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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacaataacattcttattttgaaaagttactattgtcttattgttgcttctgtttggttctcgttttctttacattaatcattggttgtgggggtttttccagTTATGAAGATTGGGGAGTGGATGAATTGATTGTAGAGGATTCATGGAAGAGGCAAGTTGGAGGTGATTGACTAACCCACGTTGGGCTGTGGGGAAATGGA

Basic information

species Vitis vinifera
transcript Vv16s0100g00530.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0100g00530.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA10G38350.2 (Glycine max), 3'ss of exon 5
gtaacaataacattcttattttgaaaagttactattgtcttattgttgcttctgtttggt----tctcgttttctttacattaatcattggttgtgggggtttttccagTTATGAAGATTGGGGAGTGGATGAATTGATTGTAGAGGATTCATGGAAGAGGCAAGTTGGAGGTGATTGACTAACCCACGTTGGGCTGTGGGGAAATGGA
       ||| ||  |     | | |  ||  | |||  ||   |  | ||  | ||| |    |   |   |  | ||  | ||||||  |||       || | ||||||||||||||||||||| |||||| ||||||| || || || |||||||||||||| || |||||||||  |    ||     | |||||||| | |  
------gtaaaatagtggccattatacttttttcttgg-ttgggggaggttaaggttgataacattatgccatactgactgtcatcattttttgcaaaa--ttctacagTTATGAAGATTGGGGAGTCGATGAACTGATTGTGGAAGACTCCTGGAAGAGGCAAGTGGGTGGTGATTGATGATTGAACTGACAGGTGTGGGGAGAGGAG

upper sequence: Vv16s0100g00530.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA20G29520.1 (Glycine max), 3'ss of exon 5
gtaacaataacattcttatt----ttgaaaagttactattgtcttattgtt---gcttctgtttggt----tctcgttttctttac-attaatcattggttgtgggggtttttccagTTATGAAGATTGGGGAGTGGATGAATTGATTGTAGAGGATTCATGGAAGAGGCAAGTTGGAGGTGATTGACTAACCCACGTTGGGCTGTGGGGAAATGGA
||||  |        ||||     ||   |||||  | ||   |   ||     | ||  | ||| |    ||  |   |  | ||  |||||||||  || ||    ||| ||||| ||||||||||||||||| |||||| ||||||| || || || |||||||||||||| || |||||||||  |    ||     | ||||||||   | |
gtaaatacttggccattatacaagttaggaagttcttttttcttggctgggggaggttaaggttgataacatcatgccatactgactgttaatcatttttt-tgcaaatttctccagCTATGAAGATTGGGGAGTTGATGAACTGATTGTGGAAGACTCCTGGAAGAGGCAAGTGGGTGGTGATTGATGATTGAACTGACAGGTGTGGGGAGGAGTA

upper sequence: Vv16s0100g00530.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: PP1S197_12V6.1 (Physcomitrella patens), 3'ss of exon 5
-----------------------------------gtaacaataacattcttattttgaa----aagttactattgtcttattgttgcttctgtttg----gttctcg---ttttctttacattaatc--attggttgtgggg-gtttttccagTTATGAAGATTGGGGAGTGGATGAATTGATTGTAGAGGATTCATGGAAGAGGCAAGTTGGAGGTGA-TTGACTAACCCACGTTGGGCTGTGGGGAAATGGA
                                   | || ||   ||   |  ||||||     | || |  ||| | ||||  |   || |||| |    |||   |   |    | | |   | ||  ||   |||||  |  || ||||||||||||||||||||| ||||| || ||||| ||||| ||||| |||| | | || || ||  | || ||  ||  || |||  |    || ||  |     
gtacgtctcatactagaataaagtacaaccaagtagcaagaagtgcaaaatatttttgaggttgacgtgaacatttttttatcttctgttttgttggtcaagttgctgaaatgcaatctgcggcagtctaatattttgtgccgtattgttccagTTATGAAGATTGGGGCGTGGACGAGTTGATCGTAGAAGATTCTTGGAGGCGCCAGGTCGGCTGAGAATTTTCTTTCCAACGGGGACGAGTTGGACATCTC-

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|110374189|gb|EC938793.1|EC938793
EST:     CGTGAGCGGAAGATACCCTTCACCATCCGCCGCTACTTGCCTGATGGAAG                         TTATGAAGATTGGGGAGTGGATGAACTGATTGTAGAGGATTCATGGAAGAG
genomic: CGTGAGCGGAAGATACCCTTCACCATCCGCCGCTACCTGCCTGATGGAAGgtaacaataa ... gtttttccagTTATGAAGATTGGGGAGTGGATGAATTGATTGTAGAGGATTCATGGAAGAG
EST: gi|351024313|gb|FQ423736.1|FQ423736
EST:     CGTGAGCGGAAGATACCCTTCACCATCCGCCGCTGCCTGCCTGATGGAAG                         TTATGAAGATTGGGGAGTGGATGAATTGATTGTAGAGGATTCATGGAAGAG
genomic: CGTGAGCGGAAGATACCCTTCACCATCCGCCGCTACCTGCCTGATGGAAGgtaacaataa ... gtttttccagTTATGAAGATTGGGGAGTGGATGAATTGATTGTAGAGGATTCATGGAAGAG
EST: gi|110686792|gb|EE064832.1|EE064832
EST:     CGTGAGCGGAAGATACCCTTCACCATCCGCCGCTACCTGCCTGATGGAAG                         TTATGAAGATTGGGGAGTGGATGAATTGATTGTAGAGGATTCATGGAAGAG
genomic: CGTGAGCGGAAGATACCCTTCACCATCCGCCGCTACCTGCCTGATGGAAGgtaacaataa ... gtttttccagTTATGAAGATTGGGGAGTGGATGAATTGATTGTAGAGGATTCATGGAAGAG
EST: gi|110368625|gb|EC932613.1|EC932613
EST:     CGTGAGCGGAAGATACCCTTCACCATCCGCCGCTACCTGCCTGATGGAAG                         TTATGAAGATTGGGGAGTGGATGAATTGATTGTAGAGGATTCATGGAAGAG
genomic: CGTGAGCGGAAGATACCCTTCACCATCCGCCGCTACCTGCCTGATGGAAGgtaacaataa ... gtttttccagTTATGAAGATTGGGGAGTGGATGAATTGATTGTAGAGGATTCATGGAAGAG
EST: gi|26265984|gb|CA817047.1|CA817047
EST:     CGTGAGCGGAAGATACCCTTCACCATCCGCCGCTACCTGCCTGATGGAAG                         TTATGAAGATTGGGGAGTGGATGAATTGATTGTAGAGGATTCATGGAAGAG
genomic: CGTGAGCGGAAGATACCCTTCACCATCCGCCGCTACCTGCCTGATGGAAGgtaacaataa ... gtttttccagTTATGAAGATTGGGGAGTGGATGAATTGATTGTAGAGGATTCATGGAAGAG
EST: gi|110413522|gb|EC979311.1|EC979311
EST:     CGTGAGCGGAAGATACCCTTCACCATCCGCCGCTACCTGCCTGATGGAAG                         TTATGAAGATTGGGGAGTGGATGAATTGATTGTAGAGGATTCATGGAAGAG
genomic: CGTGAGCGGAAGATACCCTTCACCATCCGCCGCTACCTGCCTGATGGAAGgtaacaataa ... gtttttccagTTATGAAGATTGGGGAGTGGATGAATTGATTGTAGAGGATTCATGGAAGAG
EST: gi|110386849|gb|EC951479.1|EC951479
EST:     CGTGAGCGGAAGATACCCTTCACCATCCGCCGCTACCTGCCTGATGGAAG                         TTATGAAGATTGGGGAGTGGATGAATTGATTGTAGAGGATTCATGGAAGAG
genomic: CGTGAGCGGAAGATACCCTTCACCATCCGCCGCTACCTGCCTGATGGAAGgtaacaataa ... gtttttccagTTATGAAGATTGGGGAGTGGATGAATTGATTGTAGAGGATTCATGGAAGAG
EST: gi|110729809|gb|EE106173.1|EE106173
EST:     CGTGAGCGGAAGATACCCTTCACCATCCGCCGCTACCTGCCTGATGGAAG                         TTATGAAGATTGGGGAGTGGATGAATTGATTGTAGAGGATTCATGGAAGAG
genomic: CGTGAGCGGAAGATACCCTTCACCATCCGCCGCTACCTGCCTGATGGAAGgtaacaataa ... gtttttccagTTATGAAGATTGGGGAGTGGATGAATTGATTGTAGAGGATTCATGGAAGAG
EST: gi|110365638|gb|EC928962.1|EC928962
EST:     CGTGAGCGGAAGATACCCTTCACCATCCGCCGCTACTTGCCTGATGGAAG                         TTATGAAGATTGGGGAGTGGATGAACTGATTGTAGAGGATTCATGGAAGAG
genomic: CGTGAGCGGAAGATACCCTTCACCATCCGCCGCTACCTGCCTGATGGAAGgtaacaataa ... gtttttccagTTATGAAGATTGGGGAGTGGATGAATTGATTGTAGAGGATTCATGGAAGAG
EST: gi|51050339|gb|CO818499.1|CO818499
EST:     CGTGAGCGGAAGATACCCTTCACCATCCGCCGCTACCTGCCTGATGGAAG                         TTATGAAGATTGGGGAGTGGATGAATTGATTGTAGAGGATTCATGGAAGAG
genomic: CGTGAGCGGAAGATACCCTTCACCATCCGCCGCTACCTGCCTGATGGAAGgtaacaataa ... gtttttccagTTATGAAGATTGGGGAGTGGATGAATTGATTGTAGAGGATTCATGGAAGAG
EST: gi|71888346|gb|DT037401.1|DT037401
EST:     CGTGAGCGGAAGATACCCTTCACCATCCGCCGCTACCTGCCTGATGGAAG                         TTATGAAGATTGGGGAGTGGATGAATTGATTGTAGAGGATTCATGGAAGAG
genomic: CGTGAGCGGAAGATACCCTTCACCATCCGCCGCTACCTGCCTGATGGAAGgtaacaataa ... gtttttccagTTATGAAGATTGGGGAGTGGATGAATTGATTGTAGAGGATTCATGGAAGAG
EST: gi|26263262|gb|CA814325.1|CA814325
EST:     CGTGAGCGGAAGATACCCTTCACCATCCGCCGCTACCTGCCTGATGGAAG                         TTATGAAGATTGGTGAGTGGATGAATTGATTGTAGAGGATTCATGGAAGAG
genomic: CGTGAGCGGAAGATACCCTTCACCATCCGCCGCTACCTGCCTGATGGAAGgtaacaataa ... gtttttccagTTATGAAGATTGGGGAGTGGATGAATTGATTGTAGAGGATTCATGGAAGAG
EST: gi|26262322|gb|CA813385.1|CA813385
EST:     CGTGAGCGGAAGATACCCTTCACCATCCGCCGCTACCTGCCTGATGGAAG                         TTATGAAGATTGGTGAGTGGATGAATTGATTGTAGAGGATTCATGGAAGAG
genomic: CGTGAGCGGAAGATACCCTTCACCATCCGCCGCTACCTGCCTGATGGAAGgtaacaataa ... gtttttccagTTATGAAGATTGGGGAGTGGATGAATTGATTGTAGAGGATTCATGGAAGAG
EST: gi|26263998|gb|CA815061.1|CA815061
EST:     CGTGAGCGGAAGATACCCTTCACCATCCGCCGCTACCTGCCTGATGGAAG                         TTATGAAGATTGGGGAGTGGATGAATTGATTGTAGAGGATTCATGGAAGAG
genomic: CGTGAGCGGAAGATACCCTTCACCATCCGCCGCTACCTGCCTGATGGAAGgtaacaataa ... gtttttccagTTATGAAGATTGGGGAGTGGATGAATTGATTGTAGAGGATTCATGGAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgtttggttctcgttttctttacattaatcattggttgtgggggtttttccagTTATGAAGATTGGGGAGTGGATGAATTGATTGTAGAGGATTCATGGAAGAGGCAAGTTGGAGGTGATTGACTAACCCACGTTGGGCTGTGGGGAAATGGA
                        cattaat  putative branch site (score: 3)
                                              tttttcc  putative PPT
               ttttctttacattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacaataacattcttattttgaaaagttactattgtcttattgttgcttctgtttggttctcgttttctttacattaatcattggttgtgggggtttttccagTTATGAAGATTGGGGAGTGGATGAATTGATTGTAGAGGATTCATGGAAGAGGCAAGTTGGAGGTGATTGACTAACCCACGTTGGGCTGTGGGGAAATGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG