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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagttattgtcatctttgttctcttttctcataatggaacaacttacacttagaatttcattttaatgtaaatcaagttgaccataatgatattccacagGTAACTTTTATTGAAGCTCTTGATCAGCTTATGCCTGGATTTGATCCTGAGATTGGGAAGTTGGCCCAAAGAGTTCTAATAAATCCACGGAAAATTGACT

Basic information

species Vitis vinifera
transcript Vv05s0077g01210.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0077g01210.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 5
-tagttattgtcatctttgttctcttttctcataatggaacaacttacacttagaatttcattttaatgtaaatcaagttgaccataatgatattccacagGTAACTTTTATTGAAGCTCTTGATCAGCTTATGCCTGGATTTGATCCTGAGATTGGGAAGTTGGCCCAAAGAGTTCTAATAAATCCACGGAAAATTGACT
   ||||   ||   ||     ||| | ||  |    ||  ||       ||   || | ||  || |  |  |  | ||  | | | |    ||  |||||| |||||| ||||||| ||||||||| | |||||||| ||||||||||||||||  || |||||||||||  |||| || ||||| || ||||||||||
catgttaaattctaattaaccatctatgctgttttatgattaaggcctg-ttgtcatctgatgatatttcacctgtatttacctaaatttcacttggacagGTTACTTTTGTTGAAGCACTTGATCAGTTGATGCCTGGTTTTGATCCTGAGATTGCAAAATTGGCCCAAAGGATTCTTATCAATCCTCGTAAAATTGACT

upper sequence: Vv05s0077g01210.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 3'ss of exon 5
tagttattgtcatctttg-ttctcttttctcataatggaacaacttacacttagaatttcattttaatgtaaatc--aagttgaccataatgatattccacagGTAACTTTTATTGAAGCTCTTGATCAGCTTATGCCTGGATTTGATCCTGAGATTGGGAAGTTGGCCCAAAGAGTTCTAATAAATCCACGGAAAATTGACT
|    | |  ||    || |||| ||     |  || | |  |||  ||    || |||  |||| |  |    |   | |||||  |  |   ||||  ||||| |||||| ||||||||||||| ||||| |||||||| ||||||||||| ||||  || || ||||| ||||| || || || || ||||| || ||||
tttcaacttacacaaatgattctattacagtagtattgtatcact-gcatgctgatttttgttttcacatgccccctgaattgacagtttt--cattcttcagGTTACTTTTGTTGAAGCTCTTGACCAGCTAATGCCTGGTTTTGATCCTGAAATTGCAAAATTAGCCCAGAGAGTCCTTATCAACCCTCGGAATATAGACT

upper sequence: Vv05s0077g01210.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 5
tagttattgtcatctttgttctcttttctcataatggaacaacttacacttagaatttcatt---ttaatgtaaatcaagttgaccataatgatattccacagGTAACTTTTATTGAAGCTCTTGATCAGCTTATGCCTGGATTTGATCCTGAGATTGGGAAGTTGGCCCAAAGAGTTCTAATAAATCCACGGAAAATTGACT
  | |      ||  | |    ||  |   | |   |     || |    ||  |||    |   |||||  |  | || ||   ||     | |||   ||||| |||||| ||||||||||||| ||||| |||||||||||||||||||| ||||  || || ||||| |||||||| || ||||| |||||||||||||
--gctggatgaattctagaatgctccttagacatctgt-tgcctgatgaatatgattgttctcagttaattcacttgaatttactcaattcaaaattgggcagGTTACTTTTGTTGAAGCTCTTGACCAGCTGATGCCTGGATTTGATCCTGAAATTGCAAAATTAGCCCAGAGAGTTCTTATCAATCCTCGGAAAATTGACT

upper sequence: Vv05s0077g01210.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G145595_T02 (Zea mays), 3'ss of exon 4
-----tagttattgtcatctttgttctcttttctcataatggaacaacttacacttag-aatttcattttaatgtaaatcaagttgaccataatgatattccacagGTAACTTTTATTGAAGCTCTTGATCAGCTTATGCCTGGATTTGATCCTGAGATTGGGAAGTTGGCCCAAAGAGTTCTAATAAATCCACGGAAAATTGACT
          ||||   |   |  ||||||    || ||| |  |   || |  | |  |  |  | ||| || |  ||    ||   |||  |   ||    ||||| |||||| ||||||||||||||||  | |||||||| |||||||| |||||||  || ||||| || ||  |||| || | ||| || ||||||||||
tgtttcctgaattggattacatcatctcttgatccacaattgggc--tttgctgtcaatagctggagtttcatctgtat----ttatgcattttttgatcgatcagGTTACTTTTGTTGAAGCTCTTGATCAATTAATGCCTGGGTTTGATCCCGAGATTGCAAAATTGGCGCAGAGGATTCTTATTAGTCCTCGTAAAATTGACT

upper sequence: Vv05s0077g01210.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ06739 (Selaginella moellendorffii), 3'ss of exon 5
tagttattgtcatctttgttctcttttctcataatggaacaacttacacttagaatttcattttaatgtaaatcaagttgaccataatgatattccacagGTAACTTTTATTGAAGCTCTTGATCAGCTTATGCCTGGATTTGATCCTGAGATTGGGAAGTTGGCCCAAAGAGTTCTAATAAATCCACGGAAAATTGACT
                                                 ||||  |||| | ||    |     |  | ||  |    ||| |    ||||| |||||| |||||||||| ||||| || ||||| || ||||||||||| || |||||| | || || ||  | || || || || || |||||||| |
-----------------------------------------------gtttagtttttcttctttcctttttcta--tagaatacg-cgatgt---gcagGTGACTTTTGTTGAAGCTCTGGATCAACTGATGCCAGGCTTTGATCCTGAAATCGGGAAGCTTGCTCAGAGGCTCCTGATCAACCCTCGAAAAATTGATT

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|349826900|gb|FQ418991.1|FQ418991
EST:     GTTATATTGGTCTTGAATTCAGTGATGTGTATACAGCACTTGGAAGTGAG                         GTAACTTTTATTGAAGCTCTTGATCAGCTTATGCCTGGATTTGATCCTGAG
genomic: GTTATATTGGTCTTGAATTCAGTGATGTGTATACAGCACTTGGAAGTGAGgtagcatctt ... tattccacagGTAACTTTTATTGAAGCTCTTGATCAGCTTATGCCTGGATTTGATCCTGAG
EST: gi|351031178|gb|FQ445005.1|FQ445005
EST:     GTTATATTGGTCTTGAATTCAGTGATGTGTATACAGCACTTGGAAGTGAG                         GTAACTTTTATTGAAGCTCTTGATCAGCTTATGCCTGGATTTGATCCTGAG
genomic: GTTATATTGGTCTTGAATTCAGTGATGTGTATACAGCACTTGGAAGTGAGgtagcatctt ... tattccacagGTAACTTTTATTGAAGCTCTTGATCAGCTTATGCCTGGATTTGATCCTGAG
EST: gi|71877655|gb|DT026710.1|DT026710
EST:     GTTATATTGGTCTTGAATTCAGTGATGTGTATACAGCACTTGGAAGTGAG                         GTAACTTTTATTGAAGCTCTTGATCAGCTTATGCCTGGATTTGATCCTGAG
genomic: GTTATATTGGTCTTGAATTCAGTGATGTGTATACAGCACTTGGAAGTGAGgtagcatctt ... tattccacagGTAACTTTTATTGAAGCTCTTGATCAGCTTATGCCTGGATTTGATCCTGAG
EST: gi|71877913|gb|DT026968.1|DT026968
EST:     GTTATATTGGTCTTGAATTCAGTGATGTGTATACAGCACTTGGAAGTGAG                         GTAACTTTTATTGAAGCTCTTGATCAGCTTATGCCTGGATTTGATCCTGAG
genomic: GTTATATTGGTCTTGAATTCAGTGATGTGTATACAGCACTTGGAAGTGAGgtagcatctt ... tattccacagGTAACTTTTATTGAAGCTCTTGATCAGCTTATGCCTGGATTTGATCCTGAG
EST: gi|351014262|gb|FQ434851.1|FQ434851
EST:     GTTATATTGGTCTTGAATTCAGTGATGTGTATACAGCACTTGGAAGTGAG                         GTAACTTTTATTGAAGCTCTTGATCAGCTTATGCCTGGATTTGATCCTGAG
genomic: GTTATATTGGTCTTGAATTCAGTGATGTGTATACAGCACTTGGAAGTGAGgtagcatctt ... tattccacagGTAACTTTTATTGAAGCTCTTGATCAGCTTATGCCTGGATTTGATCCTGAG
EST: gi|351023248|gb|FQ432631.1|FQ432631
EST:     GTTATATTGGTCTTGAATTCAGTGATGTGTATACAGCACTTGGAAGTGAG                         GTAACTTTTATTGAAGCTCTTGATCAGCTTATGCCTGGATTTGATCCTGAG
genomic: GTTATATTGGTCTTGAATTCAGTGATGTGTATACAGCACTTGGAAGTGAGgtagcatctt ... tattccacagGTAACTTTTATTGAAGCTCTTGATCAGCTTATGCCTGGATTTGATCCTGAG
EST: gi|71878131|gb|DT027186.1|DT027186
EST:     GTTATATTGGTCTTGAATTCAGTGATGTGTATACAGCACTTGGAAGTGAG                         GTAACTTTTATTGAAGCTCTTGATCAGCTTATGCCTGGATTTGATCCTGAG
genomic: GTTATATTGGTCTTGAATTCAGTGATGTGTATACAGCACTTGGAAGTGAGgtagcatctt ... tattccacagGTAACTTTTATTGAAGCTCTTGATCAGCTTATGCCTGGATTTGATCCTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acacttagaatttcattttaatgtaaatcaagttgaccataatgatattccacagGTAACTTTTATTGAAGCTCTTGATCAGCTTATGCCTGGATTTGATCCTGAGATTGGGAAGTTGGCCCAAAGAGTTCTAATAAATCCACGGAAAATTGACT
     tagaatttcattttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagttattgtcatctttgttctcttttctcataatggaacaacttacacttagaatttcattttaatgtaaatcaagttgaccataatgatattccacagGTAACTTTTATTGAAGCTCTTGATCAGCTTATGCCTGGATTTGATCCTGAGATTGGGAAGTTGGCCCAAAGAGTTCTAATAAATCCACGGAAAATTGACT

- - - - - - - - - - - - - - - - - -ggaacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaatcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - accataa