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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcttatttcatggttggttgtgcaatttgcttacatgtttctttgataaatatgtcatagcctcatggcatcttcctttctgtggctgtaattcctgaagGTGGAGAACCAGGAGGGTGTTATCAACTTTGATGAAATACTGCGTGAGACCGATTCATTTATGGTTGCCCGTGGTGATCTTGGAATGGAGATCCCAGTGG

Basic information

species Vitis vinifera
transcript Vv08s0056g00190.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0056g00190.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os04g58110.1 (Oryza sativa), 3'ss of exon 2
gcttatt-tcatggttggttgtgcaatttgctta-catgtttctttgataaatatgtcatagc-ctcatggcatcttcctttctgtggctgtaattcctgaagGTGGAGAACCAGGAGGGTGTTATCAACTTTGATGAAATACTGCGTGAGACCGATTCATTTATGGTTGCCCGTGGTGATCTTGGAATGGAGATCCCAGTGG
  |  |  | ||| |      |   |  ||| |   |  || |  || |   |||||    |  |   |    |||| |||    |     |  ||  |  |||| || ||||| ||||||||| | ||||| ||||| ||  || | || || ||| |||||||||||||  | |||||||||||||||||||| ||||| |
-ttcgtgatgatgataatacatatgaggtgcctggtaatttaccatgctggttatgttgctgtgcgtctaatttctttcttaactttttccttgttttt--agGTTGAAAACCAAGAGGGTGTTGTAAACTTCGATGAGATCTTGAGGGAAACGGATGCATTTATGGTTGCTAGAGGTGATCTTGGAATGGAGATTCCAGTTG

upper sequence: Vv08s0056g00190.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G150098_T01 (Zea mays), 3'ss of exon 2
----gcttatttcatggttggttgtgcaatttgcttacatgtttctttgataaatatgtcatagcctcatggcatcttcctttctgtggctgtaattcctgaagGTGGAGAACCAGGAGGGTGTTATCAACTTTGATGAAATACTGCGTGAGACCGATTCATTTATGGTTGCCCGTGGTGATCTTGGAATGGAGATCCCAGTGG
    |||   ||      |||| |     ||| ||   |      ||   | ||  |  ||| |     ||   || |   |  | ||| | |  |   || |||| |||||||| ||||||||| | ||||||||||| ||  || | ||||| ||| | |||||||||||  | |||||||| ||||||||||| ||||| |
tgacgctacatttccacctggtaggctgttttactcctaaccgaattctgttaacttcacatggatc--tgatttccttaatgatatggttctgcta--tgcagGTTGAGAACCAAGAGGGTGTTGTAAACTTTGATGAGATCTTGAGGGAGACTGATGCTTTTATGGTTGCTAGAGGTGATCTGGGAATGGAGATTCCAGTCG

upper sequence: Vv08s0056g00190.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G008714_T01 (Zea mays), 3'ss of exon 2
-gcttatttcatggttg-gttgtgcaatttgcttacatgtttct-ttgataaatatgtcatagcctcatggcatcttcctttctgtggctgtaattcctgaagGTGGAGAACCAGGAGGGTGTTATCAACTTTGATGAAATACTGCGTGAGACCGATTCATTTATGGTTGCCCGTGGTGATCTTGGAATGGAGATCCCAGTGG
  | |||| |||  |     ||| ||  | |     ||| |  | ||| | |   |||||| |     ||    ||| | |  | ||| |     |  || |||| || ||||| ||||||||| | ||||||||||| ||  || | ||||| ||| | |||||||||||  | |||||||||||||||||||| || || |
ttcatattacatcatgataatgtacatatagaacttatgatcgtgttggttatgctgtcatggatc--tgattcctttcatgatatggtttccgcta-tgcagGTTGAAAACCAAGAGGGTGTTGTAAACTTTGATGAGATCTTGAGGGAGACTGATGCTTTTATGGTTGCTAGAGGTGATCTTGGAATGGAGATTCCTGTTG

upper sequence: Vv08s0056g00190.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA05G09310.1 (Glycine max), 3'ss of exon 2
gcttatttcatggttggttgtgcaatttgcttacatgtttctttgataaatatgtcatagcctcatggcatcttcctttctgtg-------gctgtaattcctgaagGTGGAGAACCAGGAGGGTGTTATCAACTTTGATGAAATACTGCGTGAGACCGATTCATTTATGGTTGCCCGTGGTGATCTTGGAATGGAGATCCCAGTGG
      |  ||  ||  |    ||| |||| | |  |||| |||| |   | |  ||||  || | |  | |     |||| ||       ||| |  |   | ||||| ||||| |||||||| ||  | || ||||| ||||| ||||| ||||| ||| |||| ||||| || ||||||||||||||||||||||||||||| |
------tatattctttataacacaagttgcatgctagtttgtttggttttttt-ccatatgctgaagataccagttcttctctgattttatgctatgctatttaaagGTTGAGAATCAGGAGGGAGTCCTGAATTTTGACGAAATCCTGCGGGAGACTGATGCATTCATGGTGGCACGTGGTGATCTTGGAATGGAGATCCCAGTAG

upper sequence: Vv08s0056g00190.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA19G00870.2 (Glycine max), 3'ss of exon 2
--gcttattt-catggttggttgtgca-atttgcttacatgtttctttgataaatatgtcatagcctcatggcatcttcctttctgtggctgtaattcctgaagGTGGAGAACCAGGAGGGTGTTATCAACTTTGATGAAATACTGCGTGAGACCGATTCATTTATGGTTGCCCGTGGTGATCTTGGAATGGAGATCCCAGTGG
  ||  | |  | || |  ||| |  | ||   ||| | | |   | |  |   |   |       || ||  || |   |||   ||  ||||  | |||||||| ||||| ||||| || ||  | || ||||| ||||| ||||| ||||| ||| |||| ||||| || || |||||||||||||||||||||||||| |
tagcagactagcttgatctgttttatagatcatctttcttctcgttcttgtctttcaattcagaaatcctg--atttatatttgaatgattgta--tgctgaagGTTGAGAATCAGGAAGGAGTCCTGAATTTTGACGAAATCCTGCGCGAGACTGATGCATTCATGGTGGCACGAGGTGATCTTGGAATGGAGATCCCAGTTG

upper sequence: Vv08s0056g00190.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G08570.1 (Arabidopsis thaliana), 3'ss of exon 3
gcttatttcatggttggttgtgcaatttgcttacatgtttctttgataaatatgtcatagcctcatggcatcttcctttctgtggctgtaattcctgaagGTGGAGAACCAGGAGGGTGTTATCAACTTTGATGAAATACTGCGTGAGACCGATTCATTTATGGTTGCCCGTGGTGATCTTGGAATGGAGATCCCAGTGG
   || ||||   ||  |   | |    | || ||| ||   |  ||  |  | | |       ||   |   |  | ||| ||| | | |||  || |||| ||||||||||| ||||| || ||||||||||| ||  ||||||| || ||| | || |||||||||||||||||||| || |||||||| ||  | |
--gtacttcaaaattt-tcacgtatggcgattgcattttatgtatattgaggtataa-------atctgactcttttctctttgggtttgattt-tgtagGTTGAGAACCAGGAAGGTGTGATTAACTTTGATGAGATCTTGCGTGAAACAGATGCGTTCATGGTTGCCCGTGGTGATCTCGGGATGGAGATTCCGATAG

upper sequence: Vv08s0056g00190.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G63680.1 (Arabidopsis thaliana), 3'ss of exon 3
gcttatttcatggttggttgtgcaatttgcttacatgtttctttgataaatatgtcatagcctcatggcatcttcctttctgtggctgtaattcc-tgaagGTGGAGAACCAGGAGGGTGTTATCAACTTTGATGAAATACTGCGTGAGACCGATTCATTTATGGTTGCCCGTGGTGATCTTGGAATGGAGATCCCAGTGG
                   || |||  |     | | ||||  |  |   ||          | | || |   |  |   |     | | ||    | ||||| |||||||| || || ||  | || || ||||| ||  ||||||| || ||| |||| |||||||| |||||||||||||| |||||||| ||  | |
-------------------gtacaaagttacaccttatttcacttgtggctaaagttggttttaaaggtaggattgtgattagaatttttatcttattaagGTTGAGAACCAAGAAGGAGTCCTGAATTTCGATGAGATTTTGCGTGAAACTGATGCATTCATGGTTGCTCGTGGTGATCTTGGGATGGAGATTCCGATAG

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|110698076|gb|EE075678.1|EE075678
EST:     TCCGAAAGGTGCTCGGGTCTCATGCCAAGCGTATACAGTTAATGTCAAAG                         GTGGAGAACCAGGAGGGTGTTATCAACTTTGATGAAATACTGCGTGAGACC
genomic: TCCGAAAGGTGCTCGGGTCTCATGCCAAGCGTATACAGTTAATGTCAAAGgtacatgaat ... attcctgaagGTGGAGAACCAGGAGGGTGTTATCAACTTTGATGAAATACTGCGTGAGACC
EST: gi|161707167|gb|FC055571.1|FC055571
EST:     TCCGAAAGGTGCTCGGGTCTCATGCCAAGCGTATACAGTTAATGTCAAAG                         GTGGAGAACCAGGAGGGTGTTATCAACTTTGATGAAATACTGCGTGAGACC
genomic: TCCGAAAGGTGCTCGGGTCTCATGCCAAGCGTATACAGTTAATGTCAAAGgtacatgaat ... attcctgaagGTGGAGAACCAGGAGGGTGTTATCAACTTTGATGAAATACTGCGTGAGACC
EST: gi|161720977|gb|FC070692.1|FC070692
EST:     TCCGAAAGGTGCTCGGGTCTCATGCCAAGCGTATACAGTTAATGTCAAAG                         GTGGAGAACCAGGAGGGTGTTATCAACTTTGATGAAATACTGCGTGAGACC
genomic: TCCGAAAGGTGCTCGGGTCTCATGCCAAGCGTATACAGTTAATGTCAAAGgtacatgaat ... attcctgaagGTGGAGAACCAGGAGGGTGTTATCAACTTTGATGAAATACTGCGTGAGACC
EST: gi|110709558|gb|EE085123.1|EE085123
EST:     CCGAA-GGTGCCTCGG-TCTCATGCCAAGCGTATACAGTTTATGTCAAAG                         TTGGAGAAACAGGA
genomic: CCGAAAGGTGC-TCGGGTCTCATGCCAAGCGTATACAGTTAATGTCAAAGgtacatgaat ... attcctgaagGTGGAGAACCAGGA
EST: gi|110403523|gb|EC969105.1|EC969105
EST:     TCCGAAAGGTGCTCGGGTCTCATGCCAAGCGTATACAGTTAATGTCAAAG                         GTGGAGAACCAGGAGGGTGTTATCAACTTTGATGAAATACTGCGTGAGACC
genomic: TCCGAAAGGTGCTCGGGTCTCATGCCAAGCGTATACAGTTAATGTCAAAGgtacatgaat ... attcctgaagGTGGAGAACCAGGAGGGTGTTATCAACTTTGATGAAATACTGCGTGAGACC
EST: gi|71864461|gb|DT013516.1|DT013516
EST:     TCCGAAAGGTGCTCGGGTCTCATGCCAAGCGTATACAGTTAATGTCAAAG                         GTGGAGAACCAGGAGGGTGTTATCAACTTTGATGAAATACTGCGTGAGACC
genomic: TCCGAAAGGTGCTCGGGTCTCATGCCAAGCGTATACAGTTAATGTCAAAGgtacatgaat ... attcctgaagGTGGAGAACCAGGAGGGTGTTATCAACTTTGATGAAATACTGCGTGAGACC
EST: gi|27583966|gb|CB006661.1|CB006661
EST:     TCCGAAAGGTGCTCGGGTCTCATGCCAAGCGTATACAGTTAATGTCAAAG                         GTGGAGAACCAGGAGGGTGTTATCAACTTTGATGAAATACTGCGTGAGACC
genomic: TCCGAAAGGTGCTCGGGTCTCATGCCAAGCGTATACAGTTAATGTCAAAGgtacatgaat ... attcctgaagGTGGAGAACCAGGAGGGTGTTATCAACTTTGATGAAATACTGCGTGAGACC
EST: gi|71857555|gb|DT006610.1|DT006610
EST:     TATACAGTTAATGTCAAAG                         GTGGAGAACCAGGAGGGTGTTATCAACTTTGATGAAATACTGCGTGAGACC
genomic: TATACAGTTAATGTCAAAGgtacatgaat ... attcctgaagGTGGAGAACCAGGAGGGTGTTATCAACTTTGATGAAATACTGCGTGAGACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataaatatgtcatagcctcatggcatcttcctttctgtggctgtaattcctgaagGTGGAGAACCAGGAGGGTGTTATCAACTTTGATGAAATACTGCGTGAGACCGATTCATTTATGGTTGCCCGTGGTGATCTTGGAATGGAGATCCCAGTGG
 ctttgat  putative branch site (score: 5)
                                              ttcct  putative PPT
                                         tgtaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcttatttcatggttggttgtgcaatttgcttacatgtttctttgataaatatgtcatagcctcatggcatcttcctttctgtggctgtaattcctgaagGTGGAGAACCAGGAGGGTGTTATCAACTTTGATGAAATACTGCGTGAGACCGATTCATTTATGGTTGCCCGTGGTGATCTTGGAATGGAGATCCCAGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - tggttgg
- - - - - - - - - - - - - - - - acatgtt
- - - - - - - - - - - - - - - - - - - - - - -ataaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctcatg