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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggagcaaatgattggaaagtgtttattctcttttagattccaatttaaaattggactttcttctatcagGTAACAACATCAATATACAATCTTATATTGGGAAAGTTGTACTGTGATCACTATGGTACAATGCGCATACAGGGAAATCGTGAGTATTCATGTAAGCTGA

Basic information

species Vitis vinifera
transcript Vv18s0001g03790.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g03790.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G147332_T01 (Zea mays), 3'ss of exon 6
-------------------------gtatggagcaaatgattggaaa--gtgtttattctcttttagatt--ccaatttaa--aattggactttcttctatcagGTAACAACATCAATATACAATCTTATATTGGGAAAGTTGTACTGTGATCACTATGGTACAATGCGCATACAGGGAAATCGTGAGTATTCATGTAAGCTGA
||| | | | |||| || | || || | | | ||| |||||||| |||||| | | |||||| ||||| ||||| |||||||| |||||||| ||| | || || |||||||||||||| |||||||| || || ||||||||||||||||||||||| |
gtttggcttagaaaaaaccgacacaatatatatcta-tgatcagagatagtaactaatagatgattgatctatcaatttaattgattggaaatatgt---tcagGTGACAACTTCAATTTACAATCTCATATTGGGCAAGCTATATTGCGATCACTATGGTACTATGCGCATTCAAGGTAATCGTGAGTATTCATGTAAGCTTA

upper sequence: Vv18s0001g03790.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G157172_T01 (Zea mays), 3'ss of exon 7
--------------------gtatggagcaaatgattggaaagtgtttattctcttttagattccaatttaaaattggactttc--ttctat-----cagGTAACAACATCAATATACAATCTTATATTGGGAAAGTTGTACTGTGATCACTATGGTACAATGCGCATACAGGGAAATCGTGAGTATTCATGTAAGCTGA
|| | | | | || | | | | || ||| | ||| | |||| || || || || ||||| ||||| ||||| |||||||| |||||||| ||| | || || |||||||||||||| ||||||||||| || ||| |||| |||||||||||||| |
ttaaatttataatgtttgtcttaggaaaaacctagttaatatatttatgatcagaggtagtgactaatagatgattgacctatcaatttaatatgttcagGTGACAACTTCAATTTACAATCTCATATTGGGCAAGCTATATTGCGATCACTATGGTACTATGCGCATACAAGGTAATTGTGAATATTCATGTAAGCTTA

upper sequence: Vv18s0001g03790.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: EFJ15167 (Selaginella moellendorffii), 3'ss of exon 6
gtatggagcaaatgattggaaagtgtttattctcttttagattccaatttaaaattggactttcttctatcagGTAACAACATCAATATACAATCTTATATTGGGAAAGTTGTACTGTGATCACTATGGTACAATGCGCATACAGGGAAATCGTGAGTATTCATGTAAGCTGA
||| | | | ||| |||| | ||| | | |||| ||||| || |||||||| |||||||| ||| | |||||| | |||||||||||||| || ||||||||||| || ||||| || || || || ||||| |
-------------------gtagt-tcaaacggcatttggatt--ggtctaacaccgtactt------gacagGTGACCACATCAATTTACAATCTCATACTAGGAAAGCTTTACTGTGATCACTACGGCACAATGCGCATTCAAGGAAACCGCGACATGTCCTGCAAGCTTA

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|161717040|gb|FC065900.1|FC065900
EST:     GCGCTTTGACTTTGGAATTTGATGATGGAGAAACTTTTCAATGGAGTAAG                         GTAACAACATCAATATACAATCTTATATTGGGAAAGTTGTACTGTGATCAC
genomic: GCGCTTTGACTTTGGAATTTGATGATGGAGAAACTTTTCAATGGAGTAAGgtatggagca ... cttctatcagGTAACAACATCAATATACAATCTTATATTGGGAAAGTTGTACTGTGATCAC
EST: gi|161719223|gb|FC065737.1|FC065737
EST:     GCGCTTTGACTTTGGAATTTGATGATGGAGAAACTTTTCAATGGAGTAAG                         GTAACAACATCAATATACAATCTTATATTGGGAAAGTTGTACTGTGATCAC
genomic: GCGCTTTGACTTTGGAATTTGATGATGGAGAAACTTTTCAATGGAGTAAGgtatggagca ... cttctatcagGTAACAACATCAATATACAATCTTATATTGGGAAAGTTGTACTGTGATCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaagtgtttattctcttttagattccaatttaaaattggactttcttctatcagGTAACAACATCAATATACAATCTTATATTGGGAAAGTTGTACTGTGATCACTATGGTACAATGCGCATACAGGGAAATCGTGAGTATTCATGTAAGCTGA
                                         ctttcttctatc  CT-rich tract
 ttttagattccaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggagcaaatgattggaaagtgtttattctcttttagattccaatttaaaattggactttcttctatcagGTAACAACATCAATATACAATCTTATATTGGGAAAGTTGTACTGTGATCACTATGGTACAATGCGCATACAGGGAAATCGTGAGTATTCATGTAAGCTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA