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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagagattttggtttgagggacactactgcgttcatcatagtcacaacattaaagttctctattattattttaaagtctaaatgtttagaaatcgtgtaactttaaattcttaggatttaacagGTGTGTGACAAGCAGAAAGCTGTCATGTTGGCAGACATGGCACATATTAGTGGGTTGGTTGCTGCTGGTGTTATCCAATCTCCTTTTGAATATGCTGATA

Basic information

species Vitis vinifera
transcript Vv18s0001g07960.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 8
gtaagagattttggtttgagggacactactgcgttcatcatagtcacaacattaaagttctctattattattttaaagtctaaatgtttagaaatcgtgtaact--ttaaattcttagg-atttaacagGTGTGTGACAAGCAGAAAGCTGTCATGTTGGCAGACATGGCACATATTAGTGGGTTGGTTGCTGCTGGTGTTATCCAATCTCCTTTTGAATATGCTGATA
                                                | |||  | | ||| ||  |   |    | |||  |  ||  | ||||    || |  || | || ||| | | |   ||||| |||||||||||||| ||  |  |  | ||||| ||||||||||| |||||| | || || ||||||||| | | |||||||||||| ||||| ||| 
---------------------------------------------gtga-attttactgctcaatagtgcatgctgaatcttcaccttctgtaatcagtcaaataattcacttgttatgcaatctgcagGTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGTGGGCTTGTCGCAGCTGGTGTTGTTCCATCTCCTTTTGATTATGCAGATG

upper sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G135283_T03 (Zea mays), 3'ss of exon 8
---------------gtaagagattttggtttgagggacactactgcgttcatcatagtcacaacattaaagttctctat----tatt--attttaaagtctaaatgtttagaaatcgtgtaactttaaattcttaggatttaacagGTGTGTGACAAGCAGAAAGCTGTCATGTTGGCAGACATGGCACATATTAGTGGGTTGGTTGCTGCTGGTGTTATCCAATCTCCTTTTGAATATGCTGATA
                  | ||  |||  | |    ||  | |  | | |   |||  | | |  |  | ||  || ||      |||  |     |  | |   | ||||  ||||   ||| |  | | | ||| |  |  |||| | ||  |||||||||| ||  |  |  | |||||||||||||||||||||||| | ||||| ||||||||| | | |||||||||||| ||||| ||| 
gcaaggtttctttccacgatagtattttttctccaagatgcaagggagctgcacattattatattac-agagaactatacagaacattgaaccgcgatctttttttttttatcaatcaaataattccataatgttatgtgtcgacagATATGCAACAAGCAGAAGGCAATACTTCTAGCAGACATGGCACATATTAGTGGGCTTGTTGCAGCTGGTGTTGTTCCATCTCCTTTTGATTATGCAGATG

upper sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA02G38160.2 (Glycine max), 3'ss of exon 8
gtaagagattttggtttgagggacactactgcgttcatcatagtcacaacattaaagttctctattattattttaaagtctaaatgtttagaaatcgtgtaactttaaattcttaggatttaacagGTGTGTGACAAGCAGAAAGCTGTCATGTTGGCAGACATGGCACATATTAGTGGGTTGGTTGCTGCTGGTGTTATCCAATCTCCTTTTGAATATGCTGATA
                                ||  || |||      |||  ||  |      ||| | |||  ||   |  |    |    ||  || ||  ||| || |||    ||  |||||| ||||| |||||||| || ||  ||||||| || ||||||||||| ||||| ||||||||||| |||||||| |  ||||||||||| ||||| ||| 
--------------------------------gtaaattatatctgatacagaaacttaggtatttaatgtttagaacaattcagtcatgatgatattg-aatcttatatgcttgaatttgtacagGTCTGTGATAAGCAGAAGGCAGTTCTGTTGGCTGATATGGCACATATCAGTGGATTGGTTGCTGCAGGTGTTATTCCTTCTCCTTTTGATTATGCAGATG

upper sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA14G36280.1 (Glycine max), 3'ss of exon 8
gtaagagattttggtttgagggacactactgcgttcatcatagtcacaacattaaagttctctattattattttaaagtctaaatgtttagaaatcgtgtaactttaaattcttaggatttaacagGTGTGTGACAAGCAGAAAGCTGTCATGTTGGCAGACATGGCACATATTAGTGGGTTGGTTGCTGCTGGTGTTATCCAATCTCCTTTTGAATATGCTGATA
                                ||   | |||      |||  ||  |      ||| | |||  ||   |  | ||   ||     |  ||  ||  || |||    ||  | |||| ||||| |||||||| || ||  ||||||| || ||||||||||| ||||| ||||||||||| |||||||| |  ||||||||||| ||||| ||| 
--------------------------------gtaatttatatctgatacagaaacttaggtatttaatgtttagaacaattca-gtcatgatggtattgaatcttttatgcttgaatttgtatagGTCTGTGATAAGCAGAAGGCAGTTCTGTTGGCTGATATGGCACATATCAGTGGATTGGTTGCTGCCGGTGTTATTCCTTCTCCTTTTGATTATGCAGATG

upper sequence: Vv18s0001g07960.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT5G26780.3 (Arabidopsis thaliana), 3'ss of exon 8
gtaagagattttggtttgagggacactactgcgttcatcatagtcacaacattaaagttctctattattattttaaagtctaaatgtttagaaatcgtgtaactttaaattcttaggatttaacagGTGTGTGACAAGCAGAAAGCTGTCATGTTGGCAGACATGGCACATATTAGTGGGTTGGTTGCTGCTGGTGTTATCCAATCTCCTTTTGAATATGCTGATA
                                ||  |  || ||| ||||  |  |||      || |  ||  |||   |  |  |||  |  |  || |            ||  |  |  ||||| ||| ||||||| || || || |||||||| || ||||| |||||||||||||||||||||||||| ||||| |  ||||||||||| ||||| ||| 
--------------------------------gtaaagtattgtctcaactcttgagtgtgaagtt-tagttacaaaagttgcagttttcaaggttatgca------------taaaaaattgcagGTCTGTAACAAGCAAAAGGCAGTTATGTTGGCTGATATGGCTCATATTAGTGGGTTGGTTGCTGCTGGCGTTATTCCTTCTCCTTTTGAGTATGCAGATG

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|352776821|gb|FQ472708.1|FQ472708
EST:     CTGGCGCAAGTGCCTATGCACGTCTTTATGATTATGCACGTATCCGCAAG                         GTGTGTGACCAGCAGAAAGCTGTCATGTTGGCAGACAT
genomic: CTGGCGCAAGTGCCTATGCACGTCTTTATGATTATGCACGTATCCGCAAGgtaagagatt ... gatttaacagGTGTGTGACAAGCAGAAAGCTGTCATGTTGGCAGACAT
EST: gi|110383662|gb|EC948045.1|EC948045
EST:     CTGGCGCAAGTGCCTATGCACGTCTTTATGATTATGCACGTATCCGCAAG                         GTGTGTGACAAGCAGAAAGCTGTCATGTTGGCAGACATGGCACATATTAGT
genomic: CTGGCGCAAGTGCCTATGCACGTCTTTATGATTATGCACGTATCCGCAAGgtaagagatt ... gatttaacagGTGTGTGACAAGCAGAAAGCTGTCATGTTGGCAGACATGGCACATATTAGT
EST: gi|352781776|gb|FQ469074.1|FQ469074
EST:     CTGGCGCAAGTGCCTATGCACGTCTTTATGATTATGCACGTATCCGCAAG                         GTGTGTGACAAGCAGAAAGCTGTCCTGTTGGCA
genomic: CTGGCGCAAGTGCCTATGCACGTCTTTATGATTATGCACGTATCCGCAAGgtaagagatt ... gatttaacagGTGTGTGACAAGCAGAAAGCTGTCATGTTGGCA
EST: gi|110359383|gb|EC920779.1|EC920779
EST:     CTGGTGCAAGTGCCTATGCACGTCTTTATGATTATGCACGTATCCGCAAG                         GTGTGTGACAAGCAGAAAGCTGTCATGTTGGCAGACATGGCACATATTAGT
genomic: CTGGCGCAAGTGCCTATGCACGTCTTTATGATTATGCACGTATCCGCAAGgtaagagatt ... gatttaacagGTGTGTGACAAGCAGAAAGCTGTCATGTTGGCAGACATGGCACATATTAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaaagtctaaatgtttagaaatcgtgtaactttaaattcttaggatttaacagGTGTGTGACAAGCAGAAAGCTGTCATGTTGGCAGACATGGCACATATTAGTGGGTTGGTTGCTGCTGGTGTTATCCAATCTCCTTTTGAATATGCTGATA
                         gtgtaac  putative branch site (score: 3)
                            taactttaaattctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagagattttggtttgagggacactactgcgttcatcatagtcacaacattaaagttctctattattattttaaagtctaaatgtttagaaatcgtgtaactttaaattcttaggatttaacagGTGTGTGACAAGCAGAAAGCTGTCATGTTGGCAGACATGGCACATATTAGTGGGTTGGTTGCTGCTGGTGTTATCCAATCTCCTTTTGAATATGCTGATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT