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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatgtgttgtttgaatttattttttttttccgagcaaccaaacaggggctatagttagatcgaatctggttgtttgaggatcttgtttccgcgtttgcagGTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGATCGATGAGCTCAAGAACGAGGACATTCAGCTTCGATTGAACTCGATCCG

Basic information

species Vitis vinifera
transcript Vv17s0000g03870.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g03870.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 1
-----------------gatgtgttgtttgaatttattttttttttccgagcaaccaaacaggggctatagttagatcgaatctggttgtttgaggatcttgtttccgcgtttgcagGT-TCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGATCGATGAGCTCAAGAACGAGGACATTCAGCTTCGATTGAACTCGATCCG
                  | ||  ||||  | ||| |||||| ||   | | |   | | |    | | || |   || |||   || ||       |     ||| ||  |    | | | |  ||||||||||||||| ||||||||||| |||||||| ||  |||| |||||||| ||||| |||||||| ||| | ||  | |          
gatgctcttatgcagccaaagttgtgttaaagttttttttttctt---gggaatttatataattacaa-agct---tctaatgctgt-gtcctcatttaccaattcagCAATCCTTGATATACCTGATGGCTATGATTGATGAGCCTCTGTACCCAATTGCTGTACTGATTGATGAGCTTAAGAATGAGGACATCCAGTTGCGTCTAA----------

upper sequence: Vv17s0000g03870.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 1
gatgtgttgtttgaatttattttttttttccgagcaaccaaacaggggctatagttagatcgaatctggttgtttgaggatcttgtttccgcgtttgcagGTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGC--GGTTTTGATCGATGAGCTCAAGAAC---GAGGACATTCAGCTTCGATTGAACTCGATCCG----
      ||||||    | |||| |   ||| ||    |     |      || | ||      ||  |  | |||    |  |  | | |   ||  |  | ||    |||   |  ||  |   || |||  |  | |||    |  ||| | | ||  || |  |  |   ||| | |   | |   ||  || ||   |||     
-----attgtttc--ctcatttatcaattcagaaatccttgttatacctgatggctatgattgatgagcctctttatccaattgctgtactgattgacgagctcaagAATGAAGAC-ATCCAGTTGCGTCTAAACTCCATTAGAAGACTTTCAACAATT-GCACGGGCTCTTGGAGAAGAAAGAACCAGGAAGGAGCTGATTCCTTTTC

upper sequence: Vv17s0000g03870.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G164352_T05 (Zea mays), 3'ss of exon 1
--------gatgtgttgtttga---atttattttttttttccgagcaaccaaacaggggctatagttagatcgaatctggttgtttgaggatcttgtttccgcgtttgcagGTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGATCGATGAGCTCAAGAACGAGGACATTCAGCTTCGATTGAACTCGATCCG
         | || |||||  |   |||   |||| |||||  || |           | || |      |  |   || ||  |     |||   ||      |        | |  ||||||||||||||| |||||||| ||||||||||| ||  |||| || ||||||||||| || ||||| ||| | ||  | |          
tgcaaccaaaagttttgttaaacttattctattttattttcttaggattttttatatagttacaaagctcttaatattgtttcctcatttatca-attcagAAATCCTTGTTATACCTGATGGCTATGATTGATGAGCCTCTTTATCCAATTGCTGTACTGATTGACGAGCTCAAGAATGAAGACATCCAGTTGCGTCTAA----------

upper sequence: Vv17s0000g03870.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA09G31760.1 (Glycine max), 3'ss of exon 1
--------------------------------------------------------------------------------------------------------------------gatgtgttgtttgaatttattttttttttccgagcaaccaaacaggggctatagttagatcgaatctggttgtttgaggatcttgtttccgcgtttgcagGTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGATCGATGAGCTCAAGAACGAGGACATTCAGCTTCGATTGAACTCGATCCG
                                                                                                                      |||    ||  |  || |  |||| || |       |     | |  |  | ||| |||   || | || ||  ||    || | ||   | |  |  |   ||| ||||| ||| | ||| ||||||||||||| ||||| ||||||||||| ||| | ||||| |||||||||||||                   
gtgcaacaacaacactttctccttcttccctctctttacctcaacaacacttttttttttcttttgttttcaatttctctttgaactacgctccattgcttcagatcaagcatcatattgtagatttccaggttttgcttttctttccgtttctcgttttgtgtttgaaattacatc---tccgattattgcag-

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|352763871|gb|FQ465321.1|FQ465321
EST:     TCAGATCTTACTTTTCCCAAATTGCCCCTTCCTCTTCTCACATTTCCACT                         GTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGA
genomic: TCAGATCTTACTTTTCCCAAATTGCCCCTTCCTCTTCTCACATTTCCACTgtatggcctc ... gcgtttgcagGTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGA
EST: gi|110723764|gb|EE101450.1|EE101450
EST:     TCAGATCTTACTTTTCCCAAATTGCCCCTTCCTCTTCTCACATTTCCACT                         GTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGA
genomic: TCAGATCTTACTTTTCCCAAATTGCCCCTTCCTCTTCTCACATTTCCACTgtatggcctc ... gcgtttgcagGTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGA
EST: gi|71858238|gb|DT007293.1|DT007293
EST:     TCAGATCTTACTTTTCCCAAATTGCCCCTTCCTCTTCTCACATTTCCACT                         GTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGA
genomic: TCAGATCTTACTTTTCCCAAATTGCCCCTTCCTCTTCTCACATTTCCACTgtatggcctc ... gcgtttgcagGTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGA
EST: gi|352781471|gb|FQ468315.1|FQ468315
EST:     TCAGATCTTACTTTTCCCAAATTGCCCCTTCCTCTTCTCACATTTCCACT                         GTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGA
genomic: TCAGATCTTACTTTTCCCAAATTGCCCCTTCCTCTTCTCACATTTCCACTgtatggcctc ... gcgtttgcagGTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGA
EST: gi|352769561|gb|FQ468489.1|FQ468489
EST:     TCAGATCTTACTTTTCCCAAATTGCCCCTTCCTCTTCTCACATTTCCACT                         GTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGA
genomic: TCAGATCTTACTTTTCCCAAATTGCCCCTTCCTCTTCTCACATTTCCACTgtatggcctc ... gcgtttgcagGTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGA
EST: gi|37183448|gb|CF602802.1|CF602802
EST:     TCAGATCTTACTTTTCCCAAATTGCCCCTTCCTCTTCTCACATTTCCACT                         GTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGA
genomic: TCAGATCTTACTTTTCCCAAATTGCCCCTTCCTCTTCTCACATTTCCACTgtatggcctc ... gcgtttgcagGTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGA
EST: gi|22010752|gb|BQ795786.1|BQ795786
EST:     TCAGATCTTACTTTTCCCAAATTGCCCCTTCCTCTTCTCACATTTCCACT                         GTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGA
genomic: TCAGATCTTACTTTTCCCAAATTGCCCCTTCCTCTTCTCACATTTCCACTgtatggcctc ... gcgtttgcagGTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGA
EST: gi|110698010|gb|EE075532.1|EE075532
EST:     TCAGATCTTACTTTTCCCAAATTGCCCCTTCCTCTTCTCACATTTCCACT                         GTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGA
genomic: TCAGATCTTACTTTTCCCAAATTGCCCCTTCCTCTTCTCACATTTCCACTgtatggcctc ... gcgtttgcagGTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGA
EST: gi|71883706|gb|DT032761.1|DT032761
EST:     TCAGATCTTACTTTTCCCAAATTGCCCCTTCCTCTTCTCACATTTCCACT                         GTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGA
genomic: TCAGATCTTACTTTTCCCAAATTGCCCCTTCCTCTTCTCACATTTCCACTgtatggcctc ... gcgtttgcagGTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGA
EST: gi|352778272|gb|FQ465582.1|FQ465582
EST:     TCAGATCTTACTTTTCCCAAATTGCCCCTTCCTCTTCTCACATTTCCACT                         GTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGA
genomic: TCAGATCTTACTTTTCCCAAATTGCCCCTTCCTCTTCTCACATTTCCACTgtatggcctc ... gcgtttgcagGTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGA
EST: gi|352763901|gb|FQ465351.1|FQ465351
EST:     TCAGATCTTACTTTTCCCAAATTGCCCCTTCCTCTTCTCACATTTCCACT                         GTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGA
genomic: TCAGATCTTACTTTTCCCAAATTGCCCCTTCCTCTTCTCACATTTCCACTgtatggcctc ... gcgtttgcagGTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGA
EST: gi|37189319|gb|CF608668.1|CF608668
EST:     TCAGATCTTACTTTTCCCAAATTGCCCCTTCCTCTTCTCACATTTCCACT                         GTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGA
genomic: TCAGATCTTACTTTTCCCAAATTGCCCCTTCCTCTTCTCACATTTCCACTgtatggcctc ... gcgtttgcagGTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGA
EST: gi|352787201|gb|FQ477821.1|FQ477821
EST:     TCAGATCTTACTTTTCCCAAATTGCCCCTTCCTCTTCTCACATTTCCACT                         GTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGA
genomic: TCAGATCTTACTTTTCCCAAATTGCCCCTTCCTCTTCTCACATTTCCACTgtatggcctc ... gcgtttgcagGTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGA
EST: gi|352776769|gb|FQ472656.1|FQ472656
EST:     TCAGATCTTACTTTTCCCAAATTGCCCCTTCCTCTTCTCACATTTCCACT                         GTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGA
genomic: TCAGATCTTACTTTTCCCAAATTGCCCCTTCCTCTTCTCACATTTCCACTgtatggcctc ... gcgtttgcagGTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGA
EST: gi|352773443|gb|FQ472225.1|FQ472225
EST:     TCAGATCTTACTTTTCCCAAATTGCCCCTTCCTCTTCTCACATTTCCACT                         GTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGA
genomic: TCAGATCTTACTTTTCCCAAATTGCCCCTTCCTCTTCTCACATTTCCACTgtatggcctc ... gcgtttgcagGTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGA
EST: gi|352777593|gb|FQ466646.1|FQ466646
EST:     TCAGATCTTACTTTTCCCAAATTGCCCCTTCCTCTTCTCACATTTCCACT                         GTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGA
genomic: TCAGATCTTACTTTTCCCAAATTGCCCCTTCCTCTTCTCACATTTCCACTgtatggcctc ... gcgtttgcagGTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGA
EST: gi|352768313|gb|FQ469488.1|FQ469488
EST:     TCAGATCTTACTTTTCCCAAATTGCCCCTTCCTCTTCTCACATTTCCACT                         GTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGA
genomic: TCAGATCTTACTTTTCCCAAATTGCCCCTTCCTCTTCTCACATTTCCACTgtatggcctc ... gcgtttgcagGTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGA
EST: gi|156738161|gb|EV242282.1|EV242282
EST:     TCTCACATTTCCACT                         GTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGA
genomic: TCTCACATTTCCACTgtatggcctc ... gcgtttgcagGTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGA
EST: gi|352769371|gb|FQ471520.1|FQ471520
EST:     TCAGATCTTACTTTTCCCAAATTGCCCCTTCCTCTTCTCACATTTCCACT                         GTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGA
genomic: TCAGATCTTACTTTTCCCAAATTGCCCCTTCCTCTTCTCACATTTCCACTgtatggcctc ... gcgtttgcagGTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGA
EST: gi|22010753|gb|BQ795787.1|BQ795787
EST:     TCAGATCTTACTTTTCCCAAATTGCCCCTTCCTCTTCTCACATTTCCACT                         GTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGA
genomic: TCAGATCTTACTTTTCCCAAATTGCCCCTTCCTCTTCTCACATTTCCACTgtatggcctc ... gcgtttgcagGTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGA
EST: gi|352772524|gb|FQ471999.1|FQ471999
EST:     TCAGATCTTACTTTTCCCAAATTGCCCCTTCCTCTTCTCACATTTCCACT                         GTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGA
genomic: TCAGATCTTACTTTTCCCAAATTGCCCCTTCCTCTTCTCACATTTCCACTgtatggcctc ... gcgtttgcagGTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggctatagttagatcgaatctggttgtttgaggatcttgtttccgcgtttgcagGTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGATCGATGAGCTCAAGAACGAGGACATTCAGCTTCGATTGAACTCGATCCG
                                        tttccgc  CT-rich tract
     atagtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatgtgttgtttgaatttattttttttttccgagcaaccaaacaggggctatagttagatcgaatctggttgtttgaggatcttgtttccgcgtttgcagGTTCCGAGATGGCTATGATTGACGAGCCTCTGTATCCAATTGCGGTTTTGATCGATGAGCTCAAGAACGAGGACATTCAGCTTCGATTGAACTCGATCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - -ccaaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggttgt