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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttctggtgtttcccaagtaatagttgccttatgacataattgaatggatgatttgacttttttgtgtgtgagaattctaaattggtgaagttttcagGGAAGGAAGTTGTTGCGGTAGACAGCCCCATTGGTCGTTTGGGTGTAACGGTTTGCTATGATTTGAGATTCCCAGAGCTTTATCAGCAGCTAAGGTTCCT

Basic information

species Vitis vinifera
transcript Vv13s0067g03530.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0067g03530.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os12g31830.1 (Oryza sativa), 3'ss of exon 4
---tttttctggtgtttcccaagtaatagttgccttatgacataattgaatggatg-atttgacttttttgtgtgtgagaattctaaattggtgaagttttcagGGAAGGAAGTTGTTGCGGTAGACAGCCCCATTGGTCGTTTGGGTGTAACGGTTTGCTATGATTTGAGATTCCCAGAGCTTTATCAGCAGCTAAGGTTCCT
   |    ||  |  | |   ||| ||| |       ||| | |   |   || || | ||||      | | |||||   |     |||  |  | || |||||  |    || ||||| || || || ||  |||| ||  | ||  | || |||||||||||||||||||| ||||||||||| ||     |  | ||   
gattgaaactaatactgcaatagtgata-tcatggagtgagacatacgtcgggttgcagttgataacgctatatgtgatggtgt---atttatttatttatcagGTGATACTGTCGTTGCAGTGGATAGTCCTTTTGGACGACTTGGGCTTACTGTTTGCTATGATTTGAGATTTCCAGAGCTTTACCAATGTTTGCGCTTTAA

upper sequence: Vv13s0067g03530.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G145578_T01 (Zea mays), 3'ss of exon 4
tttttctggtgtttcccaagtaatagttgccttatgacataattgaatggatgatttgacttttttgtgtg--tgagaattctaaattggtgaagttttcagGGAAGGAAGTTGTTGCGGTAGACAGCCCCATTGGTCGTTTGGGTGTAACGGTTTGCTATGATTTGAGATTCCCAGAGCTTTATCAGCAGCTAAGGTTCCT
   |  |||||| |   | | | ||||     | |   |  ||||||| |   |||       | | ||||  ||   ||  |   ||       || |||||  |     ||||||| || || |||||  |||| || |||||  | || |||||||||||||||||||||||||||||||||||     |  | ||   
-aatagtggtgtcttggatgaagtagtactgctgttgtaatattgaattg-caattgattccatatatgtgattgcttatgatgttttctctctcttatcagGTGATACTATTGTTGCTGTGGATAGCCCTTTTGGACGGTTGGGGCTTACTGTTTGCTATGATTTGAGATTCCCAGAGCTTTATCAAATTTTGCGTTTTAA

upper sequence: Vv13s0067g03530.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G43950.1 (Glycine max), 3'ss of exon 4
tttttctggtgtttcccaagtaa--tagttgccttatgacataattgaatggatgatt--tgacttttttgtgtgtgagaattctaaattggtgaagttttcagGGAAGGAAGTTGTTGCGGTAGACAGCCCCATTGGTCGTTTGGGTGTAACGGTTTGCTATGATTTGAGATTCCCAGAGCTTTATCAGCAGCTAAGGTTCCT
        ||||||   |   ||  ||    |  |  || || ||   |   ||||    ||   ||||  ||||  |   ||||   ||||||| ||||||||| |||||  ||||||| |||||||| ||  |||| ||||||||  | |  |||||||||||||||||||| |||||| | || ||   |||  | |||| 
----aggagtgtttgaaagagaagataagcacacttggatatgatatgaaccatgaaggatggtgttttcatgtgaaattcttctgttttggtgatgttttcagGCAAGGATATTGTTGCAGTAGACAGTCCTGTTGGGCGTTTGGGCCTCAGTGTTTGCTATGATTTGAGATTTCCAGAGATGTACCAATTGCTGCGTTTCCA

upper sequence: Vv13s0067g03530.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA20G38690.1 (Glycine max), 3'ss of exon 6
tttttctggtgtttcccaagtaa--tagttgccttatgacataattga----atggatgatttgacttttttgtgtgtgagaattctaaattggtgaagttttcagGGAAGGAAGTTGTTGCGGTAGACAGCCCCATTGGTCGTTTGGGTGTAACGGTTTGCTATGATTTGAGATTCCCAGAGCTTTATCAGCAGCTAAGGTTCCT-
        ||||||   |   ||  ||    |  |  || || ||       ||| | |||  | ||||  ||||  |     ||||   |||| || |||||||||   |||  ||||||| |||||||| || ||||| ||||||||  | |  |||||||||||||||||||| |||||| | || ||   |||| | ||||  
--------gtgtttgaaagagaagataagcacacttggatatgatatgcaccatgaaggatggggctttcatgtgaatttc--ttctgttttggggatgttttcagGCT-GGATATTGTTGCAGTAGACAGTCCTATTGGACGTTTGGGCCTCAGTGTTTGCTATGATTTGAGATTTCCAGAGATGTACCAATTGCTACGTTTCCAA

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|71860719|gb|DT009774.1|DT009774
EST:     GGATGTTCCTGGTGGAGCGGTCTACAAGGAGAGCAGCTTTACAGAAGGAG                         GGAAGGAAGTTGTTGCGGTAGACAGCCCCATTGGTCGTTTGGGTGTAACGG
genomic: GGATGTTCCTGGTGGAGCGGTCTACAAGGAGAGCAGCTTTACAGAAGGAGgtgaattctt ... aagttttcagGGAAGGAAGTTGTTGCGGTAGACAGCCCCATTGGTCGTTTGGGTGTAACGG
EST: gi|71860659|gb|DT009714.1|DT009714
EST:     GGATGTTCCTGGTGGAGCGGTCTACAAGGAGAGCAGCTTTACAGAAGGAG                         GGAAGGAAGTTGTTGCGGTAGACAGCCCCATTGGTCGTTTGGGTGTAACGG
genomic: GGATGTTCCTGGTGGAGCGGTCTACAAGGAGAGCAGCTTTACAGAAGGAGgtgaattctt ... aagttttcagGGAAGGAAGTTGTTGCGGTAGACAGCCCCATTGGTCGTTTGGGTGTAACGG
EST: gi|294965239|gb|GW838926.1|GW838926
EST:     GGATGTNCCTGGTGGAGCGGTCTACAAGGAGAGCAGCTTTACAGAAGGAG                         GGAAGGAAGTTGTTGCGGTACACAGCCCCATTGGTCGTTTGGGTGTAACGG
genomic: GGATGTTCCTGGTGGAGCGGTCTACAAGGAGAGCAGCTTTACAGAAGGAGgtgaattctt ... aagttttcagGGAAGGAAGTTGTTGCGGTAGACAGCCCCATTGGTCGTTTGGGTGTAACGG
EST: gi|22009600|gb|BQ794634.1|BQ794634
EST:     GGATGTTCCTGG-GGAGCGGTCTACAAGGAGAGCAGC-TTACAGAAGGAG                         GGAAGGAAGTTGTTGCGGTAGACAGCCCCATTGGTCG-TTGGGTGTAACGG
genomic: GGATGTTCCTGGTGGAGCGGTCTACAAGGAGAGCAGCTTTACAGAAGGAGgtgaattctt ... aagttttcagGGAAGGAAGTTGTTGCGGTAGACAGCCCCATTGGTCGTTTGGGTGTAACGG
EST: gi|110719000|gb|EE096473.1|EE096473
EST:     GGATGTTCCTGGTGGAGCGGTCTACAAGGAGAGCAGCTTTACAGAAGGAG                         GGAAGGAAGTTGTTGCGGTAGACAGCCCCATTGGTCGTTTGGGTGTAACGG
genomic: GGATGTTCCTGGTGGAGCGGTCTACAAGGAGAGCAGCTTTACAGAAGGAGgtgaattctt ... aagttttcagGGAAGGAAGTTGTTGCGGTAGACAGCCCCATTGGTCGTTTGGGTGTAACGG
EST: gi|29785164|gb|CB341917.2|CB341917
EST:     GGATGTTCCTGGTGGAGCGGTCTACAAGGAGAGCAGCTTTACAGAAGGAG                         GGAAGGAAGTTGTTGCGGTAGACAGCCCCATTGGTCGTTTGGGTGTAACGG
genomic: GGATGTTCCTGGTGGAGCGGTCTACAAGGAGAGCAGCTTTACAGAAGGAGgtgaattctt ... aagttttcagGGAAGGAAGTTGTTGCGGTAGACAGCCCCATTGGTCGTTTGGGTGTAACGG
EST: gi|46917918|gb|CN547247.1|CN547247
EST:     GGATGTTCCTGGTGGAGCGGTCTACAAGGAGAGCAGCTTTACAGAAGGAG                         GGAAGGAAGTTGTTGCGGTAGACAGCCCCATTGGTCGTTTGGGTGTAACGG
genomic: GGATGTTCCTGGTGGAGCGGTCTACAAGGAGAGCAGCTTTACAGAAGGAGgtgaattctt ... aagttttcagGGAAGGAAGTTGTTGCGGTAGACAGCCCCATTGGTCGTTTGGGTGTAACGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatggatgatttgacttttttgtgtgtgagaattctaaattggtgaagttttcagGGAAGGAAGTTGTTGCGGTAGACAGCCCCATTGGTCGTTTGGGTGTAACGGTTTGCTATGATTTGAGATTCCCAGAGCTTTATCAGCAGCTAAGGTTCCT
                                ttctaaa  putative branch site (score: 2)
                                                ttttc  putative PPT
                              aattctaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttctggtgtttcccaagtaatagttgccttatgacataattgaatggatgatttgacttttttgtgtgtgagaattctaaattggtgaagttttcagGGAAGGAAGTTGTTGCGGTAGACAGCCCCATTGGTCGTTTGGGTGTAACGGTTTGCTATGATTTGAGATTCCCAGAGCTTTATCAGCAGCTAAGGTTCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- tttctgg
- - - - - - - -ccaagta
- - - - - - - - - - - - - -tgcctta
- - - - - - - - - - - - - - - - - - - - - -tgaatgg