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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcagaaaacccccataatcagattaattatttgctgttatgcctttttattttcagttgtctagtaaattttaccttgaggtattttttgataatgcagATCATTAATGTTTACAATCAAGAGTATGAGAGTGGTGCAGCATTCTGGCCGGATGTTCATGGGCGTATTATTGGTGCACTAATCATCTCACAGCTGCTTC

Basic information

species Vitis vinifera
transcript Vv10s0116g00940.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0116g00940.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA13G10490.1 (Glycine max), 3'ss of exon 10
atcagaaaacccccataat--cagattaattatttgctgttatgcctttttatt--ttcagttgtctagtaaattttaccttgaggtattttttgataatgcagATCATTAATGTTTACAATCAAGAGTATGAGAGTGGTGCAGCATTCTGGCCGGATGTTCATGGGCGTATTATTGGTGCACTAATCATCTCACAGCTGCTTC
  |||  | | || ||| |  |  ||  |||| |  || |||| | ||   | |  | ||   |   |  |   | ||||||    |  ||||  | ||||||||||||||| ||||| ||||| ||||||||||||||||||||||||||||| ||||| |||   |||||  |    |||||  |  |||||||| |  |||
--cagttagcacc-atagtggcttatacattaatccctattatacattagcactgatacatgagatgaagaccctgtaccttctaattgttttcca-aatgcagATCATTAACGTTTATAATCAGGAGTATGAGAGTGGTGCAGCATTCTGGCCTGATGTCCATTTCCGTATCGTGATGGCACTTCTAGTCTCACAGATAGTTC

upper sequence: Vv10s0116g00940.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA20G16230.3 (Glycine max), 3'ss of exon 5
------------------------------------------------------------------atcagaaaacccccataatcagattaat----tatttgct-----gttatgcctttttat-tttcagttgtctagtaaattttacct----tgagg------tattttttgat---------aatgcagATCATTAATGTTTACAATCAAGAGTATGAGAGTGGTGCAGCATTCTGGCCGGATGTTCATGGGCGTATTATTGGTGCACTAATCATCTCACAGCTGCTTC
                                                                  || | ||||  | || ||     ||||     || | |||      |||  || | ||||   | ||     ||||   || ||| |    ||| |      ||  || | ||         ||||||||||||||| || || ||||| ||||||||||||||||||||||||||||| ||||| |||   |||||  |    ||||| ||  |||||||| |  || 
gtcatcaggtacagagatgttaaatttatatatgcacgtttacgattctggtgccattaatcattcattaaaaaatgcacacaacacagttaacaccataatggcttatacattaatccctattatacattagcaccgtagtggtttatacatgagatgaagaccctgtaccttctaattgttttccaaatgcagATCATTAACGTATATAATCAGGAGTATGAGAGTGGTGCAGCATTCTGGCCTGATGTCCATTTCCGTATCGTGATGGCACTGATTGTCTCACAGATAGTTT

upper sequence: Vv10s0116g00940.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA20G16230.1 (Glycine max), 3'ss of exon 5
----------------------------------------------------------atcagaaaacccccataatcagattaat----tatttgct-----gttatgcctttttattt-tcagttgtctagtaaattttacct----tgagg------tattttttgat---------aatgcagATCATTAATGTTTACAATCAAGAGTATGAGAGTGGTGCAGCATTCTGGCCGGATGTTCATGGGCGTATTATTGGTGCACTAATCATCTCACAGCTGCTTC
                                                          || | ||||  | || ||     ||||     || | |||      |||  || | ||||   | ||     ||||   || ||| |    ||| |      ||  || | ||         ||||||||||||||| || || ||||| ||||||||||||||||||||||||||||| ||||| |||   |||||  |    ||||| ||  |||||||| |  || 
gtacagagatgttaaatttatatatgcacgtttacgattctggtgccattaatcattcattaaaaaatgcacacaacacagttaacaccataatggcttatacattaatccctattatacattagcaccgtagtggtttatacatgagatgaagaccctgtaccttctaattgttttccaaatgcagATCATTAACGTATATAATCAGGAGTATGAGAGTGGTGCAGCATTCTGGCCTGATGTCCATTTCCGTATCGTGATGGCACTGATTGTCTCACAGATAGTTT

upper sequence: Vv10s0116g00940.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA07G39320.1 (Glycine max), 3'ss of exon 10
-------------atcagaaaacccccata---atcagattaattatttgctgttatgcctttttattttcagttgtctagtaaattttaccttgaggtattttttgataatgcagATCATTAATGTTTACAATCAAGAGTATGAGAGTGGTGCAGCATTCTGGCCGGATGTTCATGGGCGTATTATTGGTGCACTAATCATCTCACAGCTGCTTC
              | ||||       |||    ||| | ||    | |  | ||         ||||||  |||| |   || ||        ||    |  |||   | ||||||| || |||||||| ||||||||||| ||||||||||||||||||||||| ||||| |||   ||| | |||  |||||| ||  | |||||| |  |||
gtagttccaagatgttagaattatattatacacgtcaaagtatgattgtattatttgagtcccctattttt-gttgccatatatataaggtgaagacacctactttccaattgcagATTATCAATGTTTATAATCAAGAGTACGAGAGTGGTGCAGCATTCTGGCCTGATGTCCATTTTCGTGTCATTATTGCACTGATAGTGTCACAGATAGTTC

upper sequence: Vv10s0116g00940.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA17G01400.1 (Glycine max), 3'ss of exon 9
-----------atcagaaaacccccataatcagattaa----ttatt-tgctgttatgcctttttattttcagttgtctagtaaattttaccttgaggtattt--tttgataatgcagATCATTAATGTTTACAATCAAGAGTATGAGAGTGGTGCAGCATTCTGGCCGGATGTTCATGGGCGTATTATTGGTGCACTAATCATCTCACAGCTGCTTC
           ||   | ||      || |||  | ||    | ||| |  | ||         ||||||  |||| |   || || | |  |  ||  |  |  |||   | ||||||| || |||||||| ||||||||||| ||||||||||||||||||||||| ||||| |||   ||| | |||  |||||| ||  | |||||| |  |||
gtagttccaagatgttagaattatattattcatgtcaaaggatgattgtattatttgagtcccctattttt-gttgcc--atatatataagttgaagacacctactttccaattgcagATTATCAATGTTTATAATCAAGAGTACGAGAGTGGTGCAGCATTCTGGCCTGATGTCCATTTTCGTGTCATTATTGCACTGATAGTGTCACAGATAGTTC

upper sequence: Vv10s0116g00940.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT4G04340.1 (Arabidopsis thaliana), 3'ss of exon 10
atcagaaaacccccataatcagattaattatttgctgttatgccttt--ttattttcagttgtctagtaaattttaccttgag---gtattttttgataatg-cagATCATTAATGTTTACAATCAAGAGTATGAGAGTGGTGCAGCATTCTGGCCGGATGTTCATGGGCGTATTATTGGTGCACTAATCATCTCACAGCTGCTTC
                  | |   || ||  || || |  |   |||  | |   |   | || |  ||| ||  |||||  |    | | ||||  || |  |||||||| ||||| || ||||||||||||||||| | ||| || || ||||||||||||||||| ||  ||||    ||| | ||||| || ||| ||||||
-----------------gtaaatgtagtttctttctctcctaaatttgatgaaactggctagtttgataacttgaaccttctgtttatttgttttcttattctcagATCATAAATGTGTATAATCAAGAGTATGAGAGCGCTGCTGCGTTTTGGCCGGATGTTCATGGACGGGTTATAACGGCATTGATCATATCTCAGTTGCTTC

upper sequence: Vv10s0116g00940.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT1G62320.1 (Arabidopsis thaliana), 3'ss of exon 9
atcagaaaacccccataatcagattaattatttgctgttatgcctttttattttcagttgtctagtaaattttaccttgaggtattttttgataatgcagATCATTAATGTTTACAATCAAGAGTATGAGAGTGGTGCAGCATTCTGGCCGGATGTTCATGGGCGTATTATTGGTGCACTAATCATCTCACAGCTGCTTC---------------------
              | || || |  ||  |         |  |  ||||| | |||     | ||  ||  ||         |  ||| |    ||||||||||| ||||| ||||||||  ||||||||||||  |  ||||||||||| || |||||||| ||||| ||    ||| | |||||||||||  | |||                      
------------gtaaaaacaaaggaaacaa--------actctcttttactatcaaacaacaaggtaacatt---------tggtttct----atgcagatcataaatgtgtacaatcagAAGTATGAGAGTGCGGGTGCATTCTGGCCAGACGTTCATGGACGTATAATATCGGCATTGATCATCTCACAAATCCTTTTGTTGGGATTAATGAGCACGA

upper sequence: Vv10s0116g00940.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT4G22120.1 (Arabidopsis thaliana), 3'ss of exon 8
atcagaaaacccccataatcagattaattatttgctgttatgcctttttattttcagttgtctagtaaattttaccttgaggtattttttgataatg-cagATCATTAATGTTTACAATCAAGAGTATGAGAGTGGTGCAGCATTCTGGCCGGATGTTCATGGGCGTATTATTGGTGCACTAATCATCTCACAGCTGCTTC
                        ||| | | | ||  | | | |  |    |  | ||   |   ||    |  ||| |   | |||||| |  || ||||||||||| || ||||||||||| || ||||||| |||||| || ||||| || |||||||| ||  | || |  ||| |  | || |||||| ||||||
-----------------------gtaagtttcttcttctttccttaatagggtcgaatttgttttaaagcagtttcttaaacaaatttttgtttctgtcagATCATTAACGTATACAATCAAGAATACGAGAGTGCTGCAGCGTTTTGGCCAGACGTTCATGGACGAGTCATAGCAGCATTGGTAATATCACAGTTGCTTC

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|34550981|gb|CF519185.1|CF519185
EST:     CTTTCATAATTGTTTTCTTTTGCCTGGCATATGTCGTATTCCGCCATCAG                         ATAATTAATGTTTACAATCAAGAGTATGAGAGTGGTGCAGCATTCTGGCCG
genomic: CTTTCATAATTGTTTTCTTTTGCCTGGCATATGTCGTATTCCGCCATCAGgtaaaaagtt ... gataatgcagATCATTAATGTTTACAATCAAGAGTATGAGAGTGGTGCAGCATTCTGGCCG
EST: gi|110363926|gb|EC927558.1|EC927558
EST:     TTTCATAATTG-TTTCTTTTTGCCTGGCATATGTTGTATTCCGCCATCAG                         ATAATTAATGTTTATAATCAAGAGTATGAGAGTGGTGCAGCATTCTGGCCG
genomic: TTTCATAATTGTTTTC-TTTTGCCTGGCATATGTCGTATTCCGCCATCAGgtaaaaagtt ... gataatgcagATCATTAATGTTTACAATCAAGAGTATGAGAGTGGTGCAGCATTCTGGCCG
EST: gi|30251320|gb|CB969053.1|CB969053
EST:     CGTATTCCGCCATCAG                         ATAATTAATGTTTACAATCAAGAGTATGAGAGTGGTGCAGCATTCTGGCCG
genomic: CGTATTCCGCCATCAGgtaaaaagtt ... gataatgcagATCATTAATGTTTACAATCAAGAGTATGAGAGTGGTGCAGCATTCTGGCCG
EST: gi|351028550|gb|FQ444831.1|FQ444831
EST:     CTTTCATAATTGTTTTCTTTTGCCTGGCATATGTTGTATTCCGCCATCAG                         ATAATTAATGTTTATAATCAAGAGTATGAGAGTGGTGCAGCATTCTGGCCG
genomic: CTTTCATAATTGTTTTCTTTTGCCTGGCATATGTCGTATTCCGCCATCAGgtaaaaagtt ... gataatgcagATCATTAATGTTTACAATCAAGAGTATGAGAGTGGTGCAGCATTCTGGCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttattttcagttgtctagtaaattttaccttgaggtattttttgataatgcagATCATTAATGTTTACAATCAAGAGTATGAGAGTGGTGCAGCATTCTGGCCGGATGTTCATGGGCGTATTATTGGTGCACTAATCATCTCACAGCTGCTTC
                                         ttttgat  putative branch site (score: 4)
                                       ttttttg  CT-rich tract
                                     tattttttgataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcagaaaacccccataatcagattaattatttgctgttatgcctttttattttcagttgtctagtaaattttaccttgaggtattttttgataatgcagATCATTAATGTTTACAATCAAGAGTATGAGAGTGGTGCAGCATTCTGGCCGGATGTTCATGGGCGTATTATTGGTGCACTAATCATCTCACAGCTGCTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- cagaaaa
- - - - -cccccat
- - - - - - - - aatcaga
- - - - - - - - - - - - - - - - tgctgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taccttg