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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagctctggaatacattattttaataatactgttttcttcactatttgagacactaaataattttctgaggttgccttagtttttctcatcttcaaagtttgtatcccatctgttttaatttggttctatgatgcaattcttagAATGAGAAGATGGAGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCG

Basic information

species Vitis vinifera
transcript Vv03s0091g00700.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0091g00700.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G40390.1 (Glycine max), 3'ss of exon 4
gttagctctggaatacattattttaataatactgttttcttcactatttgagacactaaataattttctgaggttgccttagtttttctcatcttcaaagtttgtatcccatctgttttaatttggttctatgatgcaattcttagAATGAGAAGATGGAGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCG
                                            ||  ||  |    || |  ||| || |  ||  |       || | || |   | || |  ||        ||    |||  |||  |  | |  |  ||||||||||||||  ||||| || ||||| ||||||||||||||| | || ||||||   ||| | 
-------------------------------------------gtaagtgttatgagaatttttttcctaaaattttccc-----ttgtaatgtatgaggtgttgatttatatgattgctttttctttccctttttcgttgtttagAATGAGAAGAATGAGACCGTGGGATCAGAAACTGAGGCATATTCCATAGCTGATATGATGTCT

upper sequence: Vv03s0091g00700.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT1G49970.1 (Arabidopsis thaliana), 3'ss of exon 4
gttagctctggaatacattattttaataatactgttttcttcactatttgagacactaaataattttctgaggttgccttagtttttctcatcttcaaagtttgtatcccatctgttttaatttggttctatgatgcaattcttagAATGAGAAGATGGAGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCG
|| ||   | ||| |    | ||| || |||   | || ||   |  | |      |     ||||  | || |  ||  | || ||    |   |||  | | ||| |  | |||||   |||| || |   |||       ||||||||||||||||| ||||||||||| ||||| ||||| ||||| || || ||| | ||  | 
gtcag---tagaaga----agtttgattata---tattgtttgttggtggtagttttctg-gatttatttagataaccc-acttgttacttttaacaagctatctattct-tttgtttccttttgcttatgccatg-------tagAATGAGAAGATGGAAACTGTTGGATCAGAAACAGAGGCTTATGCCATAGCCGATACTATTTCT
















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|110396404|gb|EC962089.1|EC962089
EST:     ACAACCCCTCAAAGCCTATATATCTCTACATAAATTCAACTGGAACACAG                         AATGAGAAGATGGAGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCT
genomic: ACAACCCCTCAAAGCCTATATATCTCTACATAAATTCAACTGGAACACAGgttagctctg ... caattcttagAATGAGAAGATGGAGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCT
EST: gi|27579693|gb|CB002388.1|CB002388
EST:     ACAACCCCTCAAAGCCTATATATCTCTACATAAATTCAACTGGAACACAG                         AATGAGAAGATGGAGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCT
genomic: ACAACCCCTCAAAGCCTATATATCTCTACATAAATTCAACTGGAACACAGgttagctctg ... caattcttagAATGAGAAGATGGAGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCT
EST: gi|110713462|gb|EE089402.1|EE089402
EST:     ACAACCCCTCAAAGCCTATATATCTCTACATNAATTCAACTGGAACACAG                         AATGAGAAGATGGAGACTGGTTGGATCTGAA-CTGANGCATATGCTATTGC
genomic: ACAACCCCTCAAAGCCTATATATCTCTACATAAATTCAACTGGAACACAGgttagctctg ... caattcttagAATGAGAAGATGGAGACTG-TTGGATCTGAAACTGAGGCATATGCTATTGC
EST: gi|26267312|gb|CA818375.1|CA818375
EST:     ACAACCCCTCAAAGCCTATATATCTCTACATAAATTCAACTGGAACACAG                         AATGAGAAGATGGAGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCT
genomic: ACAACCCCTCAAAGCCTATATATCTCTACATAAATTCAACTGGAACACAGgttagctctg ... caattcttagAATGAGAAGATGGAGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCT
EST: gi|30321875|gb|CD005137.1|CD005137
EST:     ACAACCCCTCAAAGCCTATATATCTCTACATAAATTCAACTGGAACACAG                         AATGAGAAGATGGAGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCT
genomic: ACAACCCCTCAAAGCCTATATATCTCTACATAAATTCAACTGGAACACAGgttagctctg ... caattcttagAATGAGAAGATGGAGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCT
EST: gi|110686908|gb|EE063865.1|EE063865
EST:     ACAACGCCTCAAAGCCTATATATCTCTACATAAATTCAACTGGAACACAG                         AATGAGAAGATGGAGACTGTTGGATCTGAAACTGANGCATATGCTATTGCT
genomic: ACAACCCCTCAAAGCCTATATATCTCTACATAAATTCAACTGGAACACAGgttagctctg ... caattcttagAATGAGAAGATGGAGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCT
EST: gi|28968092|gb|CB347125.1|CB347125
EST:     ACAACCCCTCAAAGCCTATATATCTCTACATAAATTCAACTGGAACACAG                         AATGAGAAGATGGAGACTGTTGGATTTGAAACTGAGGCATATGCTATTGCT
genomic: ACAACCCCTCAAAGCCTATATATCTCTACATAAATTCAACTGGAACACAGgttagctctg ... caattcttagAATGAGAAGATGGAGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCT
EST: gi|110391380|gb|EC956351.1|EC956351
EST:     ACAACCCCTCAAAGCCTATATATCTCTACATAAATTCAACTGGAACACAG                         AATGAGAAGATGGAGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCT
genomic: ACAACCCCTCAAAGCCTATATATCTCTACATAAATTCAACTGGAACACAGgttagctctg ... caattcttagAATGAGAAGATGGAGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCT
EST: gi|30321951|gb|CD005213.1|CD005213
EST:     ACAACCCCTCAAAGCCTATATATCTCTACATAAATTCAACTGGAACACAG                         AATGAGAAGATGGAGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCT
genomic: ACAACCCCTCAAAGCCTATATATCTCTACATAAATTCAACTGGAACACAGgttagctctg ... caattcttagAATGAGAAGATGGAGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCT
EST: gi|351025662|gb|FQ426676.1|FQ426676
EST:     ACAACCCCTCAAAGCCTATATATCTCTACATAAATTCAACTGGAACACAG                         AATGAGAAGATGGAGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCT
genomic: ACAACCCCTCAAAGCCTATATATCTCTACATAAATTCAACTGGAACACAGgttagctctg ... caattcttagAATGAGAAGATGGAGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCT
EST: gi|351030338|gb|FQ432276.1|FQ432276
EST:     ACAACCCCTCAAAGCCTATATATCTCTACATAAATTCAACTGGAACACAG                         AATGAGAAGATGGAGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCT
genomic: ACAACCCCTCAAAGCCTATATATCTCTACATAAATTCAACTGGAACACAGgttagctctg ... caattcttagAATGAGAAGATGGAGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCT
EST: gi|110361742|gb|EC925238.1|EC925238
EST:     ACAACCCCTCAAAGCCTATATATCTCTACATAAATTCAACTGGAACACAG                         AATGAGAAGATGGAGACTGTTGGATCTGAAATTGAGGCATATGCTATTGCT
genomic: ACAACCCCTCAAAGCCTATATATCTCTACATAAATTCAACTGGAACACAGgttagctctg ... caattcttagAATGAGAAGATGGAGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCT
EST: gi|22007314|gb|BQ792348.1|BQ792348
EST:     ACAACCCCTCAAAGCCTATATATCTCTACATAAATTCAACTGGAACACAG                         AATGAGAAGATGGAGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCT
genomic: ACAACCCCTCAAAGCCTATATATCTCTACATAAATTCAACTGGAACACAGgttagctctg ... caattcttagAATGAGAAGATGGAGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCT
EST: gi|110710998|gb|EE087695.1|EE087695
EST:     ACAACCCCTCAAAGCCTATATATCTCTACATAAATTCAACAGGAACACAG                         AATGAGAAGATGGAGACTGTTGGATCTGAAACTGAAGCATATGCTATTGCT
genomic: ACAACCCCTCAAAGCCTATATATCTCTACATAAATTCAACTGGAACACAGgttagctctg ... caattcttagAATGAGAAGATGGAGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCT
EST: gi|27578583|gb|CB001278.1|CB001278
EST:     ACAACCCCTCAAAGCCTATATATCTCTACATAAATTCAACTGGAACACAG                         AATGAGAAGATGGAGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCT
genomic: ACAACCCCTCAAAGCCTATATATCTCTACATAAATTCAACTGGAACACAGgttagctctg ... caattcttagAATGAGAAGATGGAGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCT
EST: gi|26257779|gb|CA808842.1|CA808842
EST:     ACAACCCCTCAAAGCCTATATATCTCTACATAAATTCAACTGGAACACAG                         AATGAGAAGATGGAGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCT
genomic: ACAACCCCTCAAAGCCTATATATCTCTACATAAATTCAACTGGAACACAGgttagctctg ... caattcttagAATGAGAAGATGGAGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCT
EST: gi|352795065|gb|FQ477175.1|FQ477175
EST:     ACAACCCCTCAAAGCCTATATATCTCTACATAAATTCAACTGGAACACAG                         AATGAGAAGATGGAGACTGTTGGATCTGAAACTGAAGCATATGCTATTGCT
genomic: ACAACCCCTCAAAGCCTATATATCTCTACATAAATTCAACTGGAACACAGgttagctctg ... caattcttagAATGAGAAGATGGAGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCT
EST: gi|110685602|gb|EE062466.1|EE062466
EST:     ACAACCCCTCAAAGCCTATATATCTCTACATAAATTCAACTGGAACACAG                         AATGAGAAGATGGAGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCT
genomic: ACAACCCCTCAAAGCCTATATATCTCTACATAAATTCAACTGGAACACAGgttagctctg ... caattcttagAATGAGAAGATGGAGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCT
EST: gi|26264973|gb|CA816036.1|CA816036
EST:     ACAACCCCTCAAAGCCTATATATCTCTACATAAATTCAACTGGAACACAG                         AATGAGAAGATGGTGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCT
genomic: ACAACCCCTCAAAGCCTATATATCTCTACATAAATTCAACTGGAACACAGgttagctctg ... caattcttagAATGAGAAGATGGAGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCT
EST: gi|26258048|gb|CA809111.1|CA809111
EST:     ACAACCCCTCAAAGCCTATATATCTCTACCTAAATTCAACTGGAACACAG                         AATGAGAAGATGGAGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCT
genomic: ACAACCCCTCAAAGCCTATATATCTCTACATAAATTCAACTGGAACACAGgttagctctg ... caattcttagAATGAGAAGATGGAGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCT
EST: gi|26267206|gb|CA818269.1|CA818269
EST:     ACAACCCCTCAAAGCCTATATATCTCTACATAAATTCAACTGGAACACAG                         AATGAGAAGATGGTGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCT
genomic: ACAACCCCTCAAAGCCTATATATCTCTACATAAATTCAACTGGAACACAGgttagctctg ... caattcttagAATGAGAAGATGGAGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCT
EST: gi|110388571|gb|EC953335.1|EC953335
EST:     ACAACCCCTCAAAGCCTATATATCTCTACATAAATTCAACTGGAACACAG                         AATGAGAAGATGGAGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCT
genomic: ACAACCCCTCAAAGCCTATATATCTCTACATAAATTCAACTGGAACACAGgttagctctg ... caattcttagAATGAGAAGATGGAGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCT
EST: gi|110395310|gb|EC960968.1|EC960968
EST:     ACAACCCCTCAAAGCCTATATATCTCTACATAAATTCAACTGGAACACAG                         AATGAGAAGATGGAGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCT
genomic: ACAACCCCTCAAAGCCTATATATCTCTACATAAATTCAACTGGAACACAGgttagctctg ... caattcttagAATGAGAAGATGGAGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttcaaagtttgtatcccatctgttttaatttggttctatgatgcaattcttagAATGAGAAGATGGAGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCG
                        ttttaat  putative branch site (score: 3)
                                                ttctt  putative PPT
                   atctgttttaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagctctggaatacattattttaataatactgttttcttcactatttgagacactaaataattttctgaggttgccttagtttttctcatcttcaaagtttgtatcccatctgttttaatttggttctatgatgcaattcttagAATGAGAAGATGGAGACTGTTGGATCTGAAACTGAGGCATATGCTATTGCTGATTCCATGGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT