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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatatatttgtttattttggtacatttttttctgaaaattggtccagtaatttccctgttccttttcattacaaactgattatcaaacttcatctttggcatgcagGTCATTACAATATTTTTGTTGGTGATCTTAGCCCTGAGGTTACAGATGCTACACTGTTTGCATGTTTCTCTGTTTATCCTAGCTGTTC

Basic information

species Vitis vinifera
transcript Vv11s0016g00700.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g00700.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os07g42380.1 (Oryza sativa), 3'ss of exon 5
gtatatatatttgtttattttggtacatttttttctgaaaattggtccagtaatttccctgttccttttcattacaaactgattatcaaacttcatctttggcatgcagGTCATTACAATATTTTTGTTGGTGATCTTAGCCCTGAGGTTACAGATGCTACACTGTTTGCATGTTTCTCTGTTTATCCTAGCTGTTC
            ||| ||  |        ||||| |   | |     ||| | |||      |   |||    |  |  || |    ||| || |||  |    |||||  |||| ||||||||||||||||||||||||||| |||||||| ||| |  || | |||||||  |||||||  ||| | || || ||
------------gttgatactatgtttgctttttataccagtattctcagaattttttgatataacttttggcaagacatggt----aaattttatcact--tttgcagACCATTTCAATATTTTTGTTGGTGATCTTAGCCCAGAGGTTACTGATTCCGCATTATTTGCATTCTTCTCTGGATATTCCAGTTGCTC

upper sequence: Vv11s0016g00700.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM5G835213_T02 (Zea mays), 3'ss of exon 5
---------------------gtatatatatttgtttattttg-gtacatttttttctgaa---aattggtccagtaatttccctgttccttttc---attacaaac--tgattatcaaacttcatctttggcatgcagGTCATTACAATATTTTTGTTGGTGATCTTAGCCCTGAGGTTACAGATGCTACACTGTTTGCATGTTTCTCTGTTTATCCTAGCTGTTC
                     |   |  || |  | |||||||  |   | |||| ||      || |  | |||  || |   |||    ||||   |||  || |  || |  | || ||||||||     ||||||||||||  |||||||||||||| |||||| |||| || || || ||||||||  ||||||||| ||||||||  ||  |||  || ||
gtttggaactgaagctgaagtgctgaactaatcctgtattttgtatttgtattttacttggttcaagtcatgcaggtatgtgaatgtatggtttctgaattctaagctttggtggtgaatcttcatct-----atgcagGTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGATACTCTACTTGCTC

upper sequence: Vv11s0016g00700.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G008611_T01 (Zea mays), 3'ss of exon 6
---------------------gtatatatatttgtttattttg-gtacatttttttctgaa---aattggtccagtaatttccctgttccttttc---attacaaac--tgattatcaaacttcatctttggcatgcagGTCATTACAATATTTTTGTTGGTGATCTTAGCCCTGAGGTTACAGATGCTACACTGTTTGCATGTTTCTCTGTTTATCCTAGCTGTTC
                     |   | ||| |  | ||||||   |   | |||| ||      || |  | |||  || |   |||    ||||   |||  || |  || |  | || ||||||||     ||||||||||||  |||||||||||||| |||||| |||| || || || ||||||||  ||||||||| |||||||| |||  |||  || ||
gtttggaactgaagctgaagtgctgaaataatcctgtattttatatttgtattttacttggttcaaatcatgcaggtatgtgaatgtatggtttctgaattctaagctttggtggtgaatcttcatct-----atgcagGTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGTTACTCTACTTGCTC

upper sequence: Vv11s0016g00700.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA13G17200.2 (Glycine max), 3'ss of exon 5
gtatatatatttgtttattttggtacatttttttctgaaaattggtccagtaatttccctgttccttttcattacaaactgattatcaaacttcatctttggcatgcagGTCATTACAATATTTTTGTTGGTGATCTTAGCCCTGAGGTTACAGATGCTACACTGTTTGCATGTTTCTCTGTTTATCCTAGCTGTTC
          || | |  ||     |  | |  |||||   |   |  | |   | |  ||||   |   |  ||||  | |   |      || ||||| | || ||||||| |  ||||||||||| ||||| ||||| ||||||||||||||||| ||| ||| ||| || |||||||| |||||||| |||||
---------gttatattcttgctggccatgtactctgagg-tcattttattg--tgctttgttttatggaaagacaactttacctttt--tctcttcttttggattcagGTCACTTTAATATTTTTGTCGGTGACCTTAGTCCTGAGGTTACAGATGCGACATTGTATGCTTGCTTCTCTGTATATCCTAGTTGTTC

upper sequence: Vv11s0016g00700.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA17G05530.4 (Glycine max), 3'ss of exon 6
gtatatatatttgtttattttggtacatttttttctgaaaattggtccagtaatttccctgttccttttcattacaaactgattatcaaacttcatctttggcatgcagGTCATTACAATATTTTTGTTGGTGATCTTAGCCCTGAGGTTACAGATGCTACACTGTTTGCATGTTTCTCTGTTTATCCTAGCTGTTC
         | | ||  |  |||  ||| |  || |  |  |   |  | |   | |  |||    |   |  ||||  | |   |      ||  |||| | || ||||||| |  ||||||||||| ||||| ||||| ||||||||||||||||| ||| ||| ||| || |||||||| |||||||| |||||
-------gttatattcttgctggc-catgtactttttgaggtcattttattg--tgctttgtattatggaaagacaacttcacctttt--tctctccttttggattcagGTCACTTTAATATTTTTGTCGGTGACCTTAGTCCTGAGGTTACAGATGCCACATTGTATGCTTGCTTCTCTGTATATCCTAGTTGTTC

upper sequence: Vv11s0016g00700.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ13606 (Selaginella moellendorffii), 3'ss of exon 5
gtatatatatttgtttattttggtacatttttttctgaaaattggtccagtaatttccctgttccttttcattacaaactgattatcaaacttcatctttggcatgcagGTCATTACAATATTTTTGTTGGTGATCTTAGCCCTGAGGTTACAGATGCTACACTGTTTGCATGTTTCTCTGTTTATCCTAGCTGTTC
                                                     ||   || ||  ||||  || ||      || ||  |  | ||| |  |  | |||| ||||||||||||||||| ||||||||||| |||||||| |||||||| ||||| |  ||   |||||   | |||||| | |||||
----------------------------------------------------gttgtacttttaattttgttttcat-----ttctctgagattatcgtctg--tccagGACATTACAATATTTTTGTGGGTGATCTTAGTCCTGAGGTCACAGATGCAACACTCTACGCTGCTTTCTTCATGTATCCTGGTTGTTC

upper sequence: Vv11s0016g00700.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ28907 (Selaginella moellendorffii), 3'ss of exon 5
gtatatatatttgtttattttggtacatttttttctgaaaattggtccagtaatttccctgttccttttcattacaaactgattatcaaacttcatctttggcatgcagGTCATTACAATATTTTTGTTGGTGATCTTAGCCCTGAGGTTACAGATGCTACACTGTTTGCATGTTTCTCTGTTTATCCTAGCTGTTC
                                                     ||   || ||  ||||  || ||      || ||  |  | ||| |  |  | |||| ||||||||||||||||| ||||||||||| |||||||| |||||||| ||||| |  ||   |||||   | |||||| | || ||
----------------------------------------------------gttgtacttttaatttttttttcat-----ttctctgagattatcgtctg--ttcagGACATTACAATATTTTTGTGGGTGATCTTAGTCCTGAGGTCACAGATGCAACACTCTACGCTGCTTTCTTCATGTATCCTGGTTGCTC

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|110685954|gb|EE063126.1|EE063126
EST:     AATCAAAGTTAATTGGGCATATGCTAGTAGTCAGAGAGAGGATACATCAG                         GTCATTACAATATTTTTGTTGGTGATCTTAGCCCTGAGGTTACAGATGCTA
genomic: AATCAAAGTTAATTGGGCATATGCTAGTAGTCAGAGAGAGGATACATCAGgtatatatat ... tggcatgcagGTCATTACAATATTTTTGTTGGTGATCTTAGCCCTGAGGTTACAGATGCTA
EST: gi|110728255|gb|EE103663.1|EE103663
EST:     AATCAAAGTTAATTGGGCATATGCTAGTAGTCAGAGAGAGGATACATCAG                         GTCATTACAATATTTTTGTTGGTGATCTTAGCCCTGAGGTTACAGATGCTA
genomic: AATCAAAGTTAATTGGGCATATGCTAGTAGTCAGAGAGAGGATACATCAGgtatatatat ... tggcatgcagGTCATTACAATATTTTTGTTGGTGATCTTAGCCCTGAGGTTACAGATGCTA
EST: gi|156737274|gb|EV241395.1|EV241395
EST:     AATCAAAGTTAATTGGGCATATGCTAGTAGTCAGAGAGAGGATACATCAG                         GTCATTACAATATTTTTGTTGGTGATCTTAGCCCTGAGGTTACAGATGCTA
genomic: AATCAAAGTTAATTGGGCATATGCTAGTAGTCAGAGAGAGGATACATCAGgtatatatat ... tggcatgcagGTCATTACAATATTTTTGTTGGTGATCTTAGCCCTGAGGTTACAGATGCTA
EST: gi|161705551|gb|FC057541.1|FC057541
EST:     TAGTCAGA-AAAAGATA-ATCTCGT                         GTCATTACAATATTTTTGTTGGTGATCTTAGCCCTGAGGTTACAGATGCT
genomic: TAGTCAGAGAGAGGATACATC-AG-gtatatatat ... tggcatgcagGTCATTACAATATTTTTGTTGGTGATCTTAGCCCTGAGGTTACAGATGCT
EST: gi|161705551|gb|FC057541.1|FC057541
EST:     TAGTCAGA-AAAAGATA-ATCTCGT                         GTCATTACAATATTTTTGTTGGTGATCTTAGCCCTGAGGTTACAGATGCT
genomic: TAGTCAGAGAGAGGATACATC-AG-gtatatatat ... tggcatgcagGTCATTACAATATTTTTGTTGGTGATCTTAGCCCTGAGGTTACAGATGCT
EST: gi|294966632|gb|GW839623.1|GW839623
EST:     AATCAAAGTTAATTGGGCATATGCTAGTAGTCCGAGAGAGGATACATCAG                         GTCATTACAAAATTTTTGTTGGTGATCTTAGCCCTGAGGTTAC
genomic: AATCAAAGTTAATTGGGCATATGCTAGTAGTCAGAGAGAGGATACATCAGgtatatatat ... tggcatgcagGTCATTACAATATTTTTGTTGGTGATCTTAGCCCTGAGGTTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccctgttccttttcattacaaactgattatcaaacttcatctttggcatgcagGTCATTACAATATTTTTGTTGGTGATCTTAGCCCTGAGGTTACAGATGCTACACTGTTTGCATGTTTCTCTGTTTATCCTAGCTGTTC
                      aactgat  putative branch site (score: 3)
                                    cttcatcttt  putative PPT
           ttttcatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatatatttgtttattttggtacatttttttctgaaaattggtccagtaatttccctgttccttttcattacaaactgattatcaaacttcatctttggcatgcagGTCATTACAATATTTTTGTTGGTGATCTTAGCCCTGAGGTTACAGATGCTACACTGTTTGCATGTTTCTCTGTTTATCCTAGCTGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT