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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gattggaagcactcattcatttcgtctgctgtaccactaattccacaagtttcccctctgtgcttcatgactctgatattcctttgtctaattgttttagATTGCAATGAAGGAACTTCGTGAGCGGAAGATACCCTTCACCATCCGCCGCTACCTGCCTGATGGAAG

Basic information

species Vitis vinifera
transcript Vv16s0100g00530.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0100g00530.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G013600_T01 (Zea mays), 3'ss of exon 4
-gattggaagca--ctcattcatttcgtctgctgtaccactaattccacaagtttcccctctgtgcttcatgact-ctgatattcctttgtctaattgttttagATTGCAATGAAGGAACTTCGTGAGCGGAAGATACCCTTCACCATCCGCCGCTACCTGCCTGATGGAAG
  ||  ||  ||  |||| | ||| | | | |  |      |||  |   |||||     | |||     | ||     |||||   |||   || |    |||||||| |||||||| ||| | | ||| |||||||||||||| ||| | || ||||| |||||||||||
gaatgagattcaacctcagtaattaccttt-caatggttacaatcactttagtttttatacagtgtactctaacaatccatatttacttgcacaact---ctagATTGCGATGAAGGAGCTTAGAGCGCGCAAGATACCCTTCACGATCAGACGGTACCTACCTGATGGAAG

upper sequence: Vv16s0100g00530.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G086904_T01 (Zea mays), 3'ss of exon 4
gattggaagcactcattcatttcgtctgctgtaccactaattccacaagtttcccctct-gtgcttcatgactc--tgatattcctttgtcta-attgttttagATTGCAATGAAGGAACTTCGTGAGCGGAAGATACCCTTCACCATCCGCCGCTACCTGCCTGATGGAAG
   |      | |||  | |  |     |  | | |    | |||  | |||    |||  | ||   | ||||  ||||||   | | | |  |   |||||||||||||||||||| ||  | | ||| |||||||||||||| ||| | || ||| | |||||||||||
---taatgagattcaaccttagcaatcacctttcaatggttaccatcacttttagttcttatactgtgt-actcaatgatatatatgtatttttacaattttagATTGCAATGAAGGAGCTGAGAGCGCGCAAGATACCCTTCACGATCAGACGGTACTTACCTGATGGAAG

upper sequence: Vv16s0100g00530.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA20G29520.1 (Glycine max), 3'ss of exon 4
gattggaagcactcattcatttcgtctgctgtaccactaattccacaagtttcccctctgtgcttcatgac-tctgatattcctttgtctaattgttttagATTGCAATGAAGGAACTTCGTGAGCGGAAGATACCCTTCACCATCCGCCGCTACCTGCCTGATGGAAG
  ||   |  |    ||  | |  |  | |  |  | ||         ||||     || || |  || || ||||||||    || ||  |   | | ||||||| |||||||| ||||| |||||||| |||||||| || || || |||||| |||||||||||||
-gttctcacaaaaattttctgtattagggttcaggaatatacatgtttgtttgttagctctgttatataacatctgatatctagttctcccaacttatcagATTGCTATGAAGGAGCTTCGAGAGCGGAAAATACCCTTTACAATTCGGCGCTACTTGCCTGATGGAAG

upper sequence: Vv16s0100g00530.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA10G38350.2 (Glycine max), 3'ss of exon 4
--gattggaagcactcattcatttcgtctgctgtaccactaattccacaagtttcccctctgtgcttcatgac-tctgatattcctttgtctaattgttttagATTGCAATGAAGGAACTTCGTGAGCGGAAGATACCCTTCACCATCCGCCGCTACCTGCCTGATGGAAG
  |  |  ||  | |  |  |||  |  | | | |  |   ||       ||||     || || |  || ||  |||||||    || ||| |   | | ||||||| |||||||| || || |||||||| |||||||| || || || |||||| |||||||||||||
ttgtctcaaaaaatttctgtattaggatt-caggagtatacatgtttt--gtttgttagctctgttatataacacctgatatctagttatctcaacttatcagATTGCTATGAAGGAGCTCCGAGAGCGGAAAATACCCTTTACAATTCGGCGCTACTTGCCTGATGGAAG

upper sequence: Vv16s0100g00530.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S197_12V6.1 (Physcomitrella patens), 3'ss of exon 4
-gattggaagcactcattcatttcgtctg----ctgtaccactaattc---cacaagtttcccctctgtgcttcatgactctgatattcctttgtctaattgttttagATTGCAATGAAGGAACTTCGTGAGCGGAAGATACCCTTCACCATCCGCCGCTACCTGCCTGATGGAAG
 | ||  |||| |||  |  |   || |      | ||    |||||    |  ||||| ||  |     |    | ||   |  |||  || ||  |        |||| || ||||| |||||||| |||||||| || ||||||||||| || ||||| ||||| ||||| ||
tgtttaaaagc-ctcggtggtagggttttagttttttaaagataatttagtcggaagttgccgtttacctcgcattaacagaggcatttattcgtaaa-------cagATCGCTATGAAAGAACTTCGGGAGCGGAAAATTCCCTTCACCATTCGTCGCTATCTGCCCGATGGGAG

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|110374189|gb|EC938793.1|EC938793
EST:     TGAATGCACCTGTGATGGTTGAATTGGAGGGTGAGACAGATCCACTTGAG                         ATTGCAATGAAGGAACTTCGTGAGCGGAAGATACCCTTCACCATCCGCCGC
genomic: TGAATGCGCCTGTGATGGTTGAATTGGAGGGTGAGACAGATCCACTTGAGgtatgattct ... attgttttagATTGCAATGAAGGAACTTCGTGAGCGGAAGATACCCTTCACCATCCGCCGC
EST: gi|351024313|gb|FQ423736.1|FQ423736
EST:     TGAATGCGCCTGTGATGGTTGAATTGGAGGGTGAGACAGATCCACTTGAG                         ATTGCAATGAAGGAACTTCGTGAGCGGAAGATACCCTTCACCATCCGCCGC
genomic: TGAATGCGCCTGTGATGGTTGAATTGGAGGGTGAGACAGATCCACTTGAGgtatgattct ... attgttttagATTGCAATGAAGGAACTTCGTGAGCGGAAGATACCCTTCACCATCCGCCGC
EST: gi|110686792|gb|EE064832.1|EE064832
EST:     TGAATGCGCCTGTGATGGTTGAATTGGAGGGTGAGACAGATCCACTTGAG                         ATTGCAATGAAGGAACTTCGTGAGCGGAAGATACCCTTCACCATCCGCCGC
genomic: TGAATGCGCCTGTGATGGTTGAATTGGAGGGTGAGACAGATCCACTTGAGgtatgattct ... attgttttagATTGCAATGAAGGAACTTCGTGAGCGGAAGATACCCTTCACCATCCGCCGC
EST: gi|110368625|gb|EC932613.1|EC932613
EST:     TGAATGCGCCTGTGATGGTTGAATTGGAGGGTGAGACAGATCCACTTGAG                         ATTGCAATGAAGGAACTTCGTGAGCGGAAGATACCCTTCACCATCCGCCGC
genomic: TGAATGCGCCTGTGATGGTTGAATTGGAGGGTGAGACAGATCCACTTGAGgtatgattct ... attgttttagATTGCAATGAAGGAACTTCGTGAGCGGAAGATACCCTTCACCATCCGCCGC
EST: gi|26265984|gb|CA817047.1|CA817047
EST:     TGAATGCGCCTGTGATGGTTGAATTGGAGGGTGAGACAGATCCACTTGAG                         ATTGCAATGAAGGAACTTCGTGAGCGGAAGATACCCTTCACCATCCGCCGC
genomic: TGAATGCGCCTGTGATGGTTGAATTGGAGGGTGAGACAGATCCACTTGAGgtatgattct ... attgttttagATTGCAATGAAGGAACTTCGTGAGCGGAAGATACCCTTCACCATCCGCCGC
EST: gi|110413522|gb|EC979311.1|EC979311
EST:     TGAATGCGCCTGTGATGGTTGAATTGGAGGGTGAGACAGATCCACTTGAG                         ATTGCAATGAAGGAACTTCGTGAGCGGAAGATACCCTTCACCATCCGCCGC
genomic: TGAATGCGCCTGTGATGGTTGAATTGGAGGGTGAGACAGATCCACTTGAGgtatgattct ... attgttttagATTGCAATGAAGGAACTTCGTGAGCGGAAGATACCCTTCACCATCCGCCGC
EST: gi|110386849|gb|EC951479.1|EC951479
EST:     TGAATGCGCCTGTGATGGTTGAATTGGAGGGTGAGACAGATCCACTTGAG                         ATTGCAATGAAGGAACTTCGTGAGCGGAAGATACCCTTCACCATCCGCCGC
genomic: TGAATGCGCCTGTGATGGTTGAATTGGAGGGTGAGACAGATCCACTTGAGgtatgattct ... attgttttagATTGCAATGAAGGAACTTCGTGAGCGGAAGATACCCTTCACCATCCGCCGC
EST: gi|110729809|gb|EE106173.1|EE106173
EST:     TGAATGCGCCTGTGATGGTTGAATTGGAGGGTGAGACAGATCCACTTGAG                         ATTGCAATGAAGGAACTTCGTGAGCGGAAGATACCCTTCACCATCCGCCGC
genomic: TGAATGCGCCTGTGATGGTTGAATTGGAGGGTGAGACAGATCCACTTGAGgtatgattct ... attgttttagATTGCAATGAAGGAACTTCGTGAGCGGAAGATACCCTTCACCATCCGCCGC
EST: gi|110365638|gb|EC928962.1|EC928962
EST:     TGAATGCACCTGTGATGGTTGAATTGGAGGGTGAGACAGATCCACTTGAG                         ATTGCAATGAAGGAACTTCGTGAGCGGAAGATACCCTTCACCATCCGCCGC
genomic: TGAATGCGCCTGTGATGGTTGAATTGGAGGGTGAGACAGATCCACTTGAGgtatgattct ... attgttttagATTGCAATGAAGGAACTTCGTGAGCGGAAGATACCCTTCACCATCCGCCGC
EST: gi|51050339|gb|CO818499.1|CO818499
EST:     TGAATGCGCCTGTGATGGTTGAATTGGAGGGTGAGACAGATCCACTTGAG                         ATTGCAATGAAGGAACTTCGTGAGCGGAAGATACCCTTCACCATCCGCCGC
genomic: TGAATGCGCCTGTGATGGTTGAATTGGAGGGTGAGACAGATCCACTTGAGgtatgattct ... attgttttagATTGCAATGAAGGAACTTCGTGAGCGGAAGATACCCTTCACCATCCGCCGC
EST: gi|26263262|gb|CA814325.1|CA814325
EST:     TGAATGCGCCTGTGATGGTTGAATTGGAGGGTGAGACAGATCCACTTGAG                         ATTGCAATGAAGGAACTTCGTGAGCGGAAGATACCCTTCACCATCCGCCGC
genomic: TGAATGCGCCTGTGATGGTTGAATTGGAGGGTGAGACAGATCCACTTGAGgtatgattct ... attgttttagATTGCAATGAAGGAACTTCGTGAGCGGAAGATACCCTTCACCATCCGCCGC
EST: gi|26262322|gb|CA813385.1|CA813385
EST:     TGAATGCGCCTGTGATGGTTGAATTGGAGGGTGAGACAGATCCACTTGAG                         ATTGCAATGAAGGAACTTCGTGAGCGGAAGATACCCTTCACCATCCGCCGC
genomic: TGAATGCGCCTGTGATGGTTGAATTGGAGGGTGAGACAGATCCACTTGAGgtatgattct ... attgttttagATTGCAATGAAGGAACTTCGTGAGCGGAAGATACCCTTCACCATCCGCCGC
EST: gi|26263998|gb|CA815061.1|CA815061
EST:     TGAATGCGCCTGTGATGGTTGAATTGGAGGGTGAGACAGATCCACTTGAG                         ATTGCAATGAAGGAACTTCGTGAGCGGAAGATACCCTTCACCATCCGCCGC
genomic: TGAATGCGCCTGTGATGGTTGAATTGGAGGGTGAGACAGATCCACTTGAGgtatgattct ... attgttttagATTGCAATGAAGGAACTTCGTGAGCGGAAGATACCCTTCACCATCCGCCGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagtttcccctctgtgcttcatgactctgatattcctttgtctaattgttttagATTGCAATGAAGGAACTTCGTGAGCGGAAGATACCCTTCACCATCCGCCGCTACCTGCCTGATGGAAG
                                        gtctaat  putative branch site (score: 3)
                                              ttgtttt  CT-rich tract
                                           taattgtttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gattggaagcactcattcatttcgtctgctgtaccactaattccacaagtttcccctctgtgcttcatgactctgatattcctttgtctaattgttttagATTGCAATGAAGGAACTTCGTGAGCGGAAGATACCCTTCACCATCCGCCGCTACCTGCCTGATGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - -cactcat
- - - - - - - - - - - - tctgctg
- - - - - - - - - - - - - - - - -ccactaa
- - - - - - - - - - - - - - - - - - - - - ccacaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gactctg