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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCAATCCCCAGACTCATCAGCTAAAGATATGTGATTTTGGGAGTGCAAAGAAGTTGgtatgtttattatcttccttggaatttttcaacactaatttgctatagcaggttttgaacttcatttgcctgatggtag

Basic information

species Vitis vinifera
transcript Vv15s0048g02010.t01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0048g02010.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA09G40150.1 (Glycine max), 5'ss of exon 7
GTCAATCCCCAGACTCATCAGCTAAAGATATGTGATTTTGGGAGTGCAAAGAAGTTGgtatgtttattatcttccttggaatttttcaacactaatttgctatagcaggttttgaacttcatttgcctgatggtag--------
|| |||||||||||||||||| ||||  |||||||||||||||||||||||| ||||||| ||||||| || |  ||     || ||||    ||  |  || |  || || ||  ||    |||    ||  | |        
GTTAATCCCCAGACTCATCAGTTAAAAGTATGTGATTTTGGGAGTGCAAAGATGTTGgtaagtttattttcgtttttc---cttatcaatttgaaagttgtacaatagtttgtgc-ctgagcttgtgatattattgtgctatag

upper sequence: Vv15s0048g02010.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA18G45960.1 (Glycine max), 5'ss of exon 7
GTCAATCCCCAGACTCATCAGCTAAAGATATGTGATTTTGGGAGTGCAAAGAAGTTGgtatgtttattatct-----tccttggaatttt------tcaacactaatttgctatagcaggttttgaacttcatttgcctgatggtag
 | |||||||||||||||||| ||||  |||||||||||||||||||||||| ||||||| |||| || | |     ||||||  | |||      |  |||  | |||| | |   || || |||  ||  | ||| | | |    
-TTAATCCCCAGACTCATCAGTTAAAAGTATGTGATTTTGGGAGTGCAAAGATGTTGGtaagtttgttttttgtttttccttgtcactttgaaagttgtacaacagtttg-tgtctgagcttgtgatattattgtgctttagg----

upper sequence: Vv15s0048g02010.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA03G01850.1 (Glycine max), 5'ss of exon 7
GTCAATCCCCAGACTCATCAGCTAAAGATATGTGATTTTGGGAGTGCAAAGAAGTTGgtatgtttatt-atcttcc---ttggaatttttcaacactaatttgctatagcaggttttgaacttcatttgcctgatggtag------
|| ||| | ||||| |||||| |||||||||||||||||||||||||||||  ||||||  |||  || | ||||    || ||| |||| || | || ||||  || | | | |      || ||    || || | |       
GTAAATACGCAGACACATCAGTTAAAGATATGTGATTTTGGGAGTGCAAAGGTGTTGgtgagttcctttaccttctgaatttgaacttttgaaga-tattttg--attgtatgctcctgggtttatg-atcttattgcattttcag

upper sequence: Vv15s0048g02010.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA07G08320.1 (Glycine max), 5'ss of exon 7
GTCAATCCCCAGACTCATCAGCTAAAGATATGTGATTTTGGGAGTGCAAAGAAGTTGgtatgtttatt-atcttcc---ttggaatttttcaacactaatttgctatagcaggttttgaacttcatttgcctgatggtag------
|| ||||| ||||| |||||| |||||||||||||||||||||| ||||||  ||||||| |||  || | ||||    || ||| |||| || | || ||||  || | | | |      || ||     |||| | |       
GTAAATCCGCAGACACATCAGTTAAAGATATGTGATTTTGGGAGCGCAAAGGTGTTGgtaagttcctttaccttctgaatttgaacttttgaaga-tattttg--atcgtatgctcctgcgtttatg-atatgattgcattttcag

upper sequence: Vv15s0048g02010.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: AT4G00720.1 (Arabidopsis thaliana), 5'ss of exon 7
GTCAATCCCCAGACTCATCAGCTAAAGATATGTGATTTTGGGAGTGCAAAGAAGTTGgtatgtttattatcttccttggaatttttcaacactaatttgctatagca----ggttttgaacttcatttgcctgatggtag
|| |||||||| ||||||||  |||| ||||| |||||||| || ||||||| ||||||||||| ||| | ||     || || ||  | |  | ||  |  | | |    | |    |||  | ||||| |    |   
GTTAATCCCCAAACTCATCAATTAAAAATATGCGATTTTGGAAGCGCAAAGATGTTGgtatgttcatttttttttgatgagttcttggagatgagttatcatttgaataatgatggctaacaccctttgcgtctcag---

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|349820373|gb|FQ403989.1|FQ403989
EST:     CCCAGACTCATCAGCTAAAGATATGTGATTTTGGGAGTGCAAAGAAGTTG                         GTGCCAGGTGAACCAAACATATCATATATTTGCTCAAGGTATTATAGGGCT
genomic: CCCAGACTCATCAGCTAAAGATATGTGATTTTGGGAGTGCAAAGAAGTTGgtatgtttat ... ctgatggtagGTGCCAGGTGAACCAAACATATCATATATTTGCTCAAGGTATTATAGGGCT
EST: gi|110688693|gb|EE067533.1|EE067533
EST:     CCCAGACTCATCAGCTAAAGATATGTGATTTTGGGAGTGCAAAGAAGTTG                         GTGCCAGGTGAACCAAACATATCATATATTTGCTCAAGGTATTATAGGGCT
genomic: CCCAGACTCATCAGCTAAAGATATGTGATTTTGGGAGTGCAAAGAAGTTGgtatgtttat ... ctgatggtagGTGCCAGGTGAACCAAACATATCATATATTTGCTCAAGGTATTATAGGGCT
EST: gi|32249937|gb|CD715756.1|CD715756
EST:     CCCAGACTCATCAGCTAAAGATATGTGATTTTGGGAGTGCAAAGAAGTTG                         GTGCCAGGTGAACCAAACATATCATATATTTGCTCAAGGTATTATAGGGCT
genomic: CCCAGACTCATCAGCTAAAGATATGTGATTTTGGGAGTGCAAAGAAGTTGgtatgtttat ... ctgatggtagGTGCCAGGTGAACCAAACATATCATATATTTGCTCAAGGTATTATAGGGCT
EST: gi|161713339|gb|FC063356.1|FC063356
EST:     CCCAGACTCATCAGCTAAAGATATGTGATTTTGGGAGTGCAAAGAAGTGG                         GTGCCAGGTGAACCAAACAT
genomic: CCCAGACTCATCAGCTAAAGATATGTGATTTTGGGAGTGCAAAGAAGTTGgtatgtttat ... ctgatggtagGTGCCAGGTGAACCAAACAT
EST: gi|71856597|gb|DT005652.1|DT005652
EST:     CCCAGACTCATCAGCTAAAGATATGTGATTTTGGGAGTGCAAAGAAGTTG                         GTGCCAGGTGAACCAAACATATCATATATTTGCTCAAGGTATTATAGGGCT
genomic: CCCAGACTCATCAGCTAAAGATATGTGATTTTGGGAGTGCAAAGAAGTTGgtatgtttat ... ctgatggtagGTGCCAGGTGAACCAAACATATCATATATTTGCTCAAGGTATTATAGGGCT
EST: gi|110732276|gb|EE107431.1|EE107431
EST:     CCCAGACTCATCAGCTAAAGATATGTGATTTTGGGAGTGCAAAGAAGTTG                         GTGCCAGGTGAACCAAACATATCATATATTTGCTCAAGGTATTATAGGGCT
genomic: CCCAGACTCATCAGCTAAAGATATGTGATTTTGGGAGTGCAAAGAAGTTGgtatgtttat ... ctgatggtagGTGCCAGGTGAACCAAACATATCATATATTTGCTCAAGGTATTATAGGGCT
EST: gi|27579903|gb|CB002598.1|CB002598
EST:     CCCAGACTCATCAGCTAAAGATATGTGATTTTGGGAGTGCAAAGAAGTTG                         GTGCCAGGTGAACCAAACATATCATATATTTGCTCAAGGTATTATAGGGCT
genomic: CCCAGACTCATCAGCTAAAGATATGTGATTTTGGGAGTGCAAAGAAGTTGgtatgtttat ... ctgatggtagGTGCCAGGTGAACCAAACATATCATATATTTGCTCAAGGTATTATAGGGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCAATCCCCAGACTCATCAGCTAAAGATATGTGATTTTGGGAGTGCAAAGAAGTTGgtatgtttattatcttccttggaatttttcaacactaatttgctatagcaggttttgaacttcatttgcctgatggtag

- - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT