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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGAAGCATTATTTCAGACACATGAGAACTTGGAGCATTTGGCCATGATGGAGAGGGTGTTGGGACCTCTGCCAGAGCATATGATTCGGAGGGCAAGgtaagttttctttgtgaagattatggtaaggaaacggttccatctgttggaaaagatggtacatatataaaagttgttgaacattgctaattctaaaagg...

Basic information

species Vitis vinifera
transcript Vv04s0008g04220.t01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g04220.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: LOC_Os01g40840.1 (Oryza sativa), 5'ss of exon 10
GGTGAAGCATTATTTCAGACACATGAGAACTTGGAGCATTTGGCCATGATGGAGAGGGTGTTGGGACCTCTGCCAGAGCATATGATTCGGAGGGCAAGgtaagtttt--ctttgtgaagattatggtaaggaaacggttccat--ctgttggaaaagatggtacatatataaaagttgttgaacattgctaattctaaaagg
|| |||||||| ||||| |||||||||||| | ||||| || || |||||||||||||| ||||| || || ||||| || |||||  |||  || |||||  || |  |  |||| | | ||   | | ||     |||  |  |  ||      | ||      |||||  |  |  | |||    |||  | | |    
GGGGAAGCATTGTTTCAAACACATGAGAACCTTGAGCACTTAGCAATGATGGAGAGGGTTTTGGGTCCACTCCCAGAACACATGATAAGGAAAGCCAGgtacattgtggcagtgtgcacactactttgatgatcattttcttttacctttttctgtgttgtcctcaatatagcaagtagtaaacgaatctatgtttta----

upper sequence: Vv04s0008g04220.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GRMZM2G366935_T09 (Zea mays), 5'ss of exon 9
GGTGAAGCATTATTTCAGACACATGAGAACTTGGAGCATTTGGCCATGATGGAGAGGGTGTTGGGACCTCTGCCAGAGCATATGATTCGGAGGGCAAGgtaagttttctttgtgaagattatggtaaggaaacggttccatctgttggaaaagatggtacatatataaaagttg--ttgaacattgctaattctaaaagg---
|| |||||||| |||||||||||||||||  |||| ||  | || ||||||||||| || ||||||||||| |||||||||||||| ||||   ||||||  || || ||||  |   | |   | || | |   ||  |||| ||| |  | ||| ||  | | |  || |    |||      ||  ||  | |   |   
GGGGAAGCATTGTTTCAGACACATGAGAATCTGGAACACCTAGCAATGATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAGgt--gtgttatttgcaaccttaac--ttagtagatcattttatcttttgaacgaaatg-tatttgtgttcaaatcagcttgtgataagcatatctttatttgctt

upper sequence: Vv04s0008g04220.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GRMZM2G094039_T06 (Zea mays), 5'ss of exon 8
GGTGAAGCATTATTTCAGACACATGAGAACTTGGAGCATTTGGCCATGATGGAGAGGGTGTTGGGACCTCTGCCAGAGCATATGATTCGGAGGGCAAGgtaagttttctttgtgaagattatggtaaggaaacggttccatctgttggaaaagatggtacatatataaa--agttgttgaa---cattgctaattctaaaagg-
|| |||||||| ||||||||||| |||||  |||| ||  | || |||||||||||||| ||||||||||| |||||| ||||||| ||||  |||||||  |||   |        ||  |  |  |   |   ||  |||| ||| |  | ||| ||  | |  |||  || | |||||    ||   || ||     | | 
GGGGAAGCATTGTTTCAGACACACGAGAATCTGGAACACCTAGCAATGATGGAGAGGGTTTTGGGACCTCTACCAGAGGATATGATACGGAAAGCAAGgtgcgttacttgca-----atcttaatttgcgtattattttatcttttgaatgaaatg-tatgtgttcaaatcagcttttgaagcatatctttatttgcttgatgt

upper sequence: Vv04s0008g04220.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GRMZM2G094039_T01 (Zea mays), 5'ss of exon 7
--GGTGAAGCATTATTTCAGACACATGAGAACTTGGAGCATTTGGCCATGATGGAGAGGGTGTTGGGACCTCTGCCAGAGCATATGATTCGGAGGGCAAGgtaagttttctttgtgaagattatggtaaggaaacggttccatctgttggaaaagatggtacatatataaa--agttgttgaa---cattgctaattctaaaagg-
  || |||||||| ||||||||||| |||||  |||| ||  | || |||||||||||||| ||||||||||| |||||| ||||||| ||||  |||||||  |||   |        ||  |  |  |   |   ||  |||| ||| |  | ||| ||  | |  |||  || | |||||    ||   || ||     | | 
AGGGGGAAGCATTGTTTCAGACACACGAGAATCTGGAACACCTAGCAATGATGGAGAGGGTTTTGGGACCTCTACCAGAGGATATGATACGGAAAGCAAGgtgcgttacttgca-----atcttaatttgcgtattattttatcttttgaatgaaatg-tatgtgttcaaatcagcttttgaagcatatctttatttgcttgatgt

upper sequence: Vv04s0008g04220.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA06G08480.2 (Glycine max), 5'ss of exon 9
GGTGAAGCATTATTTCAGACACATGAGAACTTGGAGCATTTGGCCATGATGGAGAGGGTGTTGGGACCTCTGCCAGAGCATATGATTCGGAGGGCAAGgtaagtttt--ctttgtgaagattatggtaaggaaacggttcca--tctgttggaaa-agatggtacatatataaaagtt----gttgaacattgctaattctaaaagg---------------------------------------------------------------------
||||||||||| |||||||| ||||| |||||||||||  |||| |||||||| || || ||||||||| | ||||||||||||||| | ||| | | ||||||  |   ||| |  |   |    |||     |  | |||  | |||| ||   | ||          |  |||||    ||  |  | ||  ||  | |||||                                                                      
GGTGAAGCATTGTTTCAGACTCATGAAAACTTGGAGCACCTGGCAATGATGGAAAGAGTTTTGGGACCTATTCCAGAGCATATGATTTGCAGGTCTAAgtaagtagtgaatttatagaacattctttaaatttcccctgccagttttgtttgaggtacatcaagaggccttccaagttatgagtcaatgactgggaaagccaaaagctgattggttatcactgaatatactaaatgtagtaacttcttttttattcatttgctcttcaatacatag

upper sequence: Vv04s0008g04220.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: PP1S132_58V6.1 (Physcomitrella patens), 5'ss of exon 10
GGTGAAGCATTATTTCAGACACATGAGAACTTGGAGCATTTGGCCATGATGGAGAGGGTGTTGGGACCTCTGCCAGAGCATATGATTCGGAGGGCAAGgtaagt----tttctttgtgaagattatggtaaggaaacggttccatctgttggaaaagatggtacatatataaaagttgttgaacattgctaattctaaaagg------------------------------------------------------------
||||| ||||| |||||||| || ||||| |||||||||||||| ||||||||  | || || || ||| | || |  || |||||   |||||||  ||||||    |   | ||| ||  || |  |           | |   | |||    |  ||            |||||   |  |||   ||    || | |                                                             
GGTGATGCATTGTTTCAGACTCACGAGAATTTGGAGCATTTGGCTATGATGGAACGAGTCTTAGGTCCTATTCCTGTACACATGATCAAGAGGGCAGAgtaagtgacatgcgtctgttaatcttttcttggcttcctctattctaatcttgtgtgatgtgtattgagccaccaagtttgagttcatgattatgagtagacgttttctatattctgtctgaaagtgtcctttggtttacgagcactttcaacgacctctgcag

upper sequence: Vv04s0008g04220.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: PP1S100_121V6.1 (Physcomitrella patens), 5'ss of exon 12
GGTGAAGCATTATTTCAGACACATGAGAACTTGGAGCATTTGGCCATGATGGAGAGGGTGTTGGGACCTCTGCCAGAGCATATGATTCGGAGGGCAAGgtaagttttcttt---gtgaagattatggtaaggaaacggttcca-----tctgttggaaaagatggtacatatataaaagtt--gttgaacattgctaattctaaaagg-----------------------------------------------------------------------
||||| ||  | |||||||| ||||||||||||||||||||||| ||||||||| |||| || || ||  | || |  || |||||  ||||||||  ||| ||||| |||   || ||  ||||  |    |||    |         |||| ||   |  |  |   |||| |   ||   | |||    ||    |     ||||                                                                       
GGTGATGCGCTGTTTCAGACTCATGAGAACTTGGAGCATTTGGCTATGATGGAGCGGGTTTTAGGTCCCATTCCCGTTCACATGATAAGGAGGGCAGAgtacgttttttttcttgttaactttattttgcccaaattactttggctatcctgtcggtttacttaatg-gtatagagtggtcacgctgagttctgtgcgtatgttaaggttttaccgactagtaaatgtctatggactttaatattgctaacatgttgtatggattacacaaatattcag

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|110378511|gb|EC943648.1|EC943648
EST:     ATGGAGAGGGTGTTGGGACCTCTGCCAGAGCATATGATTCGGAGGGCAAG                         CCGAAGTGTTGAAAAGTATTTCAGGGGAGGATCACGGTTGAATTGGCCTGA
genomic: ATGGAGAGGGTGTTGGGACCTCTGCCAGAGCATATGATTCGGAGGGCAAGgtaagttttc ... atatttgcagCCGAAGTGTTGAAAAGTATTTCAGGGGAGGATCACGGTTGAATTGGCCTGA




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGAAGCATTATTTCAGACACATGAGAACTTGGAGCATTTGGCCATGATGGAGAGGGTGTTGGGACCTCTGCCAGAGCATATGATTCGGAGGGCAAGgtaagttttctttgtgaagattatggtaaggaaacggttccatctgttggaaaagatggtacatatataaaagttgttgaacattgctaattctaaaagg

- - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aggaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tataaaa