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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actctcttttagataaggtcctctatattttgtgaggtttctgtattgtcccatacatgtcgtttcctgtaccacttgataattgtgatgtgaaattcagGTTCTTCAATCAGTGCTTCCTATTACTGATGATGAGGTTGTTCTTGGACAATACGAAGGTTACACAGATGACCCAACAGTTCCTGACCTTTCAAATACCC

Basic information

species Vitis vinifera
transcript Vv14s0171g00490.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os04g40874.1 (Oryza sativa), 3'ss of exon 9
-----------------actctcttttagataaggtcct-ctatattttgt-gaggtttctgtatt----gtcccatacat--gtcgtttcctgtaccacttgataat-----tgtgatgtgaaattcagGTTCTTCAATCAGTGCTTCCTATTACTGATGATGAGGTTGTTCTTGGACAATACGAAGGTTACACAGATGACCCAACAGTTCCTGACCTTTCAAATACCC
                 | |||||    |  ||     |  |  |  |||   |   |    || |    ||   ||   |  |||  || || ||  |||  ||||      |    ||| ||   |||||||| || || |||   ||||| |   ||||||||||||| |||||||||||||| || ||||  |||||||| ||||| || ||    ||||| ||||
gtactttacctttctctattctctacatgtcaatactatattgcagcttgccaatactataatactaagagtattatgttttagtccgtttctttagtactaaataaaaccagttccctgttaatgccagGTTCTGCAGTCCGTGAACCCTATAAAGCATGATGAGGTTGTCCTTGGACAATACGAGGGGTACAAGGATGACCCTACAGTGCCAGATGACTCAAACACCC

upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA19G24250.1 (Glycine max), 3'ss of exon 10
actctcttttagataaggtcctctatattttgtgaggtttctgtattgtcccatacatgtcgtttcctgtaccacttgataattgtgatgtgaaa--ttcagGTTCTTCAATCAGTGCTTCCTATTACTGATGATGAGGTTGTTCTTGGACAATACGAAGGTTACACAGATGACCCAACAGTTCCTGACCTTTCAAATACCC
|   | |   |  || |||   |||  ||||| || |  ||        ||  || || || | |    || ||||| ||  |||  || |||||  | ||||||||| |||||||||| |||||||  |||||||||||||||||||||||||||||||| || | ||||||||||||||| ||||||   ||||| ||||
aaaatttcacatttatggttacctagtttttgagatgagtcacagcatgcctctatatatcatatg--ataacactttatggttgctatatgaaaaatgcagGTTCTTGAATCAGTGCTCCCTATTAGAGATGATGAGGTTGTTCTTGGACAATACGAAGGCTATAAAGATGACCCAACAGTACCTGACAAGTCAAACACCC

upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA16G06850.3 (Glycine max), 3'ss of exon 10
--actctcttttagataaggtcctctatattttgtgaggtttctgtattgt-cccatacatgtcgtttcctgtaccacttgataattgtgatgtgaaattcagGTTCTTCAATCAGTGCTTCCTATTACTGATGATGAGGTTGTTCTTGGACAATACGAAGGTTACACAGATGACCCAACAGTTCCTGACCTTTCAAATACCC
  | | |     |  || |||   |||  ||||| || |  ||   |   | ||  || |  || | |    || ||||| ||  |||  | |  || | ||||||||| |||||||||| ||||||| ||||||||||||||||||||||||||| ||||| || | |||||||||||| || |||||    || || ||||
tcaatgttgcacatttatggttacctagtttttgagatgagtc-acaccatgcctctatagatcatatg--ataacactttatggttgctacggaaagtgcagGTTCTTGAATCAGTGCTCCCTATTAATGATGATGAGGTTGTTCTTGGACAATATGAAGGCTATAAAGATGACCCAACCGTACCTGATGAGTCTAACACCC

upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA19G22690.1 (Glycine max), 3'ss of exon 10
----------------------------actctcttttagataaggtcctctatattttgtgaggtttctgtattgtcccatacatgtcgt--ttcctgtaccacttgataattgtgatgtg---aaatt-cagGTTCTTCAATCAGTGCTTCCTATTACTGATGATGAGGTTGTTCTTGGACAATACGAAGGTTACACAGATGACCCAACAGTTCCTGACCTTTCAAATACCC
                              | | ||||        ||    ||    |    | ||||  |  |    ||||    || |   | || ||||||||  |  |||  ||      ||||| ||||||||| ||||||| ||||||||||  ||||||||||||||||| |||||||| ||||| || | |||||| ||||| || ||||||  |||||| || |
gtttgtctctttccattcaatttgtgtggattttttttctccctcttcagtcattcaattcttgctttccattcttgttcataatgctcatagcttctataccactttcttgttgatatacatacaaattgcagGTTCTTGAATCAGTACTTCCTATTAAAGATGATGAGGTTGTTCTAGGACAATATGAAGGCTATAAAGATGATCCAACTGTGCCTGACAATTCAAACACTC

upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT3G27300.2 (Arabidopsis thaliana), 3'ss of exon 11
-------------------actctcttttagataaggtcctctata---ttttgtgaggtttctgtat-tgtcccatacatgtcgtttcctgtaccacttgat--aattgtgatgtgaaattcagGTTCTTCAATCAGTGCTTCCTATTACTGATGATGAGGTTGTTCTTGGACAATACGAAGGTTACACAGATGACCCAACAGTTCCTGACCTTTCAAATACCC
                    | |   ||||| |     | | | ||   |   ||||  | |   | |   |      |   |   |     || ||  |||   | || | |  |||| |||||||||||||||| ||| |||| || |  ||||| ||||| |||||||||||||| ||||| || | |||||| ||||| |||||  |    ||||| || |
gtgattacagttttcttgatcacatctttagtttcaaacttttgtagaatcaagtgatatcttcatttgcattttcagccaattaatattaataacaactgactgatttcttaaatgaacttcagGTTCTTCAATCTGTGATTCCCATAAAAGATGAAGAGGTGGTTCTTGGACAATATGAAGGATATAGAGATGATCCAACTGTTCCAAATGACTCAAACACTC

upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT5G40760.1 (Arabidopsis thaliana), 3'ss of exon 10
---actctcttttagataaggtcctctatattttgtgaggtttctgtattg--tcccatacatgtcgtttcctgtaccacttgataattgtgatgtgaaattcagGTTCTTCAATCAGTGCTTCCTATTACTGATGATGAGGTTGTTCTTGGACAATACGAAGGTTACACAGATGACCCAACAGTTCCTGACCTTTCAAATACCC
   |   |||  |     || |    |  |||   |||  ||||  | |    |  ||  ||  | || ||  ||  |   |||| ||| |   ||||| ||||||| |||||||| ||| |||| || |  ||||| ||||| |||||||||||||||||||| || |  |||||    || |||||  ||   ||||| || |
ttaaaaatctccttagcgagtttacatggattggttgatatttccatttgcattttcagccaattagtctctcgttac---tgattatttta--gtgaacttcagGTGCTTCAATCTGTGGTTCCGATAAGCGATGACGAGGTAGTTCTTGGACAATACGAAGGATATAGGGATGATGATACTGTTCCAAACGACTCAAACACTC

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|30299156|gb|CB975950.1|CB975950
EST:     AGAAGCCCGTTTCTCTCAAACCTGAGCACATCCGAGATGAGAAAGTGAAG                         GTTCTTCAATCAGTGCTTCCTATTACTGATGATGAGGTTGTTCTTGGACAA
genomic: AGAAGCCCGTCTCTCTCAAACCTGAGCACATCCGAGATGAGAAAGTGAAGgtgcatactt ... tgaaattcagGTTCTTCAATCAGTGCTTCCTATTACTGATGATGAGGTTGTTCTTGGACAA
EST: gi|351015046|gb|FQ444335.1|FQ444335
EST:     AGAAACCCGTTTCTCTCAAACCTGAGCACATCCGAGATGAGAAAGTGAAG                         GTTCTTCAATCAGTGCTTCCTATTACTGATGATGAGGTTGTTCTTGGACAA
genomic: AGAAGCCCGTCTCTCTCAAACCTGAGCACATCCGAGATGAGAAAGTGAAGgtgcatactt ... tgaaattcagGTTCTTCAATCAGTGCTTCCTATTACTGATGATGAGGTTGTTCTTGGACAA
EST: gi|294967142|gb|GW840017.1|GW840017
EST:     AGAAGCCCGTCTCTCTCAAACCTGAGCACATCCGAGATGAGAAAGTGAAG                         GTTCTTCAATCAGTGCTTCCTATTACTGATGATGAGGTTGTTCTTGGACAA
genomic: AGAAGCCCGTCTCTCTCAAACCTGAGCACATCCGAGATGAGAAAGTGAAGgtgcatactt ... tgaaattcagGTTCTTCAATCAGTGCTTCCTATTACTGATGATGAGGTTGTTCTTGGACAA
EST: gi|110696408|gb|EE072500.1|EE072500
EST:     AGAAGCCCGTTTCTCTCAAACCTGAGCACATCCGAGATGAGAAAGTGAAG                         GTTCTTCAATCAGTGCTTCCTATTACTGATGATGAGGTTGTTCTTGGACAA
genomic: AGAAGCCCGTCTCTCTCAAACCTGAGCACATCCGAGATGAGAAAGTGAAGgtgcatactt ... tgaaattcagGTTCTTCAATCAGTGCTTCCTATTACTGATGATGAGGTTGTTCTTGGACAA
EST: gi|56409520|gb|CX017772.1|CX017772
EST:     AGAAGCCCGTCTCTCTCAAACCTGAGCACATCCGAGATGAGAAAGTGAAG                         GTTCTTCAATCAGTGCTTCCTATTACTGATGATGAGGTTGTTCTTGGACAA
genomic: AGAAGCCCGTCTCTCTCAAACCTGAGCACATCCGAGATGAGAAAGTGAAGgtgcatactt ... tgaaattcagGTTCTTCAATCAGTGCTTCCTATTACTGATGATGAGGTTGTTCTTGGACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtcccatacatgtcgtttcctgtaccacttgataattgtgatgtgaaattcagGTTCTTCAATCAGTGCTTCCTATTACTGATGATGAGGTTGTTCTTGGACAATACGAAGGTTACACAGATGACCCAACAGTTCCTGACCTTTCAAATACCC
                            acttgat  putative branch site (score: 5)
                              ttgataatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actctcttttagataaggtcctctatattttgtgaggtttctgtattgtcccatacatgtcgtttcctgtaccacttgataattgtgatgtgaaattcagGTTCTTCAATCAGTGCTTCCTATTACTGATGATGAGGTTGTTCTTGGACAATACGAAGGTTACACAGATGACCCAACAGTTCCTGACCTTTCAAATACCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - ccataca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccacttg