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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatctgggaatttccatataaataatgaaattgttctttttccttaattttttttacctcttcagtgtttatatgtttgtattcctacttttaacagATATCCGAGGTTGTCAATAGTATGAAAGACTTGATTGACTTCTGCAGGGAGAACAAAGTTGGGCCAATTG

Basic information

species Vitis vinifera
transcript Vv16s0100g00500.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0100g00500.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: EFJ38855 (Selaginella moellendorffii), 3'ss of exon 9
gtatgatctgggaatttccatataaataatgaaattgttctttttccttaattttttttacctcttcagtgtttatatgtttgtattcctacttttaacagATATCCGAGGTTGTCAATAGTATGAAAGACTTGATTGACTTCTGCAGGGAGAACAAAGTTGGGCCAATTG
                             | || || |   |||||   ||| |     ||    | ||   |    | ||| | |||           ||||||| ||||| || || ||||||||||| |||||||||||| |  | || |||    | || || |  |
----------------------------gtaaacttttgtattttc---aatgtacgaaactatatgagaactcgggtttttttgttc-----------agATATCAGAGGTAGTAAACAGTATGAAAGATTTGATTGACTTCAGTCGAGAAAACTCTATGGGACCCAAGG
















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|37187404|gb|CF606757.1|CF606757
EST:     AGTCGCTGAATGATCTGGGATTTTCCAAAAGATATGTGAGGTGCTTGCAG                         ATATCTGAGGTTGTCAATAGTATGAAAGACTTGATTGACTTCTGCAGGGAG
genomic: AGTCACTGAATGATCTGGGATTTTCCAAAAGATATGTGAGGTGCTTGCAGgtatgatctg ... cttttaacagATATCCGAGGTTGTCAATAGTATGAAAGACTTGATTGACTTCTGCAGGGAG
EST: gi|161705769|gb|FC056640.1|FC056640
EST:     AGTCGCTGAATGATCTGGGATTTTCCAAAAGATATGTGAGGTGCTTGCAG                         ATATCCGAAGTTGTCAATAGTATGAAAGACTTGATTGACTTCTGCAGGGAG
genomic: AGTCACTGAATGATCTGGGATTTTCCAAAAGATATGTGAGGTGCTTGCAGgtatgatctg ... cttttaacagATATCCGAGGTTGTCAATAGTATGAAAGACTTGATTGACTTCTGCAGGGAG
EST: gi|161720327|gb|FC071180.1|FC071180
EST:     AGTCGCTGAATGATCTGGGATTTTCCAAAAGATATGTGAGGTGCTTGCAG                         ATATCCGAGGTTGTCAATAGTATGAAAGACTTGATTGACTTCTGCAGGGAG
genomic: AGTCACTGAATGATCTGGGATTTTCCAAAAGATATGTGAGGTGCTTGCAGgtatgatctg ... cttttaacagATATCCGAGGTTGTCAATAGTATGAAAGACTTGATTGACTTCTGCAGGGAG
EST: gi|161708994|gb|FC058786.1|FC058786
EST:     AGTCGCTGAATGATCTGGGATTTTCCAAAAGATATGTGAGGTGCTTGCAG                         ATATCCGAGGTTGTCAATAGTATGAAAGACTTGATTGACTTCTGCAGGGAG
genomic: AGTCACTGAATGATCTGGGATTTTCCAAAAGATATGTGAGGTGCTTGCAGgtatgatctg ... cttttaacagATATCCGAGGTTGTCAATAGTATGAAAGACTTGATTGACTTCTGCAGGGAG
EST: gi|161710271|gb|FC060655.1|FC060655
EST:     AGTCGCTGAATGATCTGGGATTTTCCAAAAGATATGTGAGGTGCTTGCAG                         ATATCCGAGGTTGTCAATAGTATGAAAGACTTGATTGACTTCTGCAGGGAG
genomic: AGTCACTGAATGATCTGGGATTTTCCAAAAGATATGTGAGGTGCTTGCAGgtatgatctg ... cttttaacagATATCCGAGGTTGTCAATAGTATGAAAGACTTGATTGACTTCTGCAGGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttaattttttttacctcttcagtgtttatatgtttgtattcctacttttaacagATATCCGAGGTTGTCAATAGTATGAAAGACTTGATTGACTTCTGCAGGGAGAACAAAGTTGGGCCAATTG
 ccttaat  putative branch site (score: 4)
                                       ttcctactttt  putative PPT
                         tttatatgtttgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgatctgggaatttccatataaataatgaaattgttctttttccttaattttttttacctcttcagtgtttatatgtttgtattcctacttttaacagATATCCGAGGTTGTCAATAGTATGAAAGACTTGATTGACTTCTGCAGGGAGAACAAAGTTGGGCCAATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA