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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagacctcttgaattcatctcccgcataaagtctcatgtcttttttctattcattgcctattaaaaacaattatttacttggggtttcaattttttgcagGACAGGATTTGTCCCCAATTGACTTGATTAATGTCCAGCAATTTGCGCAGAGGGTAATGGACCTCTCTGAGTACAGGAAGAAGCTGTATGAATATCTGGT

Basic information

species Vitis vinifera
transcript Vv17s0000g01720.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g01720.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G110233_T01 (Zea mays), 3'ss of exon 4
gtagacctcttgaattcatctcccgcataaagtctcatgtcttttttctattcat--tgcctattaaaaacaattatttacttggggtttc---aattttttgcagGACAGGATTTGTCCCCAATTGACTTGATTAATGTCCAGCAATTTGCGCAGAGGGTAATGGACCTCTCTGAGTACAGGAAGAAGCTGTATGAATATCTGGT
                        | |||   |    |  ||||  | |    ||  ||  | |   |||   |  | | ||| |  |||      || ||| |||| |||||| |||| ||| |||| ||||| ||||||||||||||||| || ||||| ||| | |||||||||||  | || || || ||||||||||| ||
------------------gtaatgggatatgatgcagttactttagtttgactatcatgattgtagtaaatgttcttatgctttgttttttcttgtttgttttcagGCCAGGATCTGTCACCAGTTGATTTGATCAATGTCCAGCAATTTGCCCAAAGGGTTATGAATCTCTCTGAGTATCGCAAAAACCTTTATGAATATCTCGT

upper sequence: Vv17s0000g01720.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G144995_T01 (Zea mays), 3'ss of exon 4
gtagacctcttgaattcatctcccgcataaagtctcatgtcttttttctattcattgcctattaaaaacaattatttacttggggtttcaattttttgcagGACAGGATTTGTCCCCAATTGACTTGATTAATGTCCAGCAATTTGCGCAGAGGGTAATGGACCTCTCTGAGTACAGGAAGAAGCTGTATGAATATCTGGT
          | |    || |   |||   | | |  |   ||   | |  | ||||  || ||||  |  ||||    |     | |   || ||| |||| |||||| |||| ||| |||| ||||| ||||||||||||||||| || ||||| ||| | |||||||||||  | || || || ||||| ||||| ||
---------gtaatgggatatgatgcagtcaatttagt---ttgactatggtgattg--tagtaaatgctcttatgctttgtttttattgtttgttttcagGCCAGGATCTGTCACCAGTTGATTTGATCAATGTCCAGCAATTTGCCCAAAGGGTTATGAATCTCTCTGAGTATCGCAAAAACCTTTATGAGTATCTTGT

upper sequence: Vv17s0000g01720.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA05G03150.1 (Glycine max), 3'ss of exon 4
gtagacctcttgaattcatctcccgcataaagtctcatgtcttttt-tctattcattgcct-attaaaaacaattatttacttggggtttcaattttttgcagGACAGGATTTGTCCCCAATTGACTTGATTAATGTCCAGCAATTTGCGCAGAGGGTAATGGACCTCTCTGAGTACAGGAAGAAGCTGTATGAATATCTGGT
                        | |  || |||||| | |||   | ||    |||| | |||   |      || | |||    | |  |  |||| |||||||||||||||||||| | ||||| || |||||||| |||||||| ||||||||||||||||| ||||||||||| |||||  | ||||| || |||||
------------------------gta-gaattctcatctttttgggtttaacttttgcttcattctcagtctgaatcttctttc--tcttgacgtttt-cagGACAGGATTTGTCCCCAGTGGACTTAATCAATGTCCATCAATTTGCACAGAGGGTAATGGACCTATCTGAGTACAGAAAGAACTTATATGATTACCTGGT

upper sequence: Vv17s0000g01720.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA17G13770.1 (Glycine max), 3'ss of exon 4
gtagacctcttgaattcatctcccgcataaagtctcatgtcttttttcta-ttcattgcctattaaaaacaattatttacttggggtttcaattttttgcagGACAGGATTTGTCCCCAATTGACTTGATTAATGTCCAGCAATTTGCGCAGAGGGTAATGGACCTCTCTGAGTACAGGAAGAAGCTGTATGAATATCTGGT
              |  |  || |   |    | |   || |   || |  ||| ||  ||||   || |  || ||  ||||  ||||          |||||||||||||||||||| | |||||||| || ||||| |||||||| ||||||||||||||||| ||||||||||| || ||  ||||||| || |||||
-------------gtagaattctcatct----ttttgggtttaacttttgcttcgttctctatctgaatc--tttttctcttgatgtttt---------cagGACAGGATTTGTCCCCAGTGGACTTGATCAACGTCCATCAATTTGCACAGAGGGTAATGGACCTATCTGAGTACAGAAAAAACTTGTATGATTACCTGGT

upper sequence: Vv17s0000g01720.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA07G11560.1 (Glycine max), 3'ss of exon 4
gtagacctcttgaattcatctcccgcataaagtctcatgtcttttttctattcattgcctattaaaaacaattatttacttggggtttcaattttttgcagGACAGGATTTGTCCCCAATTGACTTGATTAATGTCCAGCAATTTGCGCAGAGGGTAATGGACCTCTCTGAGTACAGGAAGAAGCTGTATGAATATCTGGT
|||||  |||||| ||| | |      |   |  |  || ||||| |||   ||||  |||||  || |   | | |          | |  ||| | ||||||| |||||||||||| | |||||| |||||||||| ||||||||||| ||||| |||||||| ||||||||||||  |||| ||||||| || |||||
gtagaattcttgatttcttgtatt-tgtgttgcttt-tgacttttgtct---cattctctattttaatctgctttct---------cttacctttcttcagGACAAGATTTGTCCCCAGTGGACTTGGTTAATGTCCAACAATTTGCGCAAAGGGTGATGGACCTTTCTGAGTACAGGCGGAAGTTGTATGATTACCTGGT

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|110686032|gb|EE063274.1|EE063274
EST:     AGATGAAGATAAAGCAAAGGAGATTGTGGAAGCTGCCAAAGCATCCATGG                         GACAGGATTTTGTCCC
genomic: AGATGAAGATAAAGCAAAGGAGATTGTGGAAGCTGCCAAAGCATCCATGGgtagacctct ... ttttttgcagGACAGGATTT-GTCCC
EST: gi|33405708|gb|CF211335.1|CF211335
EST:     AGATGAAGATAAAGCAAAGGAGATTGTGGAAGCTGCCAAAGCATCCATGG                         GACAGGATTTGTCCCCAATTGACTTGATTAATGTCCAGCAATTTGCGCAGA
genomic: AGATGAAGATAAAGCAAAGGAGATTGTGGAAGCTGCCAAAGCATCCATGGgtagacctct ... ttttttgcagGACAGGATTTGTCCCCAATTGACTTGATTAATGTCCAGCAATTTGCGCAGA
EST: gi|33404147|gb|CF209774.1|CF209774
EST:     AGATGAAGATAAAGCAAAGGAGATTGTGGAAGCTGCCAAAGCATCCATGG                         GACAGGATTTGTCCCCAATTGACTTGATTAATGTCCAGCAATTTGCGCAGA
genomic: AGATGAAGATAAAGCAAAGGAGATTGTGGAAGCTGCCAAAGCATCCATGGgtagacctct ... ttttttgcagGACAGGATTTGTCCCCAATTGACTTGATTAATGTCCAGCAATTTGCGCAGA
EST: gi|161720525|gb|FC070912.1|FC070912
EST:     AGATGAAGATAAAGCAAAGGAGATTGTGGAAGCTGCCAAAGCATCCATGG                         GACAGGATTTGTCCCCCATTGACTTGATT
genomic: AGATGAAGATAAAGCAAAGGAGATTGTGGAAGCTGCCAAAGCATCCATGGgtagacctct ... ttttttgcagGACAGGATTTGTCCCCAATTGACTTGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctattcattgcctattaaaaacaattatttacttggggtttcaattttttgcagGACAGGATTTGTCCCCAATTGACTTGATTAATGTCCAGCAATTTGCGCAGAGGGTAATGGACCTCTCTGAGTACAGGAAGAAGCTGTATGAATATCTGGT
                                             ttttttgc  CT-rich tract
             tattaaaaacaattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagacctcttgaattcatctcccgcataaagtctcatgtcttttttctattcattgcctattaaaaacaattatttacttggggtttcaattttttgcagGACAGGATTTGTCCCCAATTGACTTGATTAATGTCCAGCAATTTGCGCAGAGGGTAATGGACCTCTCTGAGTACAGGAAGAAGCTGTATGAATATCTGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG