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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattttgagcagtttttcctcttgaatttgattgattattttgactatggctgcctatgctaaaaactgtgggtccttatcagGAATTTATTGAGGCAACTAGAGAGCCCAGTGTCACATTTTTGGTGGCCAAATTTGATGGTATATTAGGACTTGGATTTCAAGAGATTTCAGTTGGAAATG

Basic information

species Vitis vinifera
transcript Vv10s0116g01210.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0116g01210.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA17G01500.1 (Glycine max), 3'ss of exon 4
gtgattttgagcagtttttcctc----ttgaatttgattga-ttattttgactatggctgcctatgctaaaaactgtgggtccttatcagGAATTTATTGAGGCAACTAGAGAGCCCAGTGTCACATTTTTGGTGGCCAAATTTGATGGTATATTAGGACTTGGATTTCAAGAGATTTCAGTTGGAAATG
|  ||  |||   |    || ||    || | ||  || |   |  ||| |  |||  |    ||  ||  |  || |  |||   ||||||||||||||| |||||||| |||||  |||| |||||||||| |||||| |||||||||||| | |||||||||||||||||||| |||||||||||||
gcaatactgaattgcggatcatcaatgtttatttcaatagggcttctttcataatgattagtaat--tagtagttg-gtatccccttcagGAATTTATTGAAGCAACTAGGGAGCCTGGTGTTACATTTTTGGCGGCCAAGTTTGATGGTATACTGGGACTTGGATTTCAAGAGATATCAGTTGGAAATG

upper sequence: Vv10s0116g01210.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA07G39240.2 (Glycine max), 3'ss of exon 4
--------------gtgattttgagcagtttttcctcttgaatttg---attgattattttgactatg-gctgccta-----tgctaaaa--actgtgggtccttatcagGAATTTATTGAGGCAACTAGAGAGCCCAGTGTCACATTTTTGGTGGCCAAATTTGATGGTATATTAGGACTTGGATTTCAAGAGATTTCAGTTGGAAATG
               | ||  | |    || || |  | ||   ||      |  |  ||| |  ||  | ||  ||     || || |    || | | | |  |||||||||||||||| |||||||| |||||  |||| ||||||||||  ||||| |||||||||||| | |||||||||||||||||||| |||||||||||||
gtaatgctgaactgctaatcatcaatgtttatttcaatagagggtgtgagagggcttctttcataatatgttgattagtaattggtatagtgccttttgatacccatcagGAATTTATTGAAGCAACTAGGGAGCCTGGTGTTACATTTTTGGCAGCCAAGTTTGATGGTATACTGGGACTTGGATTTCAAGAGATATCAGTTGGAAATG

upper sequence: Vv10s0116g01210.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA15G11670.1 (Glycine max), 3'ss of exon 3
-------------------gtgattttgagcagtttttcctct-----------tgaatttgattgattattttgactatg-gctgcctatgctaaaaac----------tgtgggtccttatcagGAATTTATTGAGGCAACTAGAGAGCCCAGTGTCACATTTTTGGTGGCCAAATTTGATGGTATATTAGGACTTGGATTTCAAGAGATTTCAGTTGGAAATG
                      ||||        |||||||             | | ||   |||  |  ||| |  ||  | ||  ||  | |  |||          | | | ||   || ||||||||||||| ||||||||||| ||  | || |||||| |||  || || |||||||||||| |||||||||||||||||||||| ||||||||| |||
gtaatgatgattgtcaatccctatttcatttttcttttccttcacaccaacatgtcagttgagttggcttctttcataataagttgattaatcaattaacgtgaagtatgttttgatctccattagGAATTTATTGAAGCAACTAGAGAACCTGGAGTTACATTTGTGGCTGCTAAGTTTGATGGTATACTAGGACTTGGATTTCAAGAGATATCAGTTGGATATG

upper sequence: Vv10s0116g01210.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA09G00810.1 (Glycine max), 3'ss of exon 3
-------------------------------------------gtgattttgagcagtttttcctcttgaatttgattgattattttgactatggctgccta--tgctaaaaactgtg----ggtccttatcagGAATTTATTGAGGCAACTAGAGAGCCCAGTGTCACATTTTTGGTGGCCAAATTTGATGGTATATTAGGACTTGGATTTCAAGAGATTTCAGTTGGAAATG
                                                    |   ||  |  |  |||| || | ||  ||  |   |   ||  |    |  |   |  || | ||      || | || ||||||||||||| ||||||||||| ||  | || |||||| |||  || || |||||||||||| ||||||||||||||||||| || ||||||||| |||
gtaatactaattgtcaatccctatttcatttttcttttccttcacaccaacaaagtgtgatgtcagttgagttggcttctttcataatatgttgattaatcaattaacatgaagtatgttttaatcttcattagGAATTTATTGAAGCAACTAGAGAACCTGGAGTTACATTTGTGGCTGCTAAGTTTGATGGTATACTAGGACTTGGATTTCAAGATATATCAGTTGGATATG

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|110723374|gb|EE100612.1|EE100612
EST:     TCTTTAGTGAAGACAATGTGAAAGTTGGTGATCTTGTTGTGAAGAATCAG                         GAATTTATTGAGGCAACTAGAGAGCCCAGTGTCACATTTTTGGTGGCCAAA
genomic: TCTTTAGTGAAGACAATGTGAAAGTTGGTGATCTTGTTGTGAAGAATCAGgtgattttga ... tccttatcagGAATTTATTGAGGCAACTAGAGAGCCCAGTGTCACATTTTTGGTGGCCAAA
EST: gi|110703507|gb|EE080413.1|EE080413
EST:     TCTTTAGTGAAGACAATGTGAAAGTTGGTGATCTTGTTGTGAAGAATCAN                         GAATTTATTGAGGCAACTAGAGAGCCCAGTGTCACATTTTTGGTGGCCAAA
genomic: TCTTTAGTGAAGACAATGTGAAAGTTGGTGATCTTGTTGTGAAGAATCAGgtgattttga ... tccttatcagGAATTTATTGAGGCAACTAGAGAGCCCAGTGTCACATTTTTGGTGGCCAAA
EST: gi|71862953|gb|DT012008.1|DT012008
EST:     TCTTTAGTGAAGACAATGTGAAAGTTGGTGATCTTGTTGTGAAGAATCAG                         GAATTTATTGAG
genomic: TCTTTAGTGAAGACAATGTGAAAGTTGGTGATCTTGTTGTGAAGAATCAGgtgattttga ... tccttatcagGAATTTATTGAG
EST: gi|110726583|gb|EE102492.1|EE102492
EST:     TCTTTAGTGAAGACAATGTGAAAGTTGGTGATCTTGTTGTGAAGAATCAG                         GAATTTATTGAGGCAACTAGAGAGCCCAGTGTCACATTTTTGGTGGCCAAA
genomic: TCTTTAGTGAAGACAATGTGAAAGTTGGTGATCTTGTTGTGAAGAATCAGgtgattttga ... tccttatcagGAATTTATTGAGGCAACTAGAGAGCCCAGTGTCACATTTTTGGTGGCCAAA
EST: gi|71863294|gb|DT012349.1|DT012349
EST:     TCTTTAGTGAAGACAATGTGAAAGTTGGTGATCTTGTTGTGAAGAATCAG                         GAATTTATTGAGGCAACTAGAGAGCCCAGTGTCACATTTTTGGTGGCCAAA
genomic: TCTTTAGTGAAGACAATGTGAAAGTTGGTGATCTTGTTGTGAAGAATCAGgtgattttga ... tccttatcagGAATTTATTGAGGCAACTAGAGAGCCCAGTGTCACATTTTTGGTGGCCAAA
EST: gi|110723213|gb|EE100267.1|EE100267
EST:     TCTTTAGTGAAGACAATGTGAAAGTTGGTGATCTTGTTGTGAAGAATCAG                         GAATTTATTGAGGCAACTAGAGAGCCCAGTGTCACATTTTTGGTGGCCAAA
genomic: TCTTTAGTGAAGACAATGTGAAAGTTGGTGATCTTGTTGTGAAGAATCAGgtgattttga ... tccttatcagGAATTTATTGAGGCAACTAGAGAGCCCAGTGTCACATTTTTGGTGGCCAAA
EST: gi|110724471|gb|EE100330.1|EE100330
EST:     TCTTTAGTGAAGACAATGTGAAAGTTGGTGATCTTGTTGTGAAGAATCAG                         GAATTTATTGAGGCAACTAGAGAGCCCAGTGTCACATTTTTGGTGGCCAAA
genomic: TCTTTAGTGAAGACAATGTGAAAGTTGGTGATCTTGTTGTGAAGAATCAGgtgattttga ... tccttatcagGAATTTATTGAGGCAACTAGAGAGCCCAGTGTCACATTTTTGGTGGCCAAA
EST: gi|161719906|gb|FC066714.1|FC066714
EST:     GACAATGTGAAAGTTGGTGATCTTGTTGTGAAGAATCAG                         GAATTTATTGAGGCAACTAGAGAGCCCAGTGTCACATTTTTGGTGGCCAAA
genomic: GACAATGTGAAAGTTGGTGATCTTGTTGTGAAGAATCAGgtgattttga ... tccttatcagGAATTTATTGAGGCAACTAGAGAGCCCAGTGTCACATTTTTGGTGGCCAAA
EST: gi|110709179|gb|EE084415.1|EE084415
EST:     TCTTTAGTGAAGACAATGTGAAAGTTGGTGATCTTGTTGTGAAGAATCAN                         GAATTTATTGAGGCAACTAAAGAGCCCAGTGTCACATTTTTGGTGGCCAAA
genomic: TCTTTAGTGAAGACAATGTGAAAGTTGGTGATCTTGTTGTGAAGAATCAGgtgattttga ... tccttatcagGAATTTATTGAGGCAACTAGAGAGCCCAGTGTCACATTTTTGGTGGCCAAA
EST: gi|110710072|gb|EE086085.1|EE086085
EST:     TCTTTAGTGAAGACAATGTGAAAGTTGGTGATCTTGTTGTGAAGAATCAG                         GAATTTATTGAGGCAACTAGAGAGCCCAGTGTCACATTTTTGGTGGCCAAA
genomic: TCTTTAGTGAAGACAATGTGAAAGTTGGTGATCTTGTTGTGAAGAATCAGgtgattttga ... tccttatcagGAATTTATTGAGGCAACTAGAGAGCCCAGTGTCACATTTTTGGTGGCCAAA
EST: gi|110708151|gb|EE085368.1|EE085368
EST:     TCTTTAGTGAAGACAATGTGAAAGTTGGTGATCTTGTTGTGAAGAATCAG                         GAATTTATTGAGGCAACTAGAGAGCCCAGTGTCACATTTTTGGTGGCCAAA
genomic: TCTTTAGTGAAGACAATGTGAAAGTTGGTGATCTTGTTGTGAAGAATCAGgtgattttga ... tccttatcagGAATTTATTGAGGCAACTAGAGAGCCCAGTGTCACATTTTTGGTGGCCAAA
EST: gi|110723066|gb|EE099952.1|EE099952
EST:     TCTTTAGTGAAGACAATGTGAAAGTTGGTGATCTTGTTGTGAAGAATCAG                         GAATTTATTGAGGCAACTAGAGAGCCCAGTGTCACATTTTTGGTGGCCAAA
genomic: TCTTTAGTGAAGACAATGTGAAAGTTGGTGATCTTGTTGTGAAGAATCAGgtgattttga ... tccttatcagGAATTTATTGAGGCAACTAGAGAGCCCAGTGTCACATTTTTGGTGGCCAAA
EST: gi|110709842|gb|EE085666.1|EE085666
EST:     TCTTTAGTGAAGACAATGTGAAAGTTGGTGATCTTGTTGTGAAGAATCAN                         GAATTTATTGAGGCAACTAGAGAGCCCAGTGTCACATTTTTGGTGGCCAAA
genomic: TCTTTAGTGAAGACAATGTGAAAGTTGGTGATCTTGTTGTGAAGAATCAGgtgattttga ... tccttatcagGAATTTATTGAGGCAACTAGAGAGCCCAGTGTCACATTTTTGGTGGCCAAA
EST: gi|71865136|gb|DT014191.1|DT014191
EST:     TCTTTAGTGAAGACAATGTGAAAGTTGGTGATCTTGTTGTGAAGAATCAG                         GAATTTATTGAGGCAACTAGAGAGCCCAGTGTCACATTTTTGGTGGCCAAA
genomic: TCTTTAGTGAAGACAATGTGAAAGTTGGTGATCTTGTTGTGAAGAATCAGgtgattttga ... tccttatcagGAATTTATTGAGGCAACTAGAGAGCCCAGTGTCACATTTTTGGTGGCCAAA
EST: gi|110697801|gb|EE075199.1|EE075199
EST:     TCTTTAGTGAAGACAATGTGAAAGTTGGTGATCTTGTTGTGAAGAATCAN                         GAATTTATTGAGGCAACTAGAGAGCCCAGTGTCACATTTTTGGTGGCCAAA
genomic: TCTTTAGTGAAGACAATGTGAAAGTTGGTGATCTTGTTGTGAAGAATCAGgtgattttga ... tccttatcagGAATTTATTGAGGCAACTAGAGAGCCCAGTGTCACATTTTTGGTGGCCAAA
EST: gi|110723493|gb|EE100867.1|EE100867
EST:     TCTTTAGTGAAGACAATGTGAAAGTTGGTGATCTTGTTGTGAAGAATCAA                         GAATTTATTGAGGCAACTAGAGAGCCCAGTGTCACATTTTTGGTGGCCAAA
genomic: TCTTTAGTGAAGACAATGTGAAAGTTGGTGATCTTGTTGTGAAGAATCAGgtgattttga ... tccttatcagGAATTTATTGAGGCAACTAGAGAGCCCAGTGTCACATTTTTGGTGGCCAAA
EST: gi|30299773|gb|CB976567.1|CB976567
EST:     TCTTTAGTGAAGACAATGTGAAAGTTGGTGATCCTGTTGTGAAGAATCAG                         GAATTTATTGAGGCAACTAGAGAGCCCAGTGTCACATTTTTGGTGGCCAAA
genomic: TCTTTAGTGAAGACAATGTGAAAGTTGGTGATCTTGTTGTGAAGAATCAGgtgattttga ... tccttatcagGAATTTATTGAGGCAACTAGAGAGCCCAGTGTCACATTTTTGGTGGCCAAA
EST: gi|110724042|gb|EE099523.1|EE099523
EST:     TCTTTAGTGAAGACAATGTGAAAGTTGGTGATCTTGTTGTGAAGAATCAG                         GAATTTATTGAGGCAACTAGAGAGCCCAGTGTCACATTTTTGGTGGCCCAA
genomic: TCTTTAGTGAAGACAATGTGAAAGTTGGTGATCTTGTTGTGAAGAATCAGgtgattttga ... tccttatcagGAATTTATTGAGGCAACTAGAGAGCCCAGTGTCACATTTTTGGTGGCCAAA
EST: gi|352789600|gb|FQ476198.1|FQ476198
EST:     TCTTTAGTGAAGACAATGTGAAAGTTGGTGATCTTGTTGTGAAGAATCAG                         GAATTTATTGAGGCAACTAGAGAGCCCAGTGTCACATTTTTGGTGGCCAAA
genomic: TCTTTAGTGAAGACAATGTGAAAGTTGGTGATCTTGTTGTGAAGAATCAGgtgattttga ... tccttatcagGAATTTATTGAGGCAACTAGAGAGCCCAGTGTCACATTTTTGGTGGCCAAA
EST: gi|110684973|gb|EE062864.1|EE062864
EST:     TCTTTAGTGAAGACAATGTGAAAGTTGGTGATCTTGTTGTGAAGAATCAG                         GAATTTATTGAGGCAACTAGAGAGCCCAGTGTCACATTTTTGGTGGCCAAA
genomic: TCTTTAGTGAAGACAATGTGAAAGTTGGTGATCTTGTTGTGAAGAATCAGgtgattttga ... tccttatcagGAATTTATTGAGGCAACTAGAGAGCCCAGTGTCACATTTTTGGTGGCCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgattgattattttgactatggctgcctatgctaaaaactgtgggtccttatcagGAATTTATTGAGGCAACTAGAGAGCCCAGTGTCACATTTTTGGTGGCCAAATTTGATGGTATATTAGGACTTGGATTTCAAGAGATTTCAGTTGGAAATG
                             tgctaaa  putative branch site (score: 2)
                                             tccttatc  putative PPT
      attattttgactat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgattttgagcagtttttcctcttgaatttgattgattattttgactatggctgcctatgctaaaaactgtgggtccttatcagGAATTTATTGAGGCAACTAGAGAGCCCAGTGTCACATTTTTGGTGGCCAAATTTGATGGTATATTAGGACTTGGATTTCAAGAGATTTCAGTTGGAAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA