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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgtcaaaatttccattttttgtttaataaattaatttgaaatcagttttatatagtgaatgtttttttttatttttaactggaatacaaaattcatttgtaaccgtacttgtctctgatttttctttttaacttcttagATCATTGCTCAGCTTCTCTCAGAACGACTAATTCCATTTGTTGCACTTGATGTGAGGAG

Basic information

species Vitis vinifera
transcript Vv15s0046g03390.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os04g58620.1 (Oryza sativa), 3'ss of exon 15
gtattgtcaaaatttccattttttgtttaataaattaatttgaaatcagttttatatagtgaatgtttttttttatttttaactggaatacaaaattcatttgtaaccgtacttgtctctgatttttctttttaacttcttagATCATTGCTCAGCTTCTCTCAGAACGACTAATTCCATTTGTTGCACTTGATGTGAGGAG
                                      |||| ||||    | |||   |     ||| | | | | | || ||    | |   ||  |||| ||    |||   | ||  || |||            |||||| || || || || || |||||| || |||||||||||||||||||||||||  | ||
-------------------------------------gtttgtaatc---ctcataagat-----tttatctatctatctatctactttgctcgataaatttctactaatacgcctttcatatattt------------ttagATAATCGCACAACTCCTGTCAGAAAGATTAATTCCATTTGTTGCACTTGATGTTCGAAG

upper sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AT1G01790.1 (Arabidopsis thaliana), 3'ss of exon 15
gtattgtcaaaatttccattttttgtttaataaattaatttgaaatcagttttatatagtgaatgtttttttttatttttaactggaatacaaaattcatttgtaaccgtacttgtctctgatttttctttttaacttcttagATCATTGCTCAGCTTCTCTCAGAACGACTAATTCCATTTGTTGCACTTGATGTGAGGAG
            |||  || || | |  | |   | | |||    ||    ||||||   |||  | | | |  |  || | ||  |    | |  ||    ||  |    || ||  |   ||| | ||| | | || | |||| |||||||| |||||||| ||| |||| || ||||||||||| |||||||| || ||
-----------gtttatatattatctgaacttcttcagtttatgctc----ttatatga-gaacctctctgtagacattcagcttcacatgatagctcgaa-gtttctaacctcgtgaccattttctgtttgttaattgt-agATAATTGCTCAACTTCTCTCGGAAAGACTTATCCCATTTGTTGCCCTTGATGTCAGCAG
















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|110389557|gb|EC954408.1|EC954408
EST:     ATGATTTGCAAGATCATATTATCATTTGTGGATTTGGACGTGTTGGACAG                         ATCATTGCTCAGCTTCTCTCAGAACGACTAATTCCATTTGTTGCACTTGAT
genomic: ATGATTTGCAAGATCATATTATCATTTGTGGATTTGGACGTGTTGGACAGgtattgtcaa ... aacttcttagATCATTGCTCAGCTTCTCTCAGAACGACTAATTCCATTTGTTGCACTTGAT
EST: gi|34546770|gb|CF515002.1|CF515002
EST:     ATGATTTGCAAGATCATATTATCATTTGTGGATTTGGACGTGTTGGACAG                         ATCATTGCTCAGCTTCTCTCAGAACGACTAATTCCATTTGTTGCACTTGAT
genomic: ATGATTTGCAAGATCATATTATCATTTGTGGATTTGGACGTGTTGGACAGgtattgtcaa ... aacttcttagATCATTGCTCAGCTTCTCTCAGAACGACTAATTCCATTTGTTGCACTTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacaaaattcatttgtaaccgtacttgtctctgatttttctttttaacttcttagATCATTGCTCAGCTTCTCTCAGAACGACTAATTCCATTTGTTGCACTTGATGTGAGGAG
                                         ttttaac  putative branch site (score: 2)
                                  tttttctttttaactt  CT-rich tract
                                 atttttctttttaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgtcaaaatttccattttttgtttaataaattaatttgaaatcagttttatatagtgaatgtttttttttatttttaactggaatacaaaattcatttgtaaccgtacttgtctctgatttttctttttaacttcttagATCATTGCTCAGCTTCTCTCAGAACGACTAATTCCATTTGTTGCACTTGATGTGAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG