaa-agttgattgctgttcaagat-tcctattccataaatgaagaggccaaccttcttttttcattctttgctttttttaattgcacagGTCCAACACCTTCTTGGTCAGTGTGCCCAACATCTTGAAAAGGGTGAAACCCACCAAGGCCCAGCTGTACTTGGAATTGCAATGGTGGCAATGGCTGAAG
    ||    ||||| ||  || |  ||   | | | |   ||| |||   |  || | | |    | |||  | | ||||  | |||    |||   ||||| ||  | || |||||    ||  || | |||||||| || ||||||||||||||||| ||||| || ||||||||  |  |  | || ||||||||||
gtgattcccaattaacagaagaattgtgcataggttgtaggattacatttttttagcgcctatttgtttttgatgaatcttcccgttt---gatt-tgcagGTTCAGAAACTCCTTGGAATTTGCTCCGAGCATCTTGAGAAAGGTGAAACCCACCAAGGGCCAGCAGTTCTTGGAATCTCCCTAATTGCCATGGCTGAAG

upper sequence: Vv12s0028g03130.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: LOC_Os09g15750.1 (Oryza sativa), 3'ss of exon 18
--gttttgcattaaagttgattgctgttcaagattccta----ttccataaatgaagaggccaaccttcttttttcattctttgctttttttaattgcacagGTCCAACACCTTCTTGGTCAGTGTGCCCAACATCTTGAAAAGGGTGAAACCCACCAAGGCCCAGCTGTACTTGGAATTGCAATGGTGGCAATGGCTGAAG
  | ||  || | ||    |    ||| || |  |  ||    | | |||  |      ||| |  |  ||||  |     ||  |   ||| |||   ||||| ||| | || |||||    ||| || | |||||||| || ||||||||||||||||| ||||| || ||||||||  |  |  |  | ||||||||||
gtgattcccaatcaacagaagaattgtgcatggattataggattacaatattttttagtgcctatttgtttttgacgaatctt--tccgtttgatt-tgcagGTTCAAAAACTCCTTGGAATCTGTTCCGAGCATCTTGAGAAAGGTGAAACCCACCAAGGACCAGCAGTTCTTGGAATCTCCCTAATTTCCATGGCTGAAG

upper sequence: Vv12s0028g03130.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: LOC_Os02g05340.1 (Oryza sativa), 3'ss of exon 18
gttttgcattaaagttgattgctgttcaagattcctattccataaatgaagaggccaaccttcttttttcattctttgctttttttaattgcacagGTCCAACACCTTCTTGGTCAGTGTGCCCAACATCTTGAAAAGGGTGAAACCCACCAAGGCCCAGCTGTACTTGGAATTGCAATGGTGGCAATGGCTGAAG
    | | || | ||| | ||||  |  || ||| | |  | | ||      |   ||  |||    ||  |  | |||||       || | ||||| ||| | || |||||    ||  | || |||||||| || |||||||||||||| || |||||||| || ||||||||  |  | |||||||||||||
---gtac-ttcatgtttaatgct--tagaggttcttgtggcttcaa--gcttgtttaaatttcgaggttt-tgatatgcttggcaattttacgcagGTTCAAAAGCTCCTTGGGATTTGCTCACAGCATCTTGAGAAAGGTGAAACCCACCAGGGGCCAGCTGTCCTAGGAATTGCGCTTATTGCAATGGCTGAAG

upper sequence: Vv12s0028g03130.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GRMZM5G816609_T01 (Zea mays), 3'ss of exon 4
gttttgcattaaagttgattgctgttcaagattcct----attccataaatgaagaggcc---aaccttcttttttcattctttgctttttttaattgcacagGTCCAACACCTTCTTGGTCAGTGTGCCCAACATCTTGAAAAGGGTGAAACCCACCAAGGCCCAGCTGTACTTGGAATTGCAATGGTGGCAATGGCTGAAG
|| ||| || |   ||  ||  ||   | | |||      ||||  |   | |||| |      |  ||   ||   |   | |  |    |  |||   ||||| ||  | ||||||||    ||| | || |||||||| || |||||||| |||||||| |||||||| |||||||||||  |  | || ||||||||||
gtattgtat-actattctttaatggaaaggtttctagcagattcagtttttaaagaagtttaagatatttggttgatagcatgtaatcaactctatt-tgcagGTTCAGAAACTTCTTGGCATTTGTTCACAGCATCTTGAGAAAGGTGAAACACACCAAGGGCCAGCTGTCCTTGGAATTGCTCTTATTGCTATGGCTGAAG

upper sequence: Vv12s0028g03130.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA06G44340.1 (Glycine max), 3'ss of exon 18
----------------------------gttttgcattaaagttga--ttgctgttcaagattcctat-tccataaatg------aagaggccaaccttcttttttcattctttgct--ttttttaattgcacagGTCCAACACCTTCTTGGTCAGTGTGCCCAACATCTTGAAAAGGGTGAAACCCACCAAGGCCCAGCTGTACTTGGAATTGCAATGGTGGCAATGGCTGAAG
                             ||||   | |||  |||   | ||| |  |  || |||| |  |||| ||        |    || | || | |||| ||  ||||||  |  ||   |    ||||| ||| | ||  | ||||| ||| | ||||||||||| || |||||||| |||||||| || ||||| ||||||||||| ||||| || ||||||||||
gtacaatcttgtgataaactggttatgaattttttttaaaaaatgaaacttctgctgcacctttctatgtttataattgctgattgcggatgcatctttttattttaatattttgctggtgcttctttcttgcagGTTCAAAATCTGTTGGGTCATTGTTCACAACATCTTGATAAAGGTGAAACTCACCAAGGTCCTGCTGTGCTTGGAATTGCTATGGTAGCTATGGCTGAAG

upper sequence: Vv12s0028g03130.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA12G13410.1 (Glycine max), 3'ss of exon 18
-----------------------------gttttgcattaaagt-tgattgctgttcaagattcctat-tccataaatgaagaggccaaccttc-ttttttcattctttgctttttttaattgcacagGTCCAACACCTTCTTGGTCAGTGTGCCCAACATCTTGAAAAGGGTGAAACCCACCAAGGCCCAGCTGTACTTGGAATTGCAATGGTGGCAATGGCTGAAG
                             |||||   | ||| | | |   ||| |  |  || |||| |  |||| ||  || ||     ||| |||||  |||   || |  || |   |   ||||| ||| | ||  | ||||| ||| | ||||||||||| || |||||||| ||||| || || ||||| ||||||||||| ||||| || ||||||||||
gtacaatcttgtgatgaattagttatgaagttttttttaaaaatgtaacatctgctacacctttctatgtttataattgctgatgcattttttcatttttgtatttgctgatgcttctttct-tgcagGTTCAAAATCTGTTGGGTCATTGTTCACAACATCTTGATAAAGGTGAAACTCACCAGGGTCCTGCTGTGCTTGGAATTGCTATGGTAGCTATGGCTGAAG

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|161706069|gb|FC056232.1|FC056232
EST:     ATATGACGTTGCTTTCTTGTGCATATGCTGGAACTGGGAATGTGCTCAAG                         GTCCAACACCTTCTTGGTCAGTGTGCCCAACATCTTGAAAAGGGTGAAACC
genomic: ATATGACGTTGCTTTCTTGTGCATATGCTGGAACTGGGAATGTGCTCAAGgttttgcatt ... aattgcacagGTCCAACACCTTCTTGGTCAGTGTGCCCAACATCTTGAAAAGGGTGAAACC
EST: gi|110370776|gb|EC932910.1|EC932910
EST:     ATATGACGTTGCTTTCTTGTGCATATGCTGGAACTGGGAATGTGCTCAAG                         GTCCAACACCTTCTTGGTCAGTGTGCCCAACATCTTGAAAAGGGTGAAACC
genomic: ATATGACGTTGCTTTCTTGTGCATATGCTGGAACTGGGAATGTGCTCAAGgttttgcatt ... aattgcacagGTCCAACACCTTCTTGGTCAGTGTGCCCAACATCTTGAAAAGGGTGAAACC
EST: gi|37183929|gb|CF603283.1|CF603283
EST:     ATATGACGTTGCTTTCTTGTGCATATGCTGGAACTGGGAATGTGCTCAAG                         GTCCAACACCTTCTTGGTCAGTGTGCCCAACATCTTGAAAAGGGTGAAACC
genomic: ATATGACGTTGCTTTCTTGTGCATATGCTGGAACTGGGAATGTGCTCAAGgttttgcatt ... aattgcacagGTCCAACACCTTCTTGGTCAGTGTGCCCAACATCTTGAAAAGGGTGAAACC
EST: gi|37188290|gb|CF607639.1|CF607639
EST:     ATATGACGTTGCTTTCTTGTGCATATGCTGGAACTGGGAATGTGCTCAAG                         GTCCAACACCTTCTTGGTCAGTGTGCCCAACATCTTGAAAAGGGTGAAACC
genomic: ATATGACGTTGCTTTCTTGTGCATATGCTGGAACTGGGAATGTGCTCAAGgttttgcatt ... aattgcacagGTCCAACACCTTCTTGGTCAGTGTGCCCAACATCTTGAAAAGGGTGAAACC
EST: gi|110707945|gb|EE084922.1|EE084922
EST:     ATATGACGTTGCTTTCTTGTGCATATGCTGGAACTGGGAATGTGCTCAAG                         GTCCAACACCTTCTTGGTCAGTGTGCCCAACATCTTGAAAAGGGTGAAACC
genomic: ATATGACGTTGCTTTCTTGTGCATATGCTGGAACTGGGAATGTGCTCAAGgttttgcatt ... aattgcacagGTCCAACACCTTCTTGGTCAGTGTGCCCAACATCTTGAAAAGGGTGAAACC
EST: gi|30305222|gb|CB982016.1|CB982016
EST:     ATATGACGTTGCTTTCTTGTGCATATGCTGGAACTGGGAATGTGCTCAAG                         GTCCAACACCTTCTTGGTCAGTGTGCCCAACATCTTGAAAAGGGTGAAACC
genomic: ATATGACGTTGCTTTCTTGTGCATATGCTGGAACTGGGAATGTGCTCAAGgttttgcatt ... aattgcacagGTCCAACACCTTCTTGGTCAGTGTGCCCAACATCTTGAAAAGGGTGAAACC
EST: gi|110699529|gb|EE076605.1|EE076605
EST:     ATATGACGTTGCTTTCTTGTGCATATGCTGGAACTGGGAATGTGCTCAAG                         GTCCAACACCTTCTTGGTCAGTGTGCCCAACATCTTGAAAAGGGTGAAACC
genomic: ATATGACGTTGCTTTCTTGTGCATATGCTGGAACTGGGAATGTGCTCAAGgttttgcatt ... aattgcacagGTCCAACACCTTCTTGGTCAGTGTGCCCAACATCTTGAAAAGGGTGAAACC
EST: gi|30305288|gb|CB982082.1|CB982082
EST:     ATATGACGTTGCTTTCTTGTGCATATGCTGGAACTGGGAATGTGCTCAAG                         GTCCAACACCTTCTTGGTCAGTGTGCCCAACATCTTGAAAAGGGTGAAACC
genomic: ATATGACGTTGCTTTCTTGTGCATATGCTGGAACTGGGAATGTGCTCAAGgttttgcatt ... aattgcacagGTCCAACACCTTCTTGGTCAGTGTGCCCAACATCTTGAAAAGGGTGAAACC
EST: gi|37187493|gb|CF606846.1|CF606846
EST:     ATATGACGTTGCTTTCTTGTGCATATGCTGGAACTGGGAATGTGCTCAAG                         GTCCAACACCTTCTTGGTCAGTGTGCCCAACATCTTGAAAAGGGTGAAACC
genomic: ATATGACGTTGCTTTCTTGTGCATATGCTGGAACTGGGAATGTGCTCAAGgttttgcatt ... aattgcacagGTCCAACACCTTCTTGGTCAGTGTGCCCAACATCTTGAAAAGGGTGAAACC
EST: gi|161716967|gb|FC068834.1|FC068834
EST:     GCTTTCTTGTGCATATGCTGGAACTGGGAATGTGCTCAAG                         GTCCAACACCTTCTTGGTCAGTGTGCCCAACATCTTGAAAAGGGTGAAACC
genomic: GCTTTCTTGTGCATATGCTGGAACTGGGAATGTGCTCAAGgttttgcatt ... aattgcacagGTCCAACACCTTCTTGGTCAGTGTGCCCAACATCTTGAAAAGGGTGAAACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataaatgaagaggccaaccttcttttttcattctttgctttttttaattgcacagGTCCAACACCTTCTTGGTCAGTGTGCCCAACATCTTGAAAAGGGTGAAACCCACCAAGGCCCAGCTGTACTTGGAATTGCAATGGTGGCAATGGCTGAAG
                                         ttttaat  putative branch site (score: 3)
                 ccttcttttttcattc  CT-rich tract
                      ttttttcattctttgc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttgcattaaagttgattgctgttcaagattcctattccataaatgaagaggccaaccttcttttttcattctttgctttttttaattgcacagGTCCAACACCTTCTTGGTCAGTGTGCCCAACATCTTGAAAAGGGTGAAACCCACCAAGGCCCAGCTGTACTTGGAATTGCAATGGTGGCAATGGCTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG