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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgattcactttgttatcaattgttggatcttcagttgtttgttacatttgtatctgtaaatcttataactttttttttttcagTCCCTGAAGTTGCTTTCTGTTATGGCTGCAATACGTTTGGATGATTATACTGATAATATCGAGAATACTTTATCTGCTGCTTTGGTGGATAATGTGAAAA

Basic information

species Vitis vinifera
transcript Vv09s0002g02200.t01
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g02200.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA07G01230.1 (Glycine max), 3'ss of exon 18
-----gtatgattcactttgttat-caattgttggatcttcagttgtttgttacatttgtatctgtaaatcttataactttttttttttcagTCCCTGAAGTTGCTTTCTGTTATGGCTGCAATACGTTTGGATGATTAT---ACTGATAATATCGAGAATACTTTATCTGCTGCTTTGGTGGATAATGTGAAAA
     | ||||||     | ||||    || ||| || |    || ||| |||  ||| || |  ||           ||  |  ||| |||||  |||||||||| ||||||||||||||||| |||||||||||| ||   ||||| ||||| |||||    ||| | | ||| |||||||||    | |   
gtatggcatgattatgaatattatattgttattgaatttgtgcttttttattatctttttaaccata----------tttaatgctttgcagTCTTTGAAGTTGCTATCTGTTATGGCTGCAATTCGTTTGGATGATGATGACACTGACAATATTGAGAAGGTGTTAGCAGTTGCATTGGTGGATT-CATCAC--

upper sequence: Vv09s0002g02200.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA08G20610.1 (Glycine max), 3'ss of exon 18
gtatgattcactttgttatcaattgttggatcttcagttgtttgttacatttgtatctgtaaatcttataactttt--tttttttcagTCCCTGAAGTTGCTTTCTGTTATGGCTGCAATACGTTTGGATGATTAT---ACTGATAATATCGAGAATACTTTATCTGCTGCTTTGGTGGATAATGTGAAAA
||| |     | |  |||| |||  ||  ||  | | |   ||  ||  ||| ||  | |   | | |  |  |||     ||| |||||  |||||||||| ||||||||||||||||| |||||||||||| ||   ||||| ||||| |||||    ||| | | ||| |||||||||   || |   
gtacgg----catgattatgaat-attatattgttattgaatttgtatttttttaattatctttttaaccatatttaacgctttgcagTCTTTGAAGTTGCTATCTGTTATGGCTGCAATTCGTTTGGATGATGATGACACTGACAATATTGAGAAAGTGTTAGCAGTTGCCTTGGTGGATT-CGTCAC--
















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|161721528|gb|FC070082.1|FC070082
EST:     GGACTGGGAAAGAAGATATTCGTGCAATCACCAAGACTGCTCGTTCTTCT                         TCCCTGAAGTTGCTTTCTTGT-ATGGCT
genomic: GGACTGGGAAAGAAGATATTCGTGCAATCACCAAAACTGCTCGTTCTTCTgtatgattca ... tttttttcagTCCCTGAAGTTGCTTTCT-GTTATGGCT
EST: gi|161721258|gb|FC070023.1|FC070023
EST:     GGACTGGGAAAGAAGATATTCGTGCAATCACCAAGACTGCTCGTTCTTCT                         TCCCTGAAGTTGCTTTCTGTTATGGCTGCAATACGTTTGGATGATTATACT
genomic: GGACTGGGAAAGAAGATATTCGTGCAATCACCAAAACTGCTCGTTCTTCTgtatgattca ... tttttttcagTCCCTGAAGTTGCTTTCTGTTATGGCTGCAATACGTTTGGATGATTATACT
EST: gi|161716580|gb|FC065551.1|FC065551
EST:     GGACTGGGAAAGAAGATATTAGTGCAATCACCAAGACTGCTCGTTCTTCT                         TCCCTGAAGTTGCTTTCTGTTATGGCTGCAATACGTTTGGATGATTATACT
genomic: GGACTGGGAAAGAAGATATTCGTGCAATCACCAAAACTGCTCGTTCTTCTgtatgattca ... tttttttcagTCCCTGAAGTTGCTTTCTGTTATGGCTGCAATACGTTTGGATGATTATACT
EST: gi|71881154|gb|DT030209.1|DT030209
EST:     GGACTGGGAAAGAAGATATTCGTGCAATCACCAAGACTGCTCGTTCTTCT                         TCCCTGAAGTTGCTTTCTGTTATGGCTGCAATACGTTTGGATGATTATACT
genomic: GGACTGGGAAAGAAGATATTCGTGCAATCACCAAAACTGCTCGTTCTTCTgtatgattca ... tttttttcagTCCCTGAAGTTGCTTTCTGTTATGGCTGCAATACGTTTGGATGATTATACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcagttgtttgttacatttgtatctgtaaatcttataactttttttttttcagTCCCTGAAGTTGCTTTCTGTTATGGCTGCAATACGTTTGGATGATTATACTGATAATATCGAGAATACTTTATCTGCTGCTTTGGTGGATAATGTGAAAA
                                  ttataac  putative branch site (score: 2)
                                tcttataacttttttt  CT-rich tract
                 atttgtatctgtaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgattcactttgttatcaattgttggatcttcagttgtttgttacatttgtatctgtaaatcttataactttttttttttcagTCCCTGAAGTTGCTTTCTGTTATGGCTGCAATACGTTTGGATGATTATACTGATAATATCGAGAATACTTTATCTGCTGCTTTGGTGGATAATGTGAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA