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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaattggcatgccatgaccattccttggttcctaccttgttatttcatcaagtctatccatgtttaatttcagatgtatgtttgattgctggtttgcagGTACTTTCACTCTTTCAAACCTTGGAATGTTTGGTGTGGATCGGTTTGACGCAATTCTGCCACCTGGAACT

Basic information

species Vitis vinifera
transcript Vv18s0072g01000.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0072g01000.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os12g08170.1 (Oryza sativa), 3'ss of exon 3
aaaattggcatgccatgac-cattccttgg--ttcctaccttgttattt-catcaagtctatccatgtttaatttcagatgtatgtttgattgctggtttgcagGTACTTTCACTCTTTCAAACCTTGGAATGTTTGGTGTGGATCGGTTTGACGCAATTCTGCCACCTGGAACT
   |  | |     ||    ||||   ||   | |  |       || |   |     ||||| |   |  ||   | |||  ||||  ||       ||||||| || || ||| ||||||||||||| |||||||| || ||  | ||||| |||||  ||||||||||||||
--tacagactcattatagtgcatttgatgaaatgcagaagaaaacatgtatgtatgaactatctaacatctatgcta-atggttgttc-atattcaaattgcagGCACCTTTACTATTTCAAACCTTGGTATGTTTGGAGTTGACAGATTTGATGCAATCTTGCCACCTGGAACT

upper sequence: Vv18s0072g01000.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G036534_T01 (Zea mays), 3'ss of exon 3
------aaaattggcatgccatgaccattccttggttcctaccttgttatttcatcaagtctatccatgtttaatttcagatgtatgtttgattgctggtttgcagGTACTTTCACTCTTTCAAACCTTGGAATGTTTGGTGTGGATCGGTTTGACGCAATTCTGCCACCTGGAACT
      ||||  | |       |   |   | ||   | | | |  |    | | || || |||   ||| |  |     | | |    | ||      |||||||| || || |||||||| || ||||| |||||||| || ||| |||| || ||||| |||||||||||||||
gagaaaaaaacagcctcttggcggtaaccacatgaaacatgcataatatggtgaccatgt-tatttgtgtatgct-----aagaacagctcatgttcattttgcagGCACCTTTACTCTTTCGAATCTTGGTATGTTTGGAGTTGATAGGTTCGATGCAATACTGCCACCTGGAACT

upper sequence: Vv18s0072g01000.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G165176_T01 (Zea mays), 3'ss of exon 5
-aaaattggcatgccatgaccattccttggttcctaccttgttatttcatcaagtctatccat--gtttaatttcagatgtatgtttgattgctggtttgcagGTACTTTCACTCTTTCAAACCTTGGAATGTTTGGTGTGGATCGGTTTGACGCAATTCTGCCACCTGGAACT
 | |        |   | |||| |       ||  || |    | | |    |   | | | |  || ||   | |||  |     || |   |    |||||| || || ||||| || || ||||| |||||||| || ||| ||||||| ||||| |||||||||||||||
gatagcctcttggtgttaaccaataaccacatcaaacatgtagaatacggtgaccatgttcttttgtgtatgctaagaactgcacatgttcatt---ctgcagGCACGTTTACTCTCTCGAATCTTGGTATGTTTGGAGTTGATAGGTTTGATGCAATACTGCCACCTGGAACT

upper sequence: Vv18s0072g01000.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA10G35960.1 (Glycine max), 3'ss of exon 4
-aaaattggcatgccatgaccattccttggttcctaccttgttatttcatcaagtctatccatgtttaatttcagatgt--atgtttgattgctggtt--tgcagGTACTTTCACTCTTTCAAACCTTGGAATGTTTGGTGTGGATCGGTTTGACGCAATTCTGCCACCTGGAACT
 |||||    ||  | |    ||   |||  ||| |    |  |  | |   |||||     || |   || |||       || ||| ||  |  ||  |  ||||||||||||||| || || || |||||||||||||| ||||| ||||| || ||||||||||||||||||
gaaaat----atctccttgttatgg-ttgaatccaattgggccaagttaaggagtctgattctgatattttccaggccccactgattgctttttattttttatagGTACTTTCACTCTGTCCAATCTGGGAATGTTTGGTGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACT

upper sequence: Vv18s0072g01000.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA10G35960.2 (Glycine max), 3'ss of exon 4
-aaaattggcatgccatgaccattccttggttcctaccttgttatttcatcaagtctatccatgtttaatttcagatgta--tgtttgattgctggttt--gcagGTACTTTCACTCTTTCAAACCTTGGAATGTTTGGTGTGGATCGGTTTGACGCAATTCTGCCACCTGGAACT-----------------------------
 |||||    ||  | |    ||   |||  ||| |    |  |  | |   |||||     || |   || |||       || ||| ||  |  |||    ||||||||||||||| || || || |||||||||||||| ||||| ||||| || ||||||||||||||||||                             
gaaaat----atctccttgttatgg-ttgaatccaattgggccaagttaaggagtctgattctgatattttccaggccccactgattgctttttattttttatagGTACTTTCACTCTGTCCAATCTGGGAATGTTTGGTGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACTGTGAGTGTTTTACTCGTGCTCAAATATGG

upper sequence: Vv18s0072g01000.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA20G31630.1 (Glycine max), 3'ss of exon 4
aaaattggcatgccatgaccattccttggttcctaccttgttatttcatcaagtctatccatgtttaatttcagatgt--atgtttgat--tgctggtttgcagGTACTTTCACTCTTTCAAACCTTGGAATGTTTGGTGTGGATCGGTTTGACGCAATTCTGCCACCTGGAACT
    ||| | |       |   |  |||  ||| |    |  |  | |   | |||     || |   || |||       || ||| |  |  |  |||  ||||||||||||||| || || || ||||||||||| || ||||| ||||| || ||||||||||||||||||
----ttgccttagtccatcttatggttgaatccaattgggccaaattagggactctgattctgatattttccagcccccactgattgcttttatttttttatagGTACTTTCACTCTGTCCAATCTGGGAATGTTTGGCGTTGATCGCTTTGATGCTATTCTGCCACCTGGAACT

upper sequence: Vv18s0072g01000.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G34430.1 (Arabidopsis thaliana), 3'ss of exon 3
aaaattggcatgccatgaccattccttggttcctaccttgttatttcatcaagtctatccatgtttaatttcagatgtat---gtttgattgctggt--ttgcagGTACTTTCACTCTTTCAAACCTTGGAATGTTTGGTGTGGATCGGTTTGACGCAATTCTGCCACCTGGAACT
  |||     | | |  |   |    || ||      |   || | | |||| |  ||   ||||| | |   | ||| |    ||   || | |||  |||||||||| |||||||| || ||||| ||||||||||| || ||||||||||| || ||||| || |||||||| 
gtaatcctactactagaatattgaagtgatttgagtttgagtaatccttcaactagat---tgtttgagtcttgttgtttttatttcccttccgggtaattgcagGTACCTTCACTCTCTCTAACCTAGGAATGTTTGGCGTTGATCGGTTTGATGCTATTCTACCCCCTGGAACA

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|110383970|gb|EC948379.1|EC948379
EST:     GGTTGACAAGGCCCGAGCAAAGCAGCTGCAACCTCATGAATACAATACAG                         GTACTTTCACTCTTTCAAACCTTGGAATGTTTGGTGTGGATCGGTTTGACG
genomic: GGTTGACAAGGCCCGAGCAAAGCAGCTGCAACCTCATGAATACAATACAGgtatcctcat ... tggtttgcagGTACTTTCACTCTTTCAAACCTTGGAATGTTTGGTGTGGATCGGTTTGACG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatcaagtctatccatgtttaatttcagatgtatgtttgattgctggtttgcagGTACTTTCACTCTTTCAAACCTTGGAATGTTTGGTGTGGATCGGTTTGACGCAATTCTGCCACCTGGAACT
               atgtttaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaattggcatgccatgaccattccttggttcctaccttgttatttcatcaagtctatccatgtttaatttcagatgtatgtttgattgctggtttgcagGTACTTTCACTCTTTCAAACCTTGGAATGTTTGGTGTGGATCGGTTTGACGCAATTCTGCCACCTGGAACT

aaaattg
- - - - catgcca
- - - - - - - - - ccattcc
- - - - - - - - - - - - - - - -cctacct
- - - - - - - - - - - - - - - - - - - - - - - - tcaagtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgattgc