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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttcttttagttggaacctatgttatggcatttgttatatggttgatgcacttcagattcttaattaacctatctacgatgataacaaataacttaatcctgcagCTTCTCTTCATATTGATTATCCCATGTTGTTCGAACTTAGTAATCCTGCTGCTCAGCGGGTCTCCCATTGTGGAGTTCTGGAATTCATAGCTGAAGAGGG

Basic information

species Vitis vinifera
transcript Vv03s0038g00750.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g00750.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA08G05030.1 (Glycine max), 3'ss of exon 5
gttagttctttta-gttggaacctatgttatggcatttgttatatggttgatgcacttcagattcttaattaacctatctacgatgataacaaataacttaatcctgcagCTTCTCTTCATATTGATTATCCCATGTTGTTCGAACTTAGTAATCCTGCTGCTCAGCGGGTCTCCCATTGTGGAGTTCTGGAATTCATAGCTGAAGAGGG
||||||| | | | | | ||||   |||| |   ||||    ||   ||  | ||  | |   | |   || |  | || |  ||  |||||   |  |||||  |||||| ||||| ||||||||||| || |||||||| |||||  |||||  ||||||  ||||||| || |||||||| |||||||| ||||| ||||| || ||
gttagttttgtcatggttgaac---tgtttttttattttgcttacttttattccaggtgaatatatagcttgagttttcaa--attctaacatcaagtttaatt-tgcagCATCTCTGCATATTGATTACCCAATGTTGTTTGAACTCCGTAATGATGCTGCCGAGCGGGTTTCTCATTGTGGGGTTCTGGAGTTCATTGCTGAGGAAGG

upper sequence: Vv03s0038g00750.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA05G34630.2 (Glycine max), 3'ss of exon 5
gttagttctttta--gttggaacctatgttatggcatttgttatatggttgatgcacttcagattcttaattaacctatctacgatgataacaaataacttaatcctgcagCTTCTCTTCATATTGATTATCCCATGTTGTTCGAACTTAGTAATCCTGCTGCTCAGCGGGTCTCCCATTGTGGAGTTCTGGAATTCATAGCTGAAGAGGG
||||||| | | |  |||| |   | | ||||     ||  | | |  |  | ||   |     |||| | |      | |   ||  |||||   |  |||||  |||||| ||||| ||||||||||| || |||||||| |||||  |||||  ||||||  ||||||| || |||||||| |||||||| ||||| ||||| || ||
gttagttttgtcatggttgaactgttttttattttgcttacttt-tattccaggcgaatatatatcttgagt------tttcaaattctaacat-cagtttaatt-tgcagCATCTCTGCATATTGATTACCCAATGTTGTTTGAACTCCGTAATGATGCTGCCGAGCGGGTTTCTCATTGTGGGGTTCTGGAGTTCATTGCTGAGGAAGG
















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|110687487|gb|EE064951.1|EE064951
EST:     TTATAATGCCTCCCTCAGCCCTTGACCGCCTAG                         CTTCTCTTCATATTGATTATCCCATGTTGTTCGAACTTAGTAATCCTGCTG
genomic: TTATAATGCCTCCCTCAGCCCTTGACCGCCTAGgttagttctt ... aatcctgcagCTTCTCTTCATATTGATTATCCCATGTTGTTCGAACTTAGTAATCCTGCTG
EST: gi|30126806|gb|CB912145.1|CB912145
EST:     TTATAATGCCTCCCTCAGCCCTTGACCGCCTAG                         CTTCTCTTCATATTGATTATCCCATGTTGTTCGAACTTAGTAATCCTGCTG
genomic: TTATAATGCCTCCCTCAGCCCTTGACCGCCTAGgttagttctt ... aatcctgcagCTTCTCTTCATATTGATTATCCCATGTTGTTCGAACTTAGTAATCCTGCTG
EST: gi|110698550|gb|EE076176.1|EE076176
EST:     TTATAATGCCTCCCTCAGCCCTTGACCGCCTAG                         CTTCTCTTCATATTGATTATCCCATGTTGTTCGAACTTAGTAATCCTGCTG
genomic: TTATAATGCCTCCCTCAGCCCTTGACCGCCTAGgttagttctt ... aatcctgcagCTTCTCTTCATATTGATTATCCCATGTTGTTCGAACTTAGTAATCCTGCTG
EST: gi|26262376|gb|CA813439.1|CA813439
EST:     TTATAATGCCTCCCTCAGCCCTTGACCGCCTAG                         CTTCTCTTCATATTGATTATCCCATGTTGTTCGAACTTAGTAATCCTGCTG
genomic: TTATAATGCCTCCCTCAGCCCTTGACCGCCTAGgttagttctt ... aatcctgcagCTTCTCTTCATATTGATTATCCCATGTTGTTCGAACTTAGTAATCCTGCTG
EST: gi|26262164|gb|CA813227.1|CA813227
EST:     TTATAATGCCTCCCTCAGCCCTTGACCGCCTAG                         CTTCTCTTCATATTGATTATCCCATGTTGTTCGAACTTAGTAATCCTGCTG
genomic: TTATAATGCCTCCCTCAGCCCTTGACCGCCTAGgttagttctt ... aatcctgcagCTTCTCTTCATATTGATTATCCCATGTTGTTCGAACTTAGTAATCCTGCTG
EST: gi|71856948|gb|DT006003.1|DT006003
EST:     TTATAATGCCTCCCTCAGCCCTTGACCGCCTAG                         CTTCTCTTCATATTGATTATCCCATGTTGTTCGAACTTAGTAATCCTGCTG
genomic: TTATAATGCCTCCCTCAGCCCTTGACCGCCTAGgttagttctt ... aatcctgcagCTTCTCTTCATATTGATTATCCCATGTTGTTCGAACTTAGTAATCCTGCTG
EST: gi|110724233|gb|EE099882.1|EE099882
EST:     TTATAATGCCTCCCTCAGCCCTTGACCGCCTAG                         CTTCTCTTCATATTGATTATCCCATGTTGTTCGAACTTAGTAATCCTGCTG
genomic: TTATAATGCCTCCCTCAGCCCTTGACCGCCTAGgttagttctt ... aatcctgcagCTTCTCTTCATATTGATTATCCCATGTTGTTCGAACTTAGTAATCCTGCTG
EST: gi|110723124|gb|EE100074.1|EE100074
EST:     TTATAATGCCTCCCTCAGCCCTTGACCGCCTAG                         CTTCTCTTCATATTGATTATCCCATGTTGTTCGAACTTAGTAATCCTGCTG
genomic: TTATAATGCCTCCCTCAGCCCTTGACCGCCTAGgttagttctt ... aatcctgcagCTTCTCTTCATATTGATTATCCCATGTTGTTCGAACTTAGTAATCCTGCTG
EST: gi|294966730|gb|GW837749.1|GW837749
EST:     TTATAATGCCTCCCTCAGCCCTTGACCGCCTAG                         CTTCTCTTCATATTGATTATCCCATGTTGTTCGAACTTAGTAATCCTGCTG
genomic: TTATAATGCCTCCCTCAGCCCTTGACCGCCTAGgttagttctt ... aatcctgcagCTTCTCTTCATATTGATTATCCCATGTTGTTCGAACTTAGTAATCCTGCTG
EST: gi|71868328|gb|DT017383.1|DT017383
EST:     TTATAATGCCTCCCTCAGCCCTTGACCGCCTAG                         CTTCTCTTCATATTGATTATCCCATGTTGTTCGAACTTAGTAATCCTGCTG
genomic: TTATAATGCCTCCCTCAGCCCTTGACCGCCTAGgttagttctt ... aatcctgcagCTTCTCTTCATATTGATTATCCCATGTTGTTCGAACTTAGTAATCCTGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcagattcttaattaacctatctacgatgataacaaataacttaatcctgcagCTTCTCTTCATATTGATTATCCCATGTTGTTCGAACTTAGTAATCCTGCTGCTCAGCGGGTCTCCCATTGTGGAGTTCTGGAATTCATAGCTGAAGAGGG
                               ataacaaataacttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagttcttttagttggaacctatgttatggcatttgttatatggttgatgcacttcagattcttaattaacctatctacgatgataacaaataacttaatcctgcagCTTCTCTTCATATTGATTATCCCATGTTGTTCGAACTTAGTAATCCTGCTGCTCAGCGGGTCTCCCATTGTGGAGTTCTGGAATTCATAGCTGAAGAGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG