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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgagagaccatatgatatattgtaaactttgattggctgaattgtatttgtttttccactttattaaccccataaattttatgttatcctgataccttgctataaactaaggtttcctcttcttatcttttcccttaacagACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATG

Basic information

species Vitis vinifera
transcript Vv19s0090g01590.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0090g01590.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA14G02050.1 (Glycine max), 3'ss of exon 2
gtatgagagaccatatgatatattgtaaactttgattggctgaattgtatttgtttttccactttattaaccccataaattttatgttatcctgataccttgctata-aactaaggtttcctcttcttatcttttcccttaacagACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATG
                  || ||||  ||  | |     |||  || | ||  |  ||    |  |||  |  | |   |  ||||| ||  |  |    | | ||  |  |      |  | || |  |  |||   | |  ||||||||||| |||||||||||||||| ||||||||||| ||  |  |||| ||  | |||||||| |||||||
-----------------gtacattgagaatctcg-----ctgcctttttttcctgcttgttttacattggctacttggttcatatgtcattattttttgcttcaatttagtttgtaagtaattttgtagttctttatgtcattagACATTTGCAGTTTTGTCTGGAGTTCATAGTTTGGTTGTTTGCATCTTGAAAAGACTTAGAGGAAAAGATGATG

upper sequence: Vv19s0090g01590.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA02G46620.1 (Glycine max), 3'ss of exon 2
gtatgagagaccatatgatatattgtaaactttgattggctgaattgtatttgtttttccactttattaaccccataaattttatgttatcctgataccttgctataaactaaggtttcctcttcttatcttttcccttaacagACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATG
                                        |  ||||    | |   | | |||| ||  |||      |||||  ||||  |  | | ||  | || | |     |   | |  || |  |||   | |  ||||||||||| |||||||||||||||| ||||||||||| ||  |  |||| ||| | |||||||| |||||||
---------------------------------------gtacattgagaatctcgctgc-ctttttttcccctgcttgttttacattatttttttgctttaatttagattgtaagtaattgtg-ttgttctttatgtcattagACATTTGCAGTTTTGTCTGGAGTTCATAGTTTGGTTGTTTGCATCTTGAAAAGGCTTAGAGGAAAAGATGATG

upper sequence: Vv19s0090g01590.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA0121S00230.1 (Glycine max), 3'ss of exon 1
gtatgagagaccatatgatatattgtaaactttgattggctgaattgtatttgtttttccactttattaaccccataaattttatgttatcctgataccttgctataaactaaggtttcctcttcttatcttttcccttaacagACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATG
                  ||||    | |      |||  |   || |    |  |||  |||||   |||   |||  | ||     ||    || | ||  ||          | | |  || || ||||     | |  |||||||||||||||| || |||||| | ||||||||||||||  |  ||   ||  |  |||||||||||||||
-----------------gtataccagagatcaatgttgtttattttctgcccggctttttactttgcaaacttaatacctatttgaacatgtccattcattaata---------atcttcattttttgtcttcgttttcattagACATTTGCAATTTTATCCGGAGTTGATAGTTTGGTTGTCTGCATATTGGGAAGACTTCGAGGAAAGGATGATG

upper sequence: Vv19s0090g01590.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA18G09780.1 (Glycine max), 3'ss of exon 3
gtatgagagaccatatgatatattgtaaactttgattggctgaattgtatttgtttttccactttattaaccccataaattttatgttatcctgataccttgctataaactaaggtttcctcttcttatcttttcccttaacagACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATG
                  ||||    | |      |||  |   || |    |   ||  |||||   |||   |||  | ||     ||    || | ||  ||          | | |  || || |||| |   | |  |||||||||||||||| || |||||| | ||||||||||||||  |  ||   ||  | ||||||||||||||||
-----------------gtataccagagatcaatgttgtttattttctgcccggcgttttactttgcaaacttaatacctatttgaacatgtccattcattaata---------atcttcattttttgtcttctttttcattagACATTTGCAATTTTATCCGGAGTTGATAGTTTGGTTGTCTGCATATTGGGAAGACTTAGAGGAAAGGATGATG

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|26262978|gb|CA814041.1|CA814041
EST:     AGAAAAAAGGCTTTAAAGGATCCTTTGCAGAGGCCGGATCTTCTGCCAAG                         ACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAG
genomic: AGAAAAAAGGCTTTAAAGGATCCTTTGCAGAGGCCGGATCTTCTGCCAAGgtatgagaga ... cccttaacagACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAG
EST: gi|71875197|gb|DT024252.1|DT024252
EST:     AGAAAAAAGGCTTTAAAGGATCCTTTGCAGAGGCCGGATCTTCTGCCAAG                         ACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAG
genomic: AGAAAAAAGGCTTTAAAGGATCCTTTGCAGAGGCCGGATCTTCTGCCAAGgtatgagaga ... cccttaacagACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAG
EST: gi|34549393|gb|CF517625.1|CF517625
EST:     AGAAAAAAGGCTTTAAAGGATCCTTTGCAGAGGCCGGATCTTCTGCCAAG                         ACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAG
genomic: AGAAAAAAGGCTTTAAAGGATCCTTTGCAGAGGCCGGATCTTCTGCCAAGgtatgagaga ... cccttaacagACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAG
EST: gi|71876494|gb|DT025549.1|DT025549
EST:     AGAAAAAAGGCTTTAAAGGATCCTTTGCAGAGGCCGGATCTTCTGCCAAG                         ACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAG
genomic: AGAAAAAAGGCTTTAAAGGATCCTTTGCAGAGGCCGGATCTTCTGCCAAGgtatgagaga ... cccttaacagACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAG
EST: gi|51050247|gb|CO818453.1|CO818453
EST:     TTAAAGGATCC-TTGCAGAGGCCGGATC-TCTGCCAAG                         ACATTTGCAATTTTGTNNGGANTTCACAGTTTGGTTGTCTGTTTTCTGAAG
genomic: TTAAAGGATCCTTTGCAGAGGCCGGATCTTCTGCCAAGgtatgagaga ... cccttaacagACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAG
EST: gi|28961283|gb|CB340652.1|CB340652
EST:     AGAAAAAAGGCTTTAAAGGATCCTTTGCAGAGGCCGGATCTTCTGCCAAG                         ACATTTGCAACTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAG
genomic: AGAAAAAAGGCTTTAAAGGATCCTTTGCAGAGGCCGGATCTTCTGCCAAGgtatgagaga ... cccttaacagACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAG
EST: gi|28961109|gb|CB340563.1|CB340563
EST:     AGAAAAAAGGCTTTAAAGGATCCTTTGCAGAGGCCGGATCTTCTGCCAAG                         ACATTTGCAACTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAG
genomic: AGAAAAAAGGCTTTAAAGGATCCTTTGCAGAGGCCGGATCTTCTGCCAAGgtatgagaga ... cccttaacagACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAG
EST: gi|351041236|gb|FQ444213.1|FQ444213
EST:     AGAAAAAAGGCTTTAAAGGATCCTTTGCAGAGGCCGGATCTTCTGCCAAG                         ACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAG
genomic: AGAAAAAAGGCTTTAAAGGATCCTTTGCAGAGGCCGGATCTTCTGCCAAGgtatgagaga ... cccttaacagACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAG
EST: gi|110720822|gb|EE097079.1|EE097079
EST:     AGAAAAAAGGCTTTAAAGGATCCTTTGCAGAGGCCGGATCTTCTGCCAAG                         ACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAG
genomic: AGAAAAAAGGCTTTAAAGGATCCTTTGCAGAGGCCGGATCTTCTGCCAAGgtatgagaga ... cccttaacagACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAG
EST: gi|351023175|gb|FQ432558.1|FQ432558
EST:     AGAAAAAAGGCTTTAAAGGATCCTTTGCAGAGGCCGGATCTTCTGCCAAG                         ACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAG
genomic: AGAAAAAAGGCTTTAAAGGATCCTTTGCAGAGGCCGGATCTTCTGCCAAGgtatgagaga ... cccttaacagACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAG
EST: gi|26266858|gb|CA817921.1|CA817921
EST:     AGAAAAAAGGCTTTAAAGGATCCTTTGCAGAGGCCGGATCTTCTGCCAAG                         ACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAG
genomic: AGAAAAAAGGCTTTAAAGGATCCTTTGCAGAGGCCGGATCTTCTGCCAAGgtatgagaga ... cccttaacagACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAG
EST: gi|351029437|gb|FQ436831.1|FQ436831
EST:     AGAAAAAAGGCTTTAAAGGATCCTTTGCAGAGGCCGGATCTTCTGCCAAG                         ACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAG
genomic: AGAAAAAAGGCTTTAAAGGATCCTTTGCAGAGGCCGGATCTTCTGCCAAGgtatgagaga ... cccttaacagACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAG
EST: gi|71867379|gb|DT016434.1|DT016434
EST:     AGAAAAAAGGCTTTAAAGGATCCTTTGCAGAGGCCGGATCTTCTGCCAAG                         ACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAG
genomic: AGAAAAAAGGCTTTAAAGGATCCTTTGCAGAGGCCGGATCTTCTGCCAAGgtatgagaga ... cccttaacagACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAG
EST: gi|26262072|gb|CA813135.1|CA813135
EST:     AGAAAAAAGGCTTTAAAGGATCCTTTGCAGAGGCCGGATCTTCTGCCAAG                         ACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAG
genomic: AGAAAAAAGGCTTTAAAGGATCCTTTGCAGAGGCCGGATCTTCTGCCAAGgtatgagaga ... cccttaacagACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAG
EST: gi|33408488|gb|CF214115.1|CF214115
EST:     AGAAAAAAGGCTTTAAAGGATCCTTTGCAGAGGCCGGATCTTCTGCCAAG                         ACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAG
genomic: AGAAAAAAGGCTTTAAAGGATCCTTTGCAGAGGCCGGATCTTCTGCCAAGgtatgagaga ... cccttaacagACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAG
EST: gi|26261889|gb|CA812952.1|CA812952
EST:     AGAAAAAAGGCTTTAAAGGATCCTTTGCAGAGGCCGGATCTTCTGCCAAG                         ACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAG
genomic: AGAAAAAAGGCTTTAAAGGATCCTTTGCAGAGGCCGGATCTTCTGCCAAGgtatgagaga ... cccttaacagACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAG
EST: gi|34549479|gb|CF517711.1|CF517711
EST:     AGAAAAAAGGCTTTAAAGGATCCTTTGCAGAGGCCGGATCTTCTGCCAAG                         ACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAG
genomic: AGAAAAAAGGCTTTAAAGGATCCTTTGCAGAGGCCGGATCTTCTGCCAAGgtatgagaga ... cccttaacagACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAG
EST: gi|33410548|gb|CF216175.1|CF216175
EST:     AGAAAAAAGGCTTTAAAGGATCCTTTGCAGAGGCCGGATCTTCTGCCAAG                         ACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAG
genomic: AGAAAAAAGGCTTTAAAGGATCCTTTGCAGAGGCCGGATCTTCTGCCAAGgtatgagaga ... cccttaacagACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAG
EST: gi|351023375|gb|FQ432758.1|FQ432758
EST:     AGAAAAAAGGCTTTAAAGGATCCTTTGCAGAGGCCGGATCTTCTGCCAAG                         ACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAG
genomic: AGAAAAAAGGCTTTAAAGGATCCTTTGCAGAGGCCGGATCTTCTGCCAAGgtatgagaga ... cccttaacagACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctgataccttgctataaactaaggtttcctcttcttatcttttcccttaacagACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATG
 tcctgat  putative branch site (score: 3)
                          tttcctcttcttatct  putative PPT
              tataaactaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgagagaccatatgatatattgtaaactttgattggctgaattgtatttgtttttccactttattaaccccataaattttatgttatcctgataccttgctataaactaaggtttcctcttcttatcttttcccttaacagACATTTGCAATTTTGTCTGGAGTTCACAGTTTGGTTGTCTGTTTTCTGAAGAGGTTGAGAGGAAAGGATGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG