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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttggggcattacgatttgaaatgatggtcagcatttccttgctcccttttccattatttaaaagcctaattatatttatatttattttgtctctgcagGCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTGTACGTTTACTGGATCTGCCCCTTCATAGGGGCAATATTGGCTGCATGGG

Basic information

species Vitis vinifera
transcript Vv08s0007g07680.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g07680.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os01g08660.1 (Oryza sativa), 3'ss of exon 2
tgttggggcattacgat-ttgaaatgatggtcagcatttccttgctcccttttccattatttaaaagcctaattatatttatat-ttattt-tgtctctgcagGCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTGTACGTTTACTGGATCTGCCCCTTCATAGGGGCAATATTGGCTGCATGGG
   |  |   ||| | |   |   |  |  |  ||  ||  | ||| |  || |   | ||       |||||  |  ||| || |||| |     ||  ||||| ||||| ||||||||| | |||||| | || ||||||||||| || || ||||| |||||||| ||||| ||  | || ||  |  | ||||| ||||
---tctgatgttaagttgccgctcttctcatttgccctttttggctactgttccttgttttctggtaactaatcttggttaaatattatctacaattccacagGCGTTTGGCTGGGCATATGTGAACAATCGCCACAACACATGGGAGCAATTCTACGTCTACTGGATATGCCCTTTTGTTGGCGCTGTTCTTGCTGCCTGGG

upper sequence: Vv08s0007g07680.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G113470_T01 (Zea mays), 3'ss of exon 2
tgttggggcattacgatttgaaatgatggtcagcatttccttgctcccttttccattatttaaaagcctaattatatttatatttattttgtc-tctgcagGCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTGTACGTTTACTGGATCTGCCCCTTCATAGGGGCAATATTGGCTGCATGGG
 |||      | ||   ||   | ||     ||||||       ||    || | || |||||      | |||| ||| |   |   ||||| |    |||||||||| ||||||||| | ||||||||||| ||||||||||| ||| |||| || |||||||| |||||||| || ||||| ||  | |||| |||| 
cgttttcagttaaccgctttgtacgaaaacaagcattaatcctatcttgatttcctt-tttaacttgtaatttatgttttttggtcaattgtcatgaatagGCATTTGGCTGGGCATATGTTAACAATTGGCACAACACATGGGAGCAGCTGTATGTGTACTGGATATGCCCCTTTATTGGGGCCATGCTTGCTGGATGGA
















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|110723472|gb|EE100822.1|EE100822
EST:     TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCTGCCAAT                         GCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGAACAGTTG
genomic: TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCCGCCAATgtgagtatac ... gtctctgcagGCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
EST: gi|30125114|gb|CB910453.1|CB910453
EST:     TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCTGCCAAT                         GCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
genomic: TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCCGCCAATgtgagtatac ... gtctctgcagGCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
EST: gi|77580334|gb|DV219055.1|DV219055
EST:     TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCTGCCAAT                         GCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
genomic: TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCCGCCAATgtgagtatac ... gtctctgcagGCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
EST: gi|30256217|gb|CB972060.1|CB972060
EST:     TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCTGCCAAT                         GCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
genomic: TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCCGCCAATgtgagtatac ... gtctctgcagGCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
EST: gi|71856732|gb|DT005787.1|DT005787
EST:     TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCCGCCAAT                         GCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
genomic: TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCCGCCAATgtgagtatac ... gtctctgcagGCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
EST: gi|33410061|gb|CF215688.1|CF215688
EST:     TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCCGCCAAT                         GCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
genomic: TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCCGCCAATgtgagtatac ... gtctctgcagGCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
EST: gi|161717062|gb|FC064678.1|FC064678
EST:     TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCCGCCAAT                         GCATTTGGATGGGCATATATA
genomic: TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCCGCCAATgtgagtatac ... gtctctgcagGCATTTGGATGGGCATATATA
EST: gi|33409236|gb|CF214863.1|CF214863
EST:     TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCTGCCAAT                         GCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
genomic: TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCCGCCAATgtgagtatac ... gtctctgcagGCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
EST: gi|110423338|gb|EC989683.1|EC989683
EST:     ATGAATCCTGCCAAT                         GCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
genomic: ATGAATCCCGCCAATgtgagtatac ... gtctctgcagGCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
EST: gi|110712709|gb|EE087990.1|EE087990
EST:     TGGTCGTCTCAAGCTCTGCTTACACTGGGCCTTCCATGAATCCCGCCAAT                         GCATTTGGATGGGCATATATAAACAATTGGCATAACACTTGGGACCAGTTG
genomic: TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCCGCCAATgtgagtatac ... gtctctgcagGCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
EST: gi|30296753|gb|CB973547.1|CB973547
EST:     TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCCGCCAAT                         GCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
genomic: TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCCGCCAATgtgagtatac ... gtctctgcagGCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
EST: gi|110427619|gb|EC994068.1|EC994068
EST:     TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCTGCCAAT                         GCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
genomic: TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCCGCCAATgtgagtatac ... gtctctgcagGCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
EST: gi|110417541|gb|EC983606.1|EC983606
EST:     TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCTGCCAAT                         GCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
genomic: TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCCGCCAATgtgagtatac ... gtctctgcagGCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
EST: gi|110369709|gb|EC933876.1|EC933876
EST:     TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCTGCCAAT                         GCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
genomic: TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCCGCCAATgtgagtatac ... gtctctgcagGCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
EST: gi|46918109|gb|CN547438.1|CN547438
EST:     TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCCGCCAAT                         GCATTTGGATGGGCATATATAAACAATTGGCA
genomic: TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCCGCCAATgtgagtatac ... gtctctgcagGCATTTGGATGGGCATATATAAACAATTGGCA
EST: gi|110686376|gb|EE063944.1|EE063944
EST:     TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCTGCCAAT                         GCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGAACAGTTG
genomic: TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCCGCCAATgtgagtatac ... gtctctgcagGCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
EST: gi|37185155|gb|CF604508.1|CF604508
EST:     TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCTGCCAAT                         GCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
genomic: TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCCGCCAATgtgagtatac ... gtctctgcagGCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
EST: gi|29782934|gb|CB348658.2|CB348658
EST:     TGGCCGTCTCAGGCTCTGCTTACACTGGGGATTCCATGAATCCCGCCAAT                         GCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
genomic: TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCCGCCAATgtgagtatac ... gtctctgcagGCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
EST: gi|33405292|gb|CF210919.1|CF210919
EST:     TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCTGCCAAT                         GCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
genomic: TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCCGCCAATgtgagtatac ... gtctctgcagGCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
EST: gi|37190094|gb|CF609443.1|CF609443
EST:     TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCTGCCAAT                         GCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
genomic: TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCCGCCAATgtgagtatac ... gtctctgcagGCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
EST: gi|110687458|gb|EE064884.1|EE064884
EST:     GGTCGTCTCAAGCTCTGCTTACCCTGGGCCTTCCATGAATCCTGGCCA-T                         GCATTTGGATGGGCATATATAAACCATTGGGATAACAC
genomic: GGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCCG-CCAATgtgagtatac ... gtctctgcagGCATTTGGATGGGCATATATAAACAATTGGCATAACAC
EST: gi|33404298|gb|CF209925.1|CF209925
EST:     TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCTGCCAAT                         GCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
genomic: TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCCGCCAATgtgagtatac ... gtctctgcagGCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
EST: gi|110712393|gb|EE089962.1|EE089962
EST:     TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCTGCCAAT                         GCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
genomic: TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCCGCCAATgtgagtatac ... gtctctgcagGCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
EST: gi|161716098|gb|FC066824.1|FC066824
EST:     TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCTGCCAAT                         GCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
genomic: TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCCGCCAATgtgagtatac ... gtctctgcagGCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
EST: gi|110390191|gb|EC955087.1|EC955087
EST:     TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCCGCCAAT                         GCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
genomic: TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCCGCCAATgtgagtatac ... gtctctgcagGCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
EST: gi|32245907|gb|CD711726.1|CD711726
EST:     TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCTGCCAAT                         GCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
genomic: TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCCGCCAATgtgagtatac ... gtctctgcagGCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
EST: gi|110421847|gb|EC988150.1|EC988150
EST:     TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCTGCCAAT                         GCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
genomic: TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCCGCCAATgtgagtatac ... gtctctgcagGCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
EST: gi|34549854|gb|CF518086.1|CF518086
EST:     TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCTGCCAAT                         GCATTTGGATGGGCATATATAAACAATTGGCATAACACATAGGACCAGTTG
genomic: TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCCGCCAATgtgagtatac ... gtctctgcagGCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
EST: gi|33407212|gb|CF212839.1|CF212839
EST:     TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCCGCCAAT                         GCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
genomic: TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCCGCCAATgtgagtatac ... gtctctgcagGCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
EST: gi|71865839|gb|DT014894.1|DT014894
EST:     TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCCGCCAAT                         GCATTTGGATGGCCATATATAAACAATTGGCATAACACATGGCACCAGTTG
genomic: TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCCGCCAATgtgagtatac ... gtctctgcagGCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
EST: gi|110417477|gb|EC983535.1|EC983535
EST:     TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCTGCCAAT                         GCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
genomic: TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCCGCCAATgtgagtatac ... gtctctgcagGCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
EST: gi|110696997|gb|EE073598.1|EE073598
EST:     TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCTGCCAAT                         GCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
genomic: TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCCGCCAATgtgagtatac ... gtctctgcagGCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
EST: gi|110719074|gb|EE096635.1|EE096635
EST:     TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCTGCCAAT                         GCATTTGGATGGGCATATATAAACNATTGGCATAACACATGGGAACAGTTG
genomic: TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCCGCCAATgtgagtatac ... gtctctgcagGCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
EST: gi|110712833|gb|EE088226.1|EE088226
EST:     TGGTCGTCTCAAGCTCTGCTTAC-CTGGGCCTTCCATGAATCCTGCCAAT                         GC-TTTGGGATGGGCATATATAAACAAT
genomic: TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCCGCCAATgtgagtatac ... gtctctgcagGCATTTGG-ATGGGCATATATAAACAAT
EST: gi|349832344|gb|FQ420905.1|FQ420905
EST:     TGGTCGTCTCACGCTCTGCTTACACTGGGCCTTCCATGAATCCCGCCAAT                         GCATTTGGATGGGCATATATGAACAATTGGCATAACAC
genomic: TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCCGCCAATgtgagtatac ... gtctctgcagGCATTTGGATGGGCATATATAAACAATTGGCATAACAC
EST: gi|110719095|gb|EE096680.1|EE096680
EST:     TGGTCGTCTCAGGCTCTGCTTA-ACTGGGCCTTCCATGAATCCTGC-AAT                         GCATTTGAATGGGCA
genomic: TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCCGCCAATgtgagtatac ... gtctctgcagGCATTTGGATGGGCA
EST: gi|161721029|gb|FC069638.1|FC069638
EST:     TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCTGCCAAT                         GCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG
genomic: TGGTCGTCTCAGGCTCTGCTTACACTGGGCCTTCCATGAATCCCGCCAATgtgagtatac ... gtctctgcagGCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccttttccattatttaaaagcctaattatatttatatttattttgtctctgcagGCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTGTACGTTTACTGGATCTGCCCCTTCATAGGGGCAATATTGGCTGCATGGG
                    gcctaat  putative branch site (score: 3)
                                     tttattttgtctct  putative PPT
         attatttaaaagccta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgttggggcattacgatttgaaatgatggtcagcatttccttgctcccttttccattatttaaaagcctaattatatttatatttattttgtctctgcagGCATTTGGATGGGCATATATAAACAATTGGCATAACACATGGGACCAGTTGTACGTTTACTGGATCTGCCCCTTCATAGGGGCAATATTGGCTGCATGGG

-gttgggg
- - - - - - - - - - - -tgatggt
- - - - - - - - - - - - - - - - gcatttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaagcc