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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATGGACCTCCAGGGACTGGGAAAACTCTGATGGCCCGTGCATGCGCGGCTCAAACAAATGCCACTTTTCTGAAGCTGGCAGGCCCTCAACTTGTCCAGgtgggatattcttcatttgttttccttcttcattcttatttgttatttgatgccttctagggattcttgacttgttcagtatcctgaaaattctgaggtt...

Basic information

species Vitis vinifera
transcript Vv14s0060g02260.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0060g02260.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G027282_T01 (Zea mays), 5'ss of exon 5
GTATGGACCTCCAGGGACTGGGAAAACTCTGATGGCCCGTGCATGCGCGGCTCAAACAAATGCCACTTTTCTGAAGCTGGCAGGCCCTCAACTTGTCCAGgtgggatattct-tcatttgttttccttcttcattcttatttgttatttgatgccttctagggattcttgacttgttcagtatcctgaaaat--tctgaggtt
||||||||| || |||||||||||||| || ||||| ||||||||||| || || |||||||| || ||||||||  |||| || || |||||||||||||| ||  |||   ||  |    |   || | ||         |||  |      || | |   |   ||      ||    || |||    |  | || |   
GTATGGACCCCCTGGGACTGGGAAAACGCTCATGGCTCGTGCATGCGCTGCACAGACAAATGCAACATTTCTGAAATTGGCTGGTCCACAACTTGTCCAGgtaggtaattaaatccgtgaaatatattatacagatgctagggttcctaaggctctccaactaaccatttgagcattttacattctgtttgtgatttgcg---

upper sequence: Vv14s0060g02260.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA10G29250.1 (Glycine max), 5'ss of exon 5
GTATGGACCTCCAGGGACTGGGAAAACTCTGATGGCCCGTGCATGCGCGGCTCAAACAAATGCCACTTTTCTGAAGCTGGCAGGCCCTCAACTTGTCCAGgtgggatattcttcattt-gttttccttcttcattcttatttgttatttgatgccttctagggattct----tgacttgttcagtatc--ctgaaaattctgaggtt
 ||||||||||| ||||||||||||||  ||||||||||||| || || || || ||||||||||||||||||||  |||||||||||||||| ||||||||  || | | |   | | ||||| ||| |||    |||| | || | | |      |||  |||||     | || ||||  ||| |  || |  || |       
ATATGGACCTCCGGGGACTGGGAAAACATTGATGGCCCGTGCCTGTGCAGCACAGACAAATGCCACTTTTCTGAAATTGGCAGGCCCTCAACTGGTCCAGgtatgacaatttatttctagtttttctttttctccattatatatt-tgtaagcatgactaatgattccattgttacatgttt-gtaccaactaattatacca-----

upper sequence: Vv14s0060g02260.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA20G38030.1 (Glycine max), 5'ss of exon 5
GTATGGACCTCCAGGGACTGGGAAAACTCTGATGGCCCGTGCATGCGCGGCTCAAACAAATGCCACTTTTCTGAAGCTGGCAGGCCCTCAACTTGTCCAGgtgggatattcttcatttgtttt---ccttcttcattcttat-ttgttatttgatgccttctagggattcttgacttgttcagtatcctgaaaattctgaggtt
|||||||||||||||||||||||||||  ||||||| ||||| || || || || ||||||||||||||||||||  |||| ||||||||||| ||||||||  || | | |   | |  | |   | |   | ||  || |  | |||  || |    || |   ||| |    || ||   | | |  || ||| |      
GTATGGACCTCCAGGGACTGGGAAAACATTGATGGCTCGTGCCTGTGCAGCACAGACAAATGCCACTTTTCTGAAATTGGCTGGCCCTCAACTGGTCCAGgtatgacaatttatttatagtctaagcatgactaatgattctactattacatgtttgtatcaactaattatatcattattacatgttcgtaacattttcc----

upper sequence: Vv14s0060g02260.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA03G39500.1 (Glycine max), 5'ss of exon 5
GTATGGACCTCCAGGGACTGGGAAAACTCTGATGGCCCGTGCATGCGCGGCTCAAACAAATGCCACTTTTCTGAAGCTGGCAGGCCCTCAACTTGTCCAGgtgggatattcttcatttgttttccttcttcattcttat--ttgttatttgatgccttctagggattcttgacttgttcagtatcctgaaaattctgaggtt
 |||||||||||||| ||||| ||||| || || |||||||| || || || |||||||||||||||||||||||| ||||||| || || || ||||||||  ||  |  | ||||| |   | ||     |||||||  |   || |   | | || ||     | |||| |||||  | |   | ||  | ||||  ||
ATATGGACCTCCAGGAACTGGAAAAACACTAATTGCCCGTGCTTGTGCAGCACAAACAAATGCCACTTTTCTGAAGTTGGCAGGTCCACAGCTGGTCCAGgtatgac-tcttccatttttacccgtttaattttcttatcatgactagtaatttcattgtatcttattttgaattgtt-ggcaattttaatttactgaattt

upper sequence: Vv14s0060g02260.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA19G42110.1 (Glycine max), 5'ss of exon 3
-----------------GTATGGACCTCCAGGGACTGGGAAAACTCTGATGGCCCGTGCATGCGCGGCTCAAACAAATGCCACTTTTCTGAAGCTGGCAGGCCCTCAACTTGTCCAGgtgggatattcttcatttgttttccttcttcattcttatttgttatttgatgccttctagggattcttgacttgttcagtatcctgaaaattctgaggtt
                  |||||||||||||| ||||| ||||| || || |||||||| || || || |||||||||||||||||||||||| ||||||| || || || ||| |||   ||  |  | |||||   || |||  | ||| | | |    |||   ||  |  ||     | |||| |||||  |||   | ||  |||||     
CCGAAGGGAGTGCTCTTATATGGACCTCCAGGAACTGGAAAAACACTAATTGCCCGTGCTTGTGCAGCACAAACAAATGCCACTTTTCTGAAGTTGGCAGgtccacagctggtcaaggcatgac-tcttccattt---ttactttcttattatgactaa--attcattgtatctta-----ttttgaattgtt-ggtaattttaattttctg-----

upper sequence: Vv14s0060g02260.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 5
GTATGGACCTCCAGGGACTGGGAAAACTCTGATGGCCCGTGCATGCGCGGCTCAAACAAATGCCACTTTTCTGAAGCTGGCAGGCCCTCAACTTGTCCAGgtg-ggatat-tcttcatttgttttccttcttcattcttatttgttatttgatgccttctagggattcttgacttgttcagtatcctgaaaattctgaggtt--------------------------------------------------------------------------------
|||||| || ||||||||||| |||||| | ||||| ||||| ||||| || || || |||||||| || || ||  |||||||||||||| | ||||||||    |||| | |  || | | |   |   | | | | |  | | | ||     ||  |||   |  ||  | |||   | ||    || ||| |   |||                                                                                
GTATGGTCCCCCAGGGACTGGTAAAACTTTAATGGCTCGTGCCTGCGCAGCACAGACCAATGCCACCTTCCTTAAATTGGCAGGCCCTCAATTGGTCCAGgtatatatatatatatatatatatatatatatgagtatcagat-tcaattctcatctcttagaactctttaccctgtctgg-atat--aagattttagtgttctggcaacaataattacatgtgacgagctataatgatacttgattgtaatgacatgatgacatatccaatttatatacag

upper sequence: Vv14s0060g02260.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: PP1S340_7V6.1 (Physcomitrella patens), 5'ss of exon 5
GTATGGACCTCCAGGGACTGGGAAAACTCTGATGGCCCGTGCATGCGCGGCTCAAACAAATGCCACTTTTCTGAAGCTGGCAGGCCCTCAACTTGTCCAGgtgggatatt--cttcatttgttttccttcttcattcttatttgtt---atttgatgcctt-ctagggattcttgacttgttcagtatcctgaaaattctgaggtt------------------------------------------------------------------------
 ||||| || ||||| ||||| || || || ||||| ||||||||||| |||||||||||||| |||| | | ||||| || || ||||| || |||||||||   | ||   || | ||||||  ||  |  | |||  |  |||    |||      ||  |  |  ||   | |||  ||| |  | | |   |||   || |                                                                        
ATATGGCCCACCAGGTACTGGCAAGACCCTCATGGCTCGTGCATGCGCAGCTCAAACAAATGCTACTTATTTAAAGCTTGCTGGACCTCAGCTCGTCCAGgtgatttcttggttttacttgtttatcta-tggactctcgtcagttctggtttaggatgttgttttgccttaacgcctttgtcatttacttaatttttccatgggtggagtcatcttgttcatttatcctggtcaaggctcttcattgactacaagatatcctgatacgtaatcacag

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|110724320|gb|EE100046.1|EE100046
EST:     TCAAACAAATGCCACTTTTCTGAAGCTGGCAGGCCCTNCA-CTTGTCCAG                         ATGTTCATTGGGGATGGGGCGAAACTTGTCCGTGATGCCTTT
genomic: TCAAACAAATGCCACTTTTCTGAAGCTGGCAGGCCCT-CAACTTGTCCAGgtgggatatt ... atgtattcagATGTTCATTGGGGATGGGGCGAAACTTGTCCGTGATGCCTTT
EST: gi|110384620|gb|EC949072.1|EC949072
EST:     CTCAAACAAATGCCACTTTTCTGAAGCTGGCAGGCCCTCAACTTGTCCAG                         ATGTTCATTGGGGATGGGGCGAAACTTGTCCGTGATGCCTTTCAGCTTGCT
genomic: CTCAAACAAATGCCACTTTTCTGAAGCTGGCAGGCCCTCAACTTGTCCAGgtgggatatt ... atgtattcagATGTTCATTGGGGATGGGGCGAAACTTGTCCGTGATGCCTTTCAGCTTGCT
EST: gi|110387216|gb|EC951866.1|EC951866
EST:     CTCAAACAAATGCCACTTTTCTGAAGCTGGCAGGCCCTCAACTTGTCCAG                         ATGTTCATTGGGGATGGGGCGAAACTTGTCCGTGATGCCTTTCAGCTTGCT
genomic: CTCAAACAAATGCCACTTTTCTGAAGCTGGCAGGCCCTCAACTTGTCCAGgtgggatatt ... atgtattcagATGTTCATTGGGGATGGGGCGAAACTTGTCCGTGATGCCTTTCAGCTTGCT
EST: gi|110711112|gb|EE087285.1|EE087285
EST:     CTCAAACAAATGCCACTTTTCTGAAGCTGGCAGGCCCTCAACTTGTCCAG                         ATGTTCATTGGGGATGGGGCGAAACTTGTCCGTGATGCCTTTCAGCTTGCT
genomic: CTCAAACAAATGCCACTTTTCTGAAGCTGGCAGGCCCTCAACTTGTCCAGgtgggatatt ... atgtattcagATGTTCATTGGGGATGGGGCGAAACTTGTCCGTGATGCCTTTCAGCTTGCT
EST: gi|110718444|gb|EE095285.1|EE095285
EST:     CTCAAACAAATGCCACTTTTCTGAAGCTGGCAGGCCCTCAACTTGTCCAG                         ATGTTCATTGGGGATGGGGCGAAACTTGTCCGTGATGCCTTTCAGCTTGCT
genomic: CTCAAACAAATGCCACTTTTCTGAAGCTGGCAGGCCCTCAACTTGTCCAGgtgggatatt ... atgtattcagATGTTCATTGGGGATGGGGCGAAACTTGTCCGTGATGCCTTTCAGCTTGCT
EST: gi|110685213|gb|EE063376.1|EE063376
EST:     CTCAAACAAATGCCACTTTTCTGAAGCTGGCAGGCCCTCAACTTGTCCAG                         ATGTTCATTGGGGATGGGGCGAAACTTTGTC-GTGATGCCTTTCAGCTTGC
genomic: CTCAAACAAATGCCACTTTTCTGAAGCTGGCAGGCCCTCAACTTGTCCAGgtgggatatt ... atgtattcagATGTTCATTGGGGATGGGGCGAAACTT-GTCCGTGATGCCTTTCAGCTTGC
EST: gi|110724441|gb|EE100272.1|EE100272
EST:     CTCAAACAAATGCCACTTTTCTGAAGCTGGCAAGCCCTCAACTTGTCCAG                         ATGTTCATTGGGGATGGGG
genomic: CTCAAACAAATGCCACTTTTCTGAAGCTGGCAGGCCCTCAACTTGTCCAGgtgggatatt ... atgtattcagATGTTCATTGGGGATGGGG
EST: gi|110722856|gb|EE099502.1|EE099502
EST:     CTCAAACAAATGCCACTTTTCTGAAGCTGGCAAGCCCTCAACTTGTCCAG                         ATGTTCATTGGGGGATGGGGCGAAACTTGTCCG
genomic: CTCAAACAAATGCCACTTTTCTGAAGCTGGCAGGCCCTCAACTTGTCCAGgtgggatatt ... atgtattcagATGTTCATTGGGG-ATGGGGCGAAACTTGTCCG
EST: gi|30252313|gb|CB969864.1|CB969864
EST:     ACAAATGCCACTTTTTTGAAGCTGGCAGGCCCTCAACTTGTCCAG                         ATGTTCATTGGGGATGGGGTGAAACTTGTCCGTGATGCCTTTCAGCTTGCT
genomic: ACAAATGCCACTTTTCTGAAGCTGGCAGGCCCTCAACTTGTCCAGgtgggatatt ... atgtattcagATGTTCATTGGGGATGGGGCGAAACTTGTCCGTGATGCCTTTCAGCTTGCT
EST: gi|30252322|gb|CB969873.1|CB969873
EST:     CTCAAACAAATGCCACTTTTCTGAAGCTGGCAGGCCCTCAACTTGTCCAG                         ATGTTCATTGGGGATGGGGTGAAACTTGTCCGTGATGCCTTTCAGCTTGCT
genomic: CTCAAACAAATGCCACTTTTCTGAAGCTGGCAGGCCCTCAACTTGTCCAGgtgggatatt ... atgtattcagATGTTCATTGGGGATGGGGCGAAACTTGTCCGTGATGCCTTTCAGCTTGCT
EST: gi|110405468|gb|EC971009.1|EC971009
EST:     CTCAAACAAATGCCACTTTTCTGAAGCTGGCAGGCCCTCAACTTGTCCAG                         ATGTTCATTGGGGATGGGGCGAAACTTGTCCGTGATGCCTTTCAGCTTGCT
genomic: CTCAAACAAATGCCACTTTTCTGAAGCTGGCAGGCCCTCAACTTGTCCAGgtgggatatt ... atgtattcagATGTTCATTGGGGATGGGGCGAAACTTGTCCGTGATGCCTTTCAGCTTGCT
EST: gi|30255105|gb|CB971552.1|CB971552
EST:     CTCAAACAAATGCCACTTTTCTGAAGCTGGCAGGCCCTCAACTTGTCCAG                         ATGTTCATTGGGGATGGGGCGAAACTTGTCCGTGATGCCTTTCAGCTTGCT
genomic: CTCAAACAAATGCCACTTTTCTGAAGCTGGCAGGCCCTCAACTTGTCCAGgtgggatatt ... atgtattcagATGTTCATTGGGGATGGGGCGAAACTTGTCCGTGATGCCTTTCAGCTTGCT
EST: gi|30252235|gb|CB969786.1|CB969786
EST:     CTCAAACAAATGCCACTTTTCTGAAGCTGGCAGGCCCTCAACTTGTCCAG                         ATGTTCATTGGGGATGGGGTGAAACTTGTCCGTGATGCCTTTCAGCTTGCT
genomic: CTCAAACAAATGCCACTTTTCTGAAGCTGGCAGGCCCTCAACTTGTCCAGgtgggatatt ... atgtattcagATGTTCATTGGGGATGGGGCGAAACTTGTCCGTGATGCCTTTCAGCTTGCT
EST: gi|30300725|gb|CB977519.1|CB977519
EST:     TCAAACAAATGCCACTTTNTC-GAAGCTGGCAGGCCCTCAACTTGTCCAG                         ATGTTCATTGGGGATGGGGCGAAACTTGTCCGTGGTGCCTTTCAGCTTGCT
genomic: TCAAACAAATGCCACTTT-TCTGAAGCTGGCAGGCCCTCAACTTGTCCAGgtgggatatt ... atgtattcagATGTTCATTGGGGATGGGGCGAAACTTGTCCGTGATGCCTTTCAGCTTGCT
EST: gi|110375176|gb|EC940137.1|EC940137
EST:     CTGGCAGGCCCTCAACTTGTCCAG                         ATGTTCATTGGGGATGGGGCGAAACTTGTCCGTGATGCCTTTCAGCTTGCT
genomic: CTGGCAGGCCCTCAACTTGTCCAGgtgggatatt ... atgtattcagATGTTCATTGGGGATGGGGCGAAACTTGTCCGTGATGCCTTTCAGCTTGCT
EST: gi|34544589|gb|CF512821.1|CF512821
EST:     CTCGATCAAATGCCACTTTTCTGAAGCTGGCAGGCCCTCAACTTGTCCAG                         ATGTTCATTGGGGATGGGGCGAAACTTGTCCGTGATGCCTTTCAGCTTGCT
genomic: CTCAAACAAATGCCACTTTTCTGAAGCTGGCAGGCCCTCAACTTGTCCAGgtgggatatt ... atgtattcagATGTTCATTGGGGATGGGGCGAAACTTGTCCGTGATGCCTTTCAGCTTGCT
EST: gi|30252226|gb|CB969777.1|CB969777
EST:     CTCAAACAAATGCCACTTTTCTGAAGCTGGCAGGCCCTCAACTTGTCCAG                         ATGTTCATTGGGGATGGGGTGAAACTTGTCCGTGATGCCTTTCAGCTTGCT
genomic: CTCAAACAAATGCCACTTTTCTGAAGCTGGCAGGCCCTCAACTTGTCCAGgtgggatatt ... atgtattcagATGTTCATTGGGGATGGGGCGAAACTTGTCCGTGATGCCTTTCAGCTTGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATGGACCTCCAGGGACTGGGAAAACTCTGATGGCCCGTGCATGCGCGGCTCAAACAAATGCCACTTTTCTGAAGCTGGCAGGCCCTCAACTTGTCCAGgtgggatattcttcatttgttttccttcttcattcttatttgttatttgatgccttctagggattcttgacttgttcagtatcctgaaaattctgaggtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccttcttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaatt