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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatcatcaccagaatgggtgtatcttttcagtttatctcttcttattcctaattaatggattagtttccataaattgattttgttattgattctactcagTTTTGACCGTGATTGGAAAAAGATTGAGGCATTTGTTGGATCAAAGACAGTTATTCAG

Basic information

species Vitis vinifera
transcript Vv16s0050g01180.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0050g01180.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os02g45670.1 (Oryza sativa), 3'ss of exon 1
aatcatcaccagaatgggtgtatcttttcagtttatctcttctt--attcctaattaatggattagtttccataaattgattttgtta--ttgattctactcagTTTTGACCGTGATTGGAAAAAGATTGAGGCATTTGTTGGATCAAAGACAGTTATTCAG
           ||||    |||||| | ||     | |  | ||  |||         |   ||    ||    | |    | |  ||  ||| ||||  |||| ||||| ||||||||||||||||| || || ||||||||||| ||||| |||||||||
---tgctgtt-gaattcaagtatctgtacaaaaggtttgatattcaattgtaggactgtccttttacatctgatattcatgtgtaataccttgcttcttttcagCTTTGATCGTGATTGGAAAAAGATAGAAGCTTTTGTTGGATCGAAGACTGTTATTCAG

upper sequence: Vv16s0050g01180.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os06g01670.1 (Oryza sativa), 3'ss of exon 1
------------aatcatcaccagaatgggtgtatcttttcagtttatctcttcttattcctaattaatggattagtttccataaattgattttgttattgattctactcagTTTTGACCGTGATTGGAAAAAGATTGAGGCATTTGTTGGATCAAAGACAGTTATTCAG
            || ||| || ||   || | || |    | |   |    ||| |  ||||| ||| |   || |  | | | | ||| ||||  |||          ||| ||||| |||||||||||||||||||| |||| |||||| || ||||| || || |||
ttatcttgtggcaaacattacgagtggggttttaccacaactgaaaaatggttcct--tcctacttattc--tttgcattctttacttgcttttactataa--------cagGTTTGATCGTGATTGGAAAAAGATTGAAGCATATGTTGGCTCTAAGACTGTAATACAG

upper sequence: Vv16s0050g01180.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G135052_T01 (Zea mays), 3'ss of exon 1
-----aatcatcaccagaatgggtgtatcttttcagtttatctcttcttattcctaattaatggattagtttccataaattgattttgttattgattctactcagTTTTGACCGTGATTGGAAAAAGATTGAGGCATTTGTTGGATCAAAGACAGTTATTCAG
        |||   || | | |  | ||   |   ||    |   |       ||   | |   ||||  | | ||||||   | ||  | ||  |   ||  || ||||||||||| |||||||||||||| |||| |||||| || |||||||| || |||
tttaagggcatt-tcatacttgtagaatgcctcatgtcacacatctggagcagctttcttacatatta--tgctataaatccttctttcttttcgtgtaac--agCTTTGACCGTGACTGGAAAAAGATTGAAGCATATGTTGGCTCCAAGACAGTAATACAG

upper sequence: Vv16s0050g01180.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G057408_T01 (Zea mays), 3'ss of exon 1
aatcatcaccagaatgggtgtatcttttcagtt-tatctcttcttattcctaattaatggattagtttccataaatt---gattttgttattgattctact-cagTTTTGACCGTGATTGGAAAAAGATTGAGGCATTTGTTGGATCAAAGACAGTTATTCAG
    ||       | |  ||||  || | |||  |    ||       | |  || ||  | |  | |  |||  |     ||||||||  |   | |  |  |||||||| ||||||||||| || ||||| |||| |||||| |||||||| ||||| |||
----attgtttata-gtttgtaaattgtaagtgatgctactatgagaacttggttcatttaatgatatttatatttctcaaattttgtttgtttctttgttgtagTTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAG

upper sequence: Vv16s0050g01180.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA10G37520.1 (Glycine max), 3'ss of exon 1
aatcatcaccagaatgggtgtatcttttcagtttatctcttcttattcctaat-taatggattagtttccataaattgattttgttattgattc--tactcagTTTTGACCGTGATTGGAAAAAGATTGAGGCATTTGTTGGATCAAAGACAGTTATTCAG
   ||    || | |  |   ||| |||  ||||  |  ||  |   | || | | ||   || |  |      |||| |||   | || ||||  ||  ||| ||||||||||| |||||||||||||| |||||||||||||||||||||||||| |||
-tacagtgtcaaattaagataatcgttt--gttttcccttttctggccttagtatcatccttttgcattatctcattgttttgtattttcattctttatccagATTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGACAGTTATCCAG

upper sequence: Vv16s0050g01180.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA20G30250.1 (Glycine max), 3'ss of exon 1
aatcatcaccagaatgggtgtatcttttcagtttatctcttcttattcctaattaatggattagtttccataaattgattttgttattg----attctac-tcagTTTTGACCGTGATTGGAAAAAGATTGAGGCATTTGTTGGATCAAAGACAGTTATTCAG
    ||       ||  || | | ||| |  |||||  | | |  | ||    |  || ||||  |   ||   ||  |||| || ||     |||||   |||| ||||||||||| |||||||||||||| ||||||||||||||||||||||| || |||
----atttaagctatttgtttgtttttcccttttatggcct-tggtgccatccttttgcattatctcatattgttttttttttttgttccttcattctgtatcagATTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGACAGTCATCCAG

upper sequence: Vv16s0050g01180.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA09G24400.1 (Glycine max), 3'ss of exon 1
----aatcatcaccagaatgggtgtatcttttcagtttatctcttcttattcctaattaatggattagtttc-cataaattgattttgttattgattctactcagTTTTGACCGTGATTGGAAAAAGATTGAGGCATTTGTTGGATCAAAGACAGTTATTCAG
    ||| |   | ||  ||  ||| |||   |  | |    |||    |  ||| ||     | ||   || |||   ||  ||   | |||  || |  |||| ||||||||||| |||||||||||||| |||||||||||||||||||  ||||| |||
ttcaaattaaagctag--tgtttgtttctcccctttcttgaccttggggtctctatttgcc--actatcctcacattgttttgttccttcatttctttt-ttcagGTTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGAGTGTTATACAG

upper sequence: Vv16s0050g01180.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA16G29740.1 (Glycine max), 3'ss of exon 1
aatcatcaccagaatgggtgtatcttttcagtttatctcttcttattcctaattaatggattagtttccataaattgattttgttattgattctact--cagTTTTGACCGTGATTGGAAAAAGATTGAGGCATTTGTTGGATCAAAGACAGTTATTCAG
  |    |  | |    |||| | |||      | ||| |   |     |    | | |   | | ||| | | ||  |||     |   ||||  |  ||| ||||| |||||||||||||||||||| |||||||||||||||||||  ||||| |||
gtttcaaattaaagctagtgtttgtttctcccctttctttatcttggggtcgccatttg-ccactatcc-tcactttttttccccttcatttctgttttcagGTTTGATCGTGATTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGAGTGTTATACAG

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|351034613|gb|FQ457970.1|FQ457970
EST:     GAGAAGTGGACCGAGCCCGAGCACGACAAGTTCCTCGAAGCTCTTCAGCT                         TTTTGACCGTGATTGGAAAAAGATTGAGGCATTTGTTGGATCAAAGACAGT
genomic: GAGAAGTGGACCGAGCCCGAGCACGACAAGTTCCTCGAAGCTCTTCAGCTgtaagacgct ... ttctactcagTTTTGACCGTGATTGGAAAAAGATTGAGGCATTTGTTGGATCAAAGACAGT
EST: gi|351022507|gb|FQ447029.1|FQ447029
EST:     GAGAAGTGGACCGAGCCCGAGCACGACAAGTTCCTCGAAGCTCTTCAGCT                         TTTTGACCGTGATTGGAAAAAGATTGAGGCATTTGTTGGATCAAAGACAGT
genomic: GAGAAGTGGACCGAGCCCGAGCACGACAAGTTCCTCGAAGCTCTTCAGCTgtaagacgct ... ttctactcagTTTTGACCGTGATTGGAAAAAGATTGAGGCATTTGTTGGATCAAAGACAGT
EST: gi|349832942|gb|FQ423064.1|FQ423064
EST:     GAGAAGTGGACCGAGCCCGAGCACGACAAGTTCCTCGAAGCTCTTCAGCT                         TTTTGACCGTGATTGGAAAAAGATTGAGGCATTTGTTGGATCAAAGACAGT
genomic: GAGAAGTGGACCGAGCCCGAGCACGACAAGTTCCTCGAAGCTCTTCAGCTgtaagacgct ... ttctactcagTTTTGACCGTGATTGGAAAAAGATTGAGGCATTTGTTGGATCAAAGACAGT
EST: gi|351013330|gb|FQ425035.1|FQ425035
EST:     GAGAAGTGGACCGAGCCCGAGCACGACAAGTTCCTCGAAGCTCTTCAGCT                         TTTTGACCGTGATTGGAAAAAGATTGAGGCATTTGTTGGATCAAAGACAGT
genomic: GAGAAGTGGACCGAGCCCGAGCACGACAAGTTCCTCGAAGCTCTTCAGCTgtaagacgct ... ttctactcagTTTTGACCGTGATTGGAAAAAGATTGAGGCATTTGTTGGATCAAAGACAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcctaattaatggattagtttccataaattgattttgttattgattctactcagTTTTGACCGTGATTGGAAAAAGATTGAGGCATTTGTTGGATCAAAGACAGTTATTCAG
                                             ttctactc  CT-rich tract
                        ataaattgattttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatcatcaccagaatgggtgtatcttttcagtttatctcttcttattcctaattaatggattagtttccataaattgattttgttattgattctactcagTTTTGACCGTGATTGGAAAAAGATTGAGGCATTTGTTGGATCAAAGACAGTTATTCAG

- -catcacc
- - - - - - - tgggtgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccataaa