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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatagaatcatttttgggtccaatatctagatttaatcttggtgaaaggttttattttttagagagttgaagaatcaatccctgatatctatcattgcagGTCAGCTGTGTGCGTATGCTGTCAGGAGAACGTGTCCTTACTGCTGCCCATGATGGAACTGTGAAGATGTGGGATGTGAGAACTGATACGTGTGTGGCAA

Basic information

species Vitis vinifera
transcript Vv17s0000g03950.t01
intron # 25
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g03950.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: LOC_Os01g39380.3 (Oryza sativa), 3'ss of exon 26
aatagaatcatttttgggtccaatatctagatttaatcttggtgaaaggttttattttttagaga--gttgaagaatcaatccctgatatctatcattgcagGTCAGCTGTGTGCGTATGCTGTCAGGAGAACGTGTCCTTACTGCTGCCCATGATGGAACTGTGAAGATGTGGGATGTGAGAACTGATACGTGTGTGGCAA
  |  ||      | | |     |  ||| |   ||  ||  | | |   ||   ||   | | |   ||    | ||   | ||  |    |    ||||||| || | ||| || ||||| |||||||||||||| ||||||||  | |||||||| ||||| ||||||||||||||  | || ||||| ||||| || |
--tgaaaatggggtagcgggatgttgctacaccaaacattacttataacattcgcttccaaaatatccttatccagtcttacactttttgacactgctgcagGTTAGTTCTGTCCGGATGCTCTCAGGAGAACGTGTTCTTACTGCATCTCATGATGGCACTGTCAAGATGTGGGATGTACGTACCGATACTTGTGTTGCTA

upper sequence: Vv17s0000g03950.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: GRMZM2G074466_T01 (Zea mays), 3'ss of exon 6
aatagaatcatttttgggtccaatatctagatttaatcttggtgaaaggttttattttttagagagttgaagaatcaatccctgatatctatcattgcagGTCAGCTGTGTGCGTATGCTGTCAGGAGAACGTGTCCTTACTGCTGCCCATGATGGAACTGTGAAGATGTGGGATGTGAGAACTGATACGTGTGTGGCAA
    |      | ||   |  |   | |||||||  |  |     ||  || |  |  ||||  | |  ||    ||     || |   ||||  |  |||| || | ||| || ||||| ||||||||||||||||||| |||  |||||||||| ||||||||||||||||||||  | |||||||| ||||| |  |
----gtgaggctcttacatttagc-tgtagatttgtttctatgttaacattgt-ctccttagtaactccaaag--catgttttgttcaatatcggtatagGTTAGTTCTGTCCGGATGCTCTCAGGAGAACGTGTCCTTATTGCATCCCATGATGGTACTGTGAAGATGTGGGATGTCCGGACTGATACTTGTGTTGTTA

upper sequence: Vv17s0000g03950.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: GLYMA05G35210.1 (Glycine max), 3'ss of exon 8
-----------aatagaatcattt--ttgggtccaatatctagatt-taatcttggtgaa--aggttttattttttagagagt----tgaagaatcaatcc---ctgatatctatcattgcagGTCAGCTGTGTGCGTATGCTGTCAGGAGAACGTGTCCTTACTGCTGCCCATGATGGAACTGTGAAGATGTGGGATGTGAGAACTGATACGTGTGTGGCAA
             || ||  ||||  || | || | |||  | | | ||    | || ||   | |   | | |  ||| ||     |  | | | ||| |   | |  | | | |  || |||||||||||||||| ||||| || || || |||||  | |||||  |||||||||| |||||||||||||||||||| ||||| ||||  ||||| ||||
gtattttttactttaaaaatatttggtttgttctactataaacagtataggtgttgtaaattcgttacaaatatacagaaaggataattgaaacttaattcagacagccaaccaaccatgtagGTCAGCTGTGTGCGCATGCTTTCTGGGGAGCGTGTGTTAACTGCATCCCATGATGGCACTGTGAAGATGTGGGATGTAAGAACAGATAGATGTGTTGCAA

upper sequence: Vv17s0000g03950.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: GLYMA08G04510.1 (Glycine max), 3'ss of exon 25
-----------aatagaatcattt--ttgggtccaatatctagatt-taatcttggtgaaaggttttattttttagagagttga------agaatcaatcc---ctgatatctatcattgcagGTCAGCTGTGTGCGTATGCTGTCAGGAGAACGTGTCCTTACTGCTGCCCATGATGGAACTGTGAAGATGTGGGATGTGAGAACTGATACGTGTGTGGCAA
             || ||  ||||  || | || |||||  | | | ||    | || ||    ||     | || ||| | ||      | | | ||| |     |  | | | |  || |||||||||||||||| | ||| || || ||||||||  | |||||  |||||||||| || ||||||||||||||||| ||||| ||||  ||||| ||||
gtatttcttactttaaaaatatttggtttgttctaatataaacagtataggtgttgtaaattcattacaaatatacagaatggataattgaaacttaattcagatagccaaccaaccatgtagGTCAGCTGTGTGCGCACGCTCTCCGGGGAACGTGTGTTAACTGCATCCCATGATGGCACCGTGAAGATGTGGGATGTAAGAACAGATAGATGTGTTGCAA

upper sequence: Vv17s0000g03950.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: AT1G49040.3 (Arabidopsis thaliana), 3'ss of exon 25
-----aataga-atcatttttgggtccaatatctagatttaatcttggtgaaaggttttattttttagagagttgaagaatcaatccctgatatctatcattgcagGTCAGCTGTGTGCGTATGCTGTCAGGAGAACGTGTCCTTACTGCTGCCCATGATGGAACTGTGAAGATGTGGGATGTGAGAACTGATACGTGTGTGGCAA
        ||  || | |  |  | |    |   |||    ||  |  ||     ||   ||||||       || |   |  ||||   | | ||||   ||||||| || |||||    ||||| ||||| ||||||||||| |||||||| ||||||||||| || ||||||||||| ||  |||| |||| |||||| ||||
tatccgtcagtcataactcataaggcaccaaagaagaagcgatacttatggtgacttaccttttttctga--ctgtatgctacatcc---aaaactatt-ctgcagGTAAGTTGTGTCAAGATGCTTTCAGGCGAACGTGTCCTCACTGCTGCACATGATGGAACAGTTAAGATGTGGGACGTTCGAACCGATATGTGTGTTGCAA

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|110367943|gb|EC931898.1|EC931898
EST:     ATAAACAAACATCTCAACTTCTAGAAGAGCTAAAAGGCCATGATGGACAG                         GTCAGCTGTGTGCGTATGCTGTCAGGAGAACGTGTCCTTACTGCTGCCCAT
genomic: ATAAACAAACATCTCAACTTCTAGAAGAGCTAAAAGGCCATGATGGACAGgtttgagttg ... atcattgcagGTCAGCTGTGTGCGTATGCTGTCAGGAGAACGTGTCCTTACTGCTGCCCAT
EST: gi|110410864|gb|EC976558.1|EC976558
EST:     ATAAACAAACATCTCAACTTCTAGAAGAGCTAAAAGGCCATGATGGACAG                         GTCAGCTGTGTGCGTATGCTGTCAGGAGAACGTGTCCTTACTGCTGCCCAT
genomic: ATAAACAAACATCTCAACTTCTAGAAGAGCTAAAAGGCCATGATGGACAGgtttgagttg ... atcattgcagGTCAGCTGTGTGCGTATGCTGTCAGGAGAACGTGTCCTTACTGCTGCCCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaggttttattttttagagagttgaagaatcaatccctgatatctatcattgcagGTCAGCTGTGTGCGTATGCTGTCAGGAGAACGTGTCCTTACTGCTGCCCATGATGGAACTGTGAAGATGTGGGATGTGAGAACTGATACGTGTGTGGCAA
                                  ccctgat  putative branch site (score: 4)
     tttattttttagaga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatagaatcatttttgggtccaatatctagatttaatcttggtgaaaggttttattttttagagagttgaagaatcaatccctgatatctatcattgcagGTCAGCTGTGTGCGTATGCTGTCAGGAGAACGTGTCCTTACTGCTGCCCATGATGGAACTGTGAAGATGTGGGATGTGAGAACTGATACGTGTGTGGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
aatagaa
- - - - - -ttttggg
- - - - - - - - - - - - - - - - - - -cttggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caatccc