Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgagttgttcgttgacatgtgtacaaaaagactgcatttgcttgttttataatctctctccaaccttcttgaaaacttgattttctcttgtgcttaaagGGCCCTTTTATCAATGGGAAAGACATATCTGCTGTTGACTTGTCTCTTGGACCAAAACTATACCATCTAGAGATTGCTTTGGGGCATTACAAGAAGTGGA

Basic information

species Vitis vinifera
transcript Vv14s0006g00630.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0006g00630.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA11G33700.2 (Glycine max), 3'ss of exon 4
ttgagttgttcgttgacatgtgtacaaaaagactgcatttgct--tgttttataatctctctccaaccttcttgaaaacttgattttctcttgtgcttaaagGGCCCTTTTATCAATGGGAAAGACATATCTGCTGTTGACTTGTCTCTTGGACCAAAACTATACCATCTAGAGATTGCTTTGGGGCATTACAAGAAGTGGA
 ||||     | ||   || | ||   |||| ||||| |   |      ||  |    |  || |   |  || |     ||||||| | |  |  ||| |||| ||||| ||||| || |  || |||||||| | |||| | || ||||||||||| ||||||||| |||||||||||||||||||||| ||||| ||||
-tgaggaagccttttttatat-tatctaaagtctgcactgtttaacaaattgcaggaaccttctactttatttaattgactgattttttttcctctttatagGGTCCTTTCATCAACGGTAGTGAGATATCTGCAGCTGACCTATCACTTGGACCAAAGCTATACCATTTAGAGATTGCTTTGGGGCATTATAAGAAATGGA

upper sequence: Vv14s0006g00630.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA18G04510.1 (Glycine max), 3'ss of exon 4
ttgagttgttcgttgacatgtgtacaaaaagactgcatttgcttg------ttttataatctctctccaaccttcttgaaaacttgattttctcttgtgcttaaagGGCCCTTTTATCAATGGGAAAGACATATCTGCTGTTGACTTGTCTCTTGGACCAAAACTATACCATCTAGAGATTGCTTTGGGGCATTACAAGAAGTGGA
  |      |  |||  ||   ||   |||| ||||||| ||||       |  |  || ||    ||  | || || ||        | | | |  |  ||  |||| ||||| ||||| || |  || |||||||| | |||| | || ||||||||||| ||||||||| | |||||||||||||||||||| ||||| ||| 
-aggaaacctttttgttat---tatctaaagtctgcatt-gcttaacaagttgctggaaccttctgcctgctttatttaattgactgatctttttcctctttgtaGGGTCCTTTCATCAACGGTAGTGAGATATCTGCAGCTGACCTATCACTTGGACCAAAGCTATACCATTTGGAGATTGCTTTGGGGCATTATAAGAAATGG-
















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|110719968|gb|EE095537.1|EE095537
EST:     AGACATTACTGAACGAGCTAGCTTCTTTTGATGATTATATAAAAGAAA-T                         GGCCCTTTTATCAATGGGAAAGAC-TATCTGCTGTTGACTTGTCTCTTGGG
genomic: AGACATTACTGAACGAGCTAGCTTCTTTTGATGATTATATAAAAGAAAATgtgagtcttc ... gtgcttaaagGGCCCTTTTATCAATGGGAAAGACATATCTGCTGTTGACTTGTCTCTTGG-
EST: gi|349817724|gb|FQ407713.1|FQ407713
EST:     AGACATTACTGAACGAGCTAGCTTCTTTTGATGATTATATAAAAGAAAAT                         GGCCCTTTTATCAATGGGAAAGACATATCTGCTGTTGACTTGTCTCTTGGA
genomic: AGACATTACTGAACGAGCTAGCTTCTTTTGATGATTATATAAAAGAAAATgtgagtcttc ... gtgcttaaagGGCCCTTTTATCAATGGGAAAGACATATCTGCTGTTGACTTGTCTCTTGGA
EST: gi|33402764|gb|CF208391.1|CF208391
EST:     AGACATTACTGAACGAGCTAGCTTCTTTTGATGATTATATAAAAGAAAAT                         GGCCCTTTTATCAATGGGAAAGACATATCTGCTGTTGACTTGTCTCTTGGA
genomic: AGACATTACTGAACGAGCTAGCTTCTTTTGATGATTATATAAAAGAAAATgtgagtcttc ... gtgcttaaagGGCCCTTTTATCAATGGGAAAGACATATCTGCTGTTGACTTGTCTCTTGGA
EST: gi|26265541|gb|CA816604.1|CA816604
EST:     AGACATTACTGAACGAGCTAGCTTCTTTTGATGATTATATAAAAGAAAAT                         GGCCCTTTTATCAATGGGAAAGACATATCTGCTGTTGACTTGTCTCTTGGA
genomic: AGACATTACTGAACGAGCTAGCTTCTTTTGATGATTATATAAAAGAAAATgtgagtcttc ... gtgcttaaagGGCCCTTTTATCAATGGGAAAGACATATCTGCTGTTGACTTGTCTCTTGGA
EST: gi|351024071|gb|FQ423494.1|FQ423494
EST:     AGACATTACTGAACGAGCTAGCTTCTTTTGATGATTATATAAAAGAAAAT                         GGCCCTTTTATCAATGGGAAAGACATATCTGCTGTTGACTTGTCTCTTGGA
genomic: AGACATTACTGAACGAGCTAGCTTCTTTTGATGATTATATAAAAGAAAATgtgagtcttc ... gtgcttaaagGGCCCTTTTATCAATGGGAAAGACATATCTGCTGTTGACTTGTCTCTTGGA
EST: gi|33404427|gb|CF210054.1|CF210054
EST:     AGACATTACTGAACGAGCTAGCTTCTTTTGATGATTATATAAAAGAAAAT                         GGCCCTTTTATCAATGGGAAAGACATATCTGCTGTTGACTTGTCTCTTGGA
genomic: AGACATTACTGAACGAGCTAGCTTCTTTTGATGATTATATAAAAGAAAATgtgagtcttc ... gtgcttaaagGGCCCTTTTATCAATGGGAAAGACATATCTGCTGTTGACTTGTCTCTTGGA
EST: gi|349826855|gb|FQ418946.1|FQ418946
EST:     AGACATTACTGAACGAGCTAGCTTCTTTTGATGATTATATAAAAGAAAAT                         GGCCCTTTTATCAATGGGAAAGACATATCTGCTGTTGACTTGTCTCTTGAA
genomic: AGACATTACTGAACGAGCTAGCTTCTTTTGATGATTATATAAAAGAAAATgtgagtcttc ... gtgcttaaagGGCCCTTTTATCAATGGGAAAGACATATCTGCTGTTGACTTGTCTCTTGGA
EST: gi|110691855|gb|EE070437.1|EE070437
EST:     AGACATTACTGAACGAGCTAGCTTCTTTTGATGATTATATAAAAGAAAAT                         GGCCCTTTTATCAATGGGAAAGACATATCTGCTGTTGACTTGTCTCTTGGA
genomic: AGACATTACTGAACGAGCTAGCTTCTTTTGATGATTATATAAAAGAAAATgtgagtcttc ... gtgcttaaagGGCCCTTTTATCAATGGGAAAGACATATCTGCTGTTGACTTGTCTCTTGGA
EST: gi|351046545|gb|FQ453161.1|FQ453161
EST:     AGACATTACTGAACGAGCTAGCTTCTTTTGATGATTATATAAAAGAAAAT                         GGCCCTTTTATCAATGGGNNNNNNNTATCTGCTGTTGACTTGTCTCTTGGA
genomic: AGACATTACTGAACGAGCTAGCTTCTTTTGATGATTATATAAAAGAAAATgtgagtcttc ... gtgcttaaagGGCCCTTTTATCAATGGGAAAGACATATCTGCTGTTGACTTGTCTCTTGGA
EST: gi|294966595|gb|GW837730.1|GW837730
EST:     AGACATTACTGAACGAGCTAGCTTCTTTTGATGATTATATAAAAGAAAAT                         GGCCCTTT-ATCAATGGGAAA
genomic: AGACATTACTGAACGAGCTAGCTTCTTTTGATGATTATATAAAAGAAAATgtgagtcttc ... gtgcttaaagGGCCCTTTTATCAATGGGAAA
EST: gi|77577773|gb|DV217632.1|DV217632
EST:     AGACATTACTGAACGAGCTAGCTTCTTTTGATGATTATATAAAAGAAAAT                         GGCCCTTTTATCAATGGGAAAGACATATCTGCTGTTGACTTGTCTCTTGGA
genomic: AGACATTACTGAACGAGCTAGCTTCTTTTGATGATTATATAAAAGAAAATgtgagtcttc ... gtgcttaaagGGCCCTTTTATCAATGGGAAAGACATATCTGCTGTTGACTTGTCTCTTGGA
EST: gi|26261684|gb|CA812747.1|CA812747
EST:     AGACATTACTGAACGAGCTAGCTTCTTTTGATGATTATATAAAAGAAAAT                         GGCCCTTTTATCAATGGGAAAGACATATCTGCTGTTGACTTGTCTCTTGGA
genomic: AGACATTACTGAACGAGCTAGCTTCTTTTGATGATTATATAAAAGAAAATgtgagtcttc ... gtgcttaaagGGCCCTTTTATCAATGGGAAAGACATATCTGCTGTTGACTTGTCTCTTGGA
EST: gi|26263937|gb|CA815000.1|CA815000
EST:     AGACATTACTGAACGAGCTAGCTTCTTTTGATGATTATATAAAAGAAAAT                         GGCCCTTTTATCAATGGGAAAGACATATCTGCTGTTGACTTGTCTCTTGGA
genomic: AGACATTACTGAACGAGCTAGCTTCTTTTGATGATTATATAAAAGAAAATgtgagtcttc ... gtgcttaaagGGCCCTTTTATCAATGGGAAAGACATATCTGCTGTTGACTTGTCTCTTGGA
EST: gi|349809187|gb|FQ398960.1|FQ398960
EST:     AGACATTACTGAACGAGCTAGCTTCTTTTGATGATTATATAAAAGAAAAT                         GGCCCTTTTATCAATGGGAAAGACATATCTGCTGTTGACTTGTCTCTTGGA
genomic: AGACATTACTGAACGAGCTAGCTTCTTTTGATGATTATATAAAAGAAAATgtgagtcttc ... gtgcttaaagGGCCCTTTTATCAATGGGAAAGACATATCTGCTGTTGACTTGTCTCTTGGA
EST: gi|349827950|gb|FQ422818.1|FQ422818
EST:     AGACATTACTGAACGAGCTAGCTTCTTTTGATGATTATATAAAAGAAAAT                         GGCCCTTTTATCAATGGGAAAGACATATCTGCTGTTGACTTGTCTCTTGGA
genomic: AGACATTACTGAACGAGCTAGCTTCTTTTGATGATTATATAAAAGAAAATgtgagtcttc ... gtgcttaaagGGCCCTTTTATCAATGGGAAAGACATATCTGCTGTTGACTTGTCTCTTGGA
EST: gi|349814904|gb|FQ410127.1|FQ410127
EST:     AGACATTACTGAACGAGCTAGCTTCTTTTGATGATTATATAAAAGAAAAT                         GGCCCTTTTATCAATGGGAAAGACATATCTGCTGTTGACTTGTCTCTTGGA
genomic: AGACATTACTGAACGAGCTAGCTTCTTTTGATGATTATATAAAAGAAAATgtgagtcttc ... gtgcttaaagGGCCCTTTTATCAATGGGAAAGACATATCTGCTGTTGACTTGTCTCTTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttataatctctctccaaccttcttgaaaacttgattttctcttgtgcttaaagGGCCCTTTTATCAATGGGAAAGACATATCTGCTGTTGACTTGTCTCTTGGACCAAAACTATACCATCTAGAGATTGCTTTGGGGCATTACAAGAAGTGGA
                              acttgat  putative branch site (score: 5)
                                    ttttctcttgtgctt  CT-rich tract
                                ttgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgagttgttcgttgacatgtgtacaaaaagactgcatttgcttgttttataatctctctccaaccttcttgaaaacttgattttctcttgtgcttaaagGGCCCTTTTATCAATGGGAAAGACATATCTGCTGTTGACTTGTCTCTTGGACCAAAACTATACCATCTAGAGATTGCTTTGGGGCATTACAAGAAGTGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - catgtgt
- - - - - - - - - - - - -aaaaaga
- - - - - - - - - - - - - - - - - -catttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaact