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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggtaatatgaaattatgtgttaaagtagatttatttaggttagtatcatttgcatttatattctttttgtctgccattacacactgactccagacatttattttccagGGTCAACTGCTAACTTTGGTTGAATATACATTACTGTTGTATCGTGCCTTGTTGCCAGCACCTGTCTGGTATCGTTTTTTCTTGAACAAAGAATATGGGA

Basic information

species Vitis vinifera
transcript Vv08s0056g00440.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0056g00440.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os05g25180.1 (Oryza sativa), 3'ss of exon 4
gtaaggtaatatgaaattatgtgttaaagtagatttatttaggttagtatcatttgcatttatattctttttgtctgccattacacactga--ctccagacatttatttt-ccagGGTCAACTGCTAACTTTGGTTGAATATACATTACTGTTGTATCGTGCCTTGTTGCCAGCACCTGTCTGGTATCGTTTTTTCTTGAACAAAGAATATGGGA
               ||  ||  ||  ||   ||||  |||  ||||   | |||  | ||  |  |||  |   ||    |     ||||  ||| |    | | |||| | |||||||| |||||||  | || |||||     | ||  | |||||||||||||||||| | ||||| ||||| ||||| ||  ||||||| ||||||||||
--------------tatcttgaattctagcttattt-cttattttagatccttttatagttgcaagcttagtagttggttctgacttctgaggctcaaactttctgttttgctagGGTCAAATGCTAACCCTTGTGGAATACCTTCTGCTCCTATATCGTGCCTTGTTGCCAACTCCTGTTTGGTACCGTTTCTTTCTGAACAAGGAATATGGGA

upper sequence: Vv08s0056g00440.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G141216_T02 (Zea mays), 3'ss of exon 4
--------------------gtaaggtaatatgaaattatgtgttaaagtagatttattta---------ggttagtatcatttgcatttatattctttttgtctgccattacaca-ctgactccagacatttattttccagGGTCAACTGCTAACTTTGGTTGAATATACATTACTGTTGTATCGTGCCTTGTTGCCAGCACCTGTCTGGTATCGTTTTTTCTTGAACAAAGAATATGGGA
                     |     | | |    | || | ||   ||  ||||  | |         |||  |  |  ||| | | |  ||  |  | ||| |  |    | | |  | |     |  ||  | | ||||||||| || | ||  | || ||||||    |||| ||||||||||| || |||||  ||||||| ||||| ||||||||| ||||||| || ||||| |
gtaaaccatctacatttgttatcctacatttttctgtgatatattttggtgaatttcctcaataactcatggtgtggtttgtttacttctgcataatcgtagtcggagacgctataaccaattttctccccttgctgttcagGGTCAAATGTTGACGATTGTGGAATATTTTCTACTTTTGTATCGTGCATTATTGCCTACACCTGTGTGGTACCGTTTTTTCCTGAACAAGGAGTATGGAA

upper sequence: Vv08s0056g00440.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G061980_T01 (Zea mays), 3'ss of exon 4
gtaaggtaatatgaaattatgtgttaaagtagatttatttaggttagtatcatttgcatttatattctttttgtctgccattacacactgactccagacatttattttccagGGTCAACTGCTAACTTTGGTTGAATATACATTACTGTTGTATCGTGCCTTGTTGCCAGCACCTGTCTGGTATCGTTTTTTCTTGAACAAAGAATATGGGA
  |   |  | |  | | |  |||   | |   ||   ||  ||||| |  |           |||  | |||       ||||||  | ||| || |   ||  |||  |||| ||| || ||||  | || || ||     | ||  | |||||||| ||||||||| |  |||| ||||||||||| ||  ||||||| ||||||||||
-aacattgttgtacagtaacatgtgtgaattttttcccttctgttagaacaacca--------attagtattgcagaatgttacac--taactaca-attcttcctttttagGGCCAAATGTTAACCCTTGTGGAGTACCTTCTGCTTCTTTATCGTGCTTTGTTGCCAACTTCTGTTTGGTATCGTTTCTTTCTGAACAAGGAATATGGGA

upper sequence: Vv08s0056g00440.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA18G45010.1 (Glycine max), 3'ss of exon 4
gtaaggtaatatgaaattatgtgttaaagtagatttatttaggttagtatcatttgcatttatattctttttgtc-tgccattacacactgac--tccagacatttattttccagGGTCAACTGCTAACTTTGGTTGAATATACATTACTGTTGTATCGTGCCTTGTTGCCAGCACCTGTCTGGTATCGTTTTTTCTTGAACAAAGAATATGGGA
                 ||| | ||  |  |  |||  |   |||| |    |  | || |||||  | ||| || || |||||||  ||||   | |   ||||| |||  ||||||||| |||| ||||| ||||||||     | ||| | || ||||||||||||||| |||| || ||||||||||| ||| |||||||||||||||| |
------------tctgctatcttttgtaaca--tttcctggagtta-tgggttcaggatctatatcatctttctcatgtcattacattctgatggtactatcatttttttgtcagGGTCAAATGCTGACTTTAGTTGAATACCTCCTCCTGCTTTACCGTGCCTTGTTGCCAACACCAGTTTGGTATCGTTTCTTCCTGAACAAAGAATATGGAA

upper sequence: Vv08s0056g00440.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G01960.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaaggtaatatgaaattatgtgttaaagtagatttatttaggttagtatcatttgcatttatattctttttgtctgccattacacactgactccagacatttattttc----cagGGTCAACTGCTAACTTTGGTTGAATATACATTACTGTTGTATCGTGCCTTGTTGCCAGCACCTGTCTGGTATCGTTTTTTCTTGAACAAAGAATATGGGA
|| | |||  |  | ||| | | |         ||   |    | ||| |||||||   |     ||  | || |  |  |   | ||  | |   |  ||| | || |    ||||||||| ||||||||||||||||||||    | ||  |||||||  | ||  ||||  | ||||| ||||| ||||| || |||||||| || ||||| |
gtgatgtagaaaaatattct-tctctgtcccctttagctgtattcagtttcatttggcatggc--tcactgtggcgtctctgggatacataatttggttattcacttccaatgcagGGTCAATTGCTAACTTTGGTTGAATATTTCATGCTTCTGTATCGCTCTTTACTGCCTACCCCTGTATGGTACCGTTTCTTTTTGAACAAGGATTATGGAA

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|110730035|gb|EE106655.1|EE106655
EST:     TTCTATTGATGTACTACAAGAACAGCAGAGGCAGAAATTATCGTAAACAG                         GGTCAACTGCTAACTTTGGTTGAATATACATTACTGTTGTATCGTGCCTTG
genomic: TTCTATTGATGTACTACAAGAACAGCAGAGGCAGAAATTATCGTAAACAGgtaaggtaat ... tattttccagGGTCAACTGCTAACTTTGGTTGAATATACATTACTGTTGTATCGTGCCTTG
EST: gi|37184416|gb|CF603770.1|CF603770
EST:     TTCTATTGATGTACTACAAGAACAGCAGAGGCAGAAATTATCGTAAACAG                         GGTCAACTGCTAACTTTGGTTGAATATACATTACTGTTGTATCGTGCCTTG
genomic: TTCTATTGATGTACTACAAGAACAGCAGAGGCAGAAATTATCGTAAACAGgtaaggtaat ... tattttccagGGTCAACTGCTAACTTTGGTTGAATATACATTACTGTTGTATCGTGCCTTG
EST: gi|30253236|gb|CB970787.1|CB970787
EST:     TTCTATTGATGTACTACAAGAACAGCAGAGGCAGAAATTATCGTAAACAG                         GGTCAACTGCTAACTTTGGTTGAATATACATTACTGTTGTATCGTGCCTTG
genomic: TTCTATTGATGTACTACAAGAACAGCAGAGGCAGAAATTATCGTAAACAGgtaaggtaat ... tattttccagGGTCAACTGCTAACTTTGGTTGAATATACATTACTGTTGTATCGTGCCTTG
EST: gi|110729839|gb|EE106235.1|EE106235
EST:     TTCTATTGATGTACTACAAGAACAGCAGAGGCAGAAATTATCGTAAACAG                         GGTCAACTGCTAACTTTGGTTGAATATACATTACTGTTGTATCGTGCCTTG
genomic: TTCTATTGATGTACTACAAGAACAGCAGAGGCAGAAATTATCGTAAACAGgtaaggtaat ... tattttccagGGTCAACTGCTAACTTTGGTTGAATATACATTACTGTTGTATCGTGCCTTG
EST: gi|161708174|gb|FC056515.1|FC056515
EST:     TTCTATTGATGTACTACAAGAACAGCAGAGGCAGAAATTATCGTAAACAG                         GGTCAACTGCTAACTTTGGTTGAATAT
genomic: TTCTATTGATGTACTACAAGAACAGCAGAGGCAGAAATTATCGTAAACAGgtaaggtaat ... tattttccagGGTCAACTGCTAACTTTGGTTGAATAT
EST: gi|161721710|gb|FC071108.1|FC071108
EST:     CTACAAGAACAGCAGAGGCAGAAATTATCGTAAACAG                         GGTCAACTGCTAACTTTGGTTGAATATACATTACTGTTGTATCGTGCCTTG
genomic: CTACAAGAACAGCAGAGGCAGAAATTATCGTAAACAGgtaaggtaat ... tattttccagGGTCAACTGCTAACTTTGGTTGAATATACATTACTGTTGTATCGTGCCTTG
EST: gi|110390287|gb|EC955189.1|EC955189
EST:     TTCTATTGATGTACTACAAGAACAGCAGAGGCAGAAATTATCGTAAACAG                         GGTCAACTGCTAACTTTGGTTGAATATACATTACTGTTGTATCGTGCCTTG
genomic: TTCTATTGATGTACTACAAGAACAGCAGAGGCAGAAATTATCGTAAACAGgtaaggtaat ... tattttccagGGTCAACTGCTAACTTTGGTTGAATATACATTACTGTTGTATCGTGCCTTG
EST: gi|110396248|gb|EC961929.1|EC961929
EST:     TTCTATTGATGTACTACAAGAACAGCAGAGGCAGAAATTATCGTAAACAG                         GGTCAACTGCTAACTTTGGTTGAATATACATTACTGTTGTATCGTGCCTTG
genomic: TTCTATTGATGTACTACAAGAACAGCAGAGGCAGAAATTATCGTAAACAGgtaaggtaat ... tattttccagGGTCAACTGCTAACTTTGGTTGAATATACATTACTGTTGTATCGTGCCTTG
EST: gi|30253079|gb|CB970630.1|CB970630
EST:     TTCTATTGATGTACTACAAGAACAGCAGAGGCAGAAATTATCGTAAACAG                         GGTCAACTGCTAACTTTGGTTGAATATACATTACTGTTGTATCGTGCCTTG
genomic: TTCTATTGATGTACTACAAGAACAGCAGAGGCAGAAATTATCGTAAACAGgtaaggtaat ... tattttccagGGTCAACTGCTAACTTTGGTTGAATATACATTACTGTTGTATCGTGCCTTG
EST: gi|161719084|gb|FC069337.1|FC069337
EST:     TTCTATTGATGTACTACAAGAACAGCAGAGGCAGAAATTATCGTAAACAG                         GGTCAACTGCTAACTTTGGTTGAATATACATTACTGTTGTATCGTGCCTTG
genomic: TTCTATTGATGTACTACAAGAACAGCAGAGGCAGAAATTATCGTAAACAGgtaaggtaat ... tattttccagGGTCAACTGCTAACTTTGGTTGAATATACATTACTGTTGTATCGTGCCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttatattctttttgtctgccattacacactgactccagacatttattttccagGGTCAACTGCTAACTTTGGTTGAATATACATTACTGTTGTATCGTGCCTTGTTGCCAGCACCTGTCTGGTATCGTTTTTTCTTGAACAAAGAATATGGGA
                            cactgac  putative branch site (score: 2)
                                           tttattttcc  putative PPT
                                        acatttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggtaatatgaaattatgtgttaaagtagatttatttaggttagtatcatttgcatttatattctttttgtctgccattacacactgactccagacatttattttccagGGTCAACTGCTAACTTTGGTTGAATATACATTACTGTTGTATCGTGCCTTGTTGCCAGCACCTGTCTGGTATCGTTTTTTCTTGAACAAAGAATATGGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA