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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtggcccacccattgctgcctcttgagttgacagttctattatgtcgtctcatttgtttaactctgtgttgtctactttgcttacagCTCCTCTGGGTTAATCTTATCATGGATACTCTTGGAGCACTTGCATTGGCCACTGAACCACCAACAGATCACCTGATGCACAGGCCTCCAGTTGGTCGAA

Basic information

species Vitis vinifera
transcript Vv11s0052g00320.t01
intron # 29
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 29
lower sequence: LOC_Os02g08010.1 (Oryza sativa), 3'ss of exon 10
---------gttggtggcccacccattgctgcctcttgagttgacagttctattatgtcgtctcat--ttgtttaactctgtgttgtctactttgcttacagCTCCTCTGGGTTAATCTTATCATGGATACTCTTGGAGCACTTGCATTGGCCACTGAACCACCAACAGATCACCTGATGCACAGGCCTCCAGTTGGTCGAA
         ||| |||        |||   |   ||| | |  |  | | |   | |||| | |||   ||  |   |   |   || |  | |   |  |||| || ||||| ||||| || ||||| || ||||| |||||||||||||| ||||||||||||||||| || || ||| |  |||| || ||||| || |
ggggaaattgttagtgaaaatgaaattaa-gatacttaactgtattgatttgc-acgtcggcacatggctgaatgttttacttccgtttgttgttgatttagCTTCTTTGGGTCAATCTCATTATGGACACACTTGGTGCACTTGCATTGGCTACTGAACCACCAACAGACCAACTTATGAAGCGGCCACCTGTTGGACGGA

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 29
lower sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 27
gttggtggcccacccattgctgcctcttga--gttgacagttctattatgtcgtctcatttgtttaactctgtgttgtctactttgcttacagCTCCTCTGGGTTAATCTTATCATGGATACTCTTGGAGCACTTGCATTGGCCACTGAACCACCAACAGATCACCTGATGCACAGGCCTCCAGTTGGTCGAA
||| |  || ||  |  || |   |  |||  | | |||      |||||   |   |||   |    | ||  | | ||  || |||  ||||| || |||||||| || |||||||||||||| || || |||||| |||| || |||||||| || || || || ||||| || || ||||||||  |||
gtttg-agctcatactctgtttgttactgatagataacacggaagttatggt-taatattctctctcttttgcttgggcttgttggctggcagCTACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAA

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 29
lower sequence: GRMZM5G893864_T01 (Zea mays), 3'ss of exon 6
-----------gttggtggcccacccattgctgcc-tcttgagttgacagttctattatgtcgtctcatttgt-ttaactctgtgttgtctactttgcttacagCTCCTCTGGGTTAATCTTATCATGGATACTCTTGGAGCACTTGCATTGGCCACTGAACCACCAACAGATCACCTGATGCACAGGCCTCCAGTTGGTCGAA
           |||  ||  | |    | | |    | || || |   | ||  |   ||    |  |    | ||| ||   | ||||    |||   ||||||| |||||||||||||| |||||||| || || || || ||||| ||||| |||||||||||||||||||| || |||    |||| |||||||| || |
caaaccaagttgttaatgaacaaagtgtagttaaagtattaagcttctatttgaaagttggacaccaacaaatattagcttccttttgt----tttttatacagCTTCTCTGGGTTAATCTCATCATGGACACACTCGGTGCTCTTGCTTTGGCTACTGAACCACCAACAGATCAACTTATGAGGCGGCCACCAGTTGGACGGA

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 29
lower sequence: GLYMA17G06520.1 (Glycine max), 3'ss of exon 29
gttggtggcccacccattgctgcct--cttgagttgacagttctattatgtcgtctcatttgtttaactctgtgttgtctactttgcttacagCTCCTCTGGGTTAATCTTATCATGGATACTCTTGGAGCACTTGCATTGGCCACTGAACCACCAACAGATCACCTGATGCACAGGCCTCCAGTTGGTCGAA
||| |    | |    |  ||  ||   ||| | |  |   | ||||  |  | ||    |  | |||| |   ||   || |||    |||||| |||||||| ||||||||||||||||||||||||||| | || ||||| |||||||||||||| |||  ||||||| |      ||||   |||||||
gtttgctttctatttgtctctaactggtttgtgctccctcatttattcagaaggctatccttatgaactataccttcattaatttatcaacagCTTCTCTGGGTAAATCTTATCATGGATACTCTTGGAGCATTAGCCTTGGCAACTGAACCACCAACTGATTCCCTGATGGATCAAAGTCCAAAGGGTCGAA

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 29
lower sequence: GLYMA13G00420.1 (Glycine max), 3'ss of exon 27
gttggtggcccacccattgctgcct--cttgagttgacagttctattatgtcgtctcatttgtttaactctgtgttgtctactttgcttacagCTCCTCTGGGTTAATCTTATCATGGATACTCTTGGAGCACTTGCATTGGCCACTGAACCACCAACAGATCACCTGATGCACAGGCCTCCAGTTGGTCGAA
||| |    | |    |  ||  |    ||| | |  |   | ||||  |  | ||    |  | |||| |   ||   || |||    |||||| |||||||| ||||||||||||||||||||||||||| | || ||||| |||||||| ||||| |||   |||||| |       ||    |||| ||
gtttgatttctatttgtctctaaccggtttgtgctccctcatttattcagaaggctatccttatgaactataccttcattaatttctcaacagCTTCTCTGGGTAAATCTTATCATGGATACTCTTGGAGCATTAGCCTTGGCAACTGAACCGCCAACTGATTCTCTGATGGATCAAAGCCCTAAGGGTCAAA

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 29
lower sequence: GLYMA15G18180.1 (Glycine max), 3'ss of exon 26
gttggtggcccacccattgctgcctcttgagttgacagttctattatgtcgtctcatttgtttaactctgtgttgtctactttgcttacagCTCCTCTGGGTTAATCTTATCATGGATACTCTTGGAGCACTTGCATTGGCCACTGAACCACCAACAGATCACCTGATGCACAGGCCTCCAGTTGGTCGAA
    || | |   |  || ||   ||| |  |   |     ||||| |||        |  | |  |     |    | ||||   || |||| || ||||| |||||||||||||||||||| |||||||| ||  |||| |||||||||||||| |||||||| ||| |  |  | ||||| |||||||
----gttgactttctttttctctttctaggttatgctcacgtattaagtcaggatgagtcatgacattaaaatctgttgctttctctatagCTTCTTTGGGTAAATCTTATCATGGATACTCTGGGAGCACTAGCCCTGGCAACTGAACCACCAACTGATCACCTCATGGATCGATCCCCAGTGGGTCGAA

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 29
lower sequence: GLYMA09G06890.1 (Glycine max), 3'ss of exon 26
gttggtggcccacccattgctgcctcttgagttgacagttctattatgtc-gtctcatttgtttaactctgtgttgtctactttgcttacagCTCCTCTGGGTTAATCTTATCATGGATACTCTTGGAGCACTTGCATTGGCCACTGAACCACCAACAGATCACCTGATGCACAGGCCTCCAGTTGGTCGAA
    || | |   |  ||  |   ||| |  |   |   | ||||| ||| |  | |    |    ||      ||| | ||||   || |||| || ||||| |||||||||||||||||||| ||||| || ||  |||| |||||||||||||| |||||||| ||| |  |  ||||||| |||||||
----gttgactttctttttttctttctaggttatgctcatgtattaagtcaggatgagccatgatgctaaaatctgt-tgctttctctatagCTTCTTTGGGTGAATCTTATCATGGATACTCTGGGAGCGCTGGCCCTGGCAACTGAACCACCAACTGATCACCTCATGGATCGAACTCCAGTGGGTCGAA

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 29
lower sequence: AT5G57110.2 (Arabidopsis thaliana), 3'ss of exon 28
------gttggtggcccacccattgctgcctcttgagttgacagttctattatgtcgtctca-tttgtttaactctgtgttgtctactttg-cttacagCTCCTCTGGGTTAATCTTATCATGGATACTCTTGGAGCACTTGCATTGGCCACTGAACCACCAACAGATCACCTGATGCACAGGCCTCCAGTTGGTCGAA
      |||  ||   ||   |  |||   | |  |  |  |  |     ||  |  | | | |||| | |  | | ||  || | ||||  | ||||||| |||||||||||||| || ||||| |||||||||||| | || ||||| ||||||||||| || |||||||| |||   ||||||||||||||  |||
gtttgagtttctgttgcattta--gctctttttgaatatctctctctctctaaatattataagtttgctcatatatttggcgttttctttaacatacagCTTCTCTGGGTTAATCTGATAATGGACACTCTTGGAGCATTGGCTTTGGCTACTGAACCACCCACTGATCACCTCATGGGGAGGCCTCCAGTTGGCAGAA

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 29
lower sequence: AT4G29900.1 (Arabidopsis thaliana), 3'ss of exon 28
------gttggtggcccacccattgctgcctcttgagttgacagttctattatgtcgtctcatttgtttaactctgtgttgtctactttgcttacagCTCCTCTGGGTTAATCTTATCATGGATACTCTTGGAGCACTTGCATTGGCCACTGAACCACCAACAGATCACCTGATGCACAGGCCTCCAGTTGGTCGAA
        | || |        |  ||   |||    |  |||    ||||          | ||| | ||    || || ||   |     |  ||||||| ||||| |||||||| |||||||||||||| || ||||| || |||||||| |||||||| |||||| | ||| |  |  | || |||||  |||
gttcgaaatagtagttttatactctctctttctcatctgcacaaaagtatt-cacttcagaacttggtaaaaa--gtcttatcccttacctatgtagCTCCTTTGGGTCAATCTTATAATGGATACTCTTGGGGCTCTTGCTTTAGCCACTGAGCCACCAACCGATCACTTAATGGATCGAGCGCCTGTTGGCAGAA

upper sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 29
lower sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 23
gttggtggcccacccattgctgcctcttgagttgacagttctattatgtcgtctcatttgtttaactctgtgttgtctactttgcttacagCTCCTCTGGGTTAATCTTATCATGGATACTCTTGGAGCACTTGCATTGGCCACTGAACCACCAACAGATCACCTGATGCACAGGCCTCCAGTTGGTCGAA
                                 |  |||  |  | | |||| |||| |||| |  |   | |       |||   ||||||| || ||||| |||||||| ||||||||| | ||||| || || || |||||||||||||| |||||  || | ||| | ||||| || || || || |
---------------------------------gtgagtcgttatctctcgtttcatctgttcagtt---tataagtcgtttt--ctacagCTGCTTTGGGTAAATCTTATTATGGATACTTTGGGAGCGCTCGCTTTAGCCACTGAACCACCTACAGACGACTTAATGGATAGGCCGCCCGTGGGACGCA

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|30299117|gb|CB975911.1|CB975911
EST:     ATGTCGTGGCAGCAATTTCCTCTGGCAATGTTCCACTAAATGCAGTGCAG                         CTCCTTTGGGTTAATTTTATAATGGATACTCTTGGAGCACTTGCATTGGCC
genomic: ATGTCGTGGCAGCAATTTCCTCTGGCAATGTTCCACTAAATGCAGTGCAGgttggtggcc ... ttgcttacagCTCCTCTGGGTTAATCTTATCATGGATACTCTTGGAGCACTTGCATTGGCC
EST: gi|30299189|gb|CB975983.1|CB975983
EST:     ATGTCGTGGCAGCAATTTCCTCTGGCAATGTTCCACTAAATGCAGTGCAG                         CTCCTCTGGGTTAATCTTATAATGGATACTCTTGGAGCACTTGCATTGGCC
genomic: ATGTCGTGGCAGCAATTTCCTCTGGCAATGTTCCACTAAATGCAGTGCAGgttggtggcc ... ttgcttacagCTCCTCTGGGTTAATCTTATCATGGATACTCTTGGAGCACTTGCATTGGCC
EST: gi|30299258|gb|CB976052.1|CB976052
EST:     ATGTCGTGGCAGCAATTTCCTCTGGCAATGTTCCACTAAATGCAGTGCAG                         CTCCTTTGGGTTAATTTTATAATGGATACTCTTGGAGCACTTGCATTGGCC
genomic: ATGTCGTGGCAGCAATTTCCTCTGGCAATGTTCCACTAAATGCAGTGCAGgttggtggcc ... ttgcttacagCTCCTCTGGGTTAATCTTATCATGGATACTCTTGGAGCACTTGCATTGGCC
EST: gi|71883815|gb|DT032870.1|DT032870
EST:     ATGTCGTGGCAGCAATTTCCTCTGGCAATGTTCCACTAAATGCAGTGCAG                         CTCCTCTGGGTTAATCTTATCATGGATACTCTTGGAGCACTTGCATTGGCC
genomic: ATGTCGTGGCAGCAATTTCCTCTGGCAATGTTCCACTAAATGCAGTGCAGgttggtggcc ... ttgcttacagCTCCTCTGGGTTAATCTTATCATGGATACTCTTGGAGCACTTGCATTGGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttctattatgtcgtctcatttgtttaactctgtgttgtctactttgcttacagCTCCTCTGGGTTAATCTTATCATGGATACTCTTGGAGCACTTGCATTGGCCACTGAACCACCAACAGATCACCTGATGCACAGGCCTCCAGTTGGTCGAA
                       gtttaac  putative branch site (score: 3)
                                       tctacttt  putative PPT
                   atttgtttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggtggcccacccattgctgcctcttgagttgacagttctattatgtcgtctcatttgtttaactctgtgttgtctactttgcttacagCTCCTCTGGGTTAATCTTATCATGGATACTCTTGGAGCACTTGCATTGGCCACTGAACCACCAACAGATCACCTGATGCACAGGCCTCCAGTTGGTCGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA