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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatatttttgtacaatctcatgttttgaaacatcaaatccaagtctataatctgacgatggctaattgtctgtttcttttcttttttctttttctttcagGGATACTGCAGGACAGGAAAGGTTCAGGAGTCTGATCCCAAGTTACATTAGGGACTCCTCTGTTGCAGTCATTGTATATGATGTTGCAA

Basic information

species Vitis vinifera
transcript Vv15s0021g00640.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0021g00640.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os07g31370.1 (Oryza sativa), 3'ss of exon 2
aatatttttgtacaatctcatgttttgaaaca--tcaaatcca--agtctataatctgacgatggcta---attgtctgtttcttttcttttttctttttctttcagGGATACTGCAGGACAGGAAAGGTTCAGGAGTCTGATCCCAAGTTACATTAGGGACTCCTCTGTTGCAGTCATTGTATATGATGTTGCAA
         |||  ||  ||| |||||   ||  || | |       ||||     ||   || |  |   ||| |||  | | |||  | ||| |||||||  ||||||||| || || |||||| | ||||||||| |||| ||||| || || || ||||| || ||||| ||||| |||| |||||||||||
---------gtatgatggcatcttttgctgcatttccagttagttgttctactccttgggaatcggcaggcattatcttatgcattttgtatttttttttctg-cagGGATACAGCTGGTCAGGAACGATTCAGGAGTTTGATTCCAAGCTATATCAGAGACTCTTCCGTTGCTGTCATCGTATTTGATGTTGCAA

upper sequence: Vv15s0021g00640.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G169694_T01 (Zea mays), 3'ss of exon 2
aatatttttgtacaatctcatgttttgaaacatcaaatccaagtctataatctgacgatggctaattgtctgtttcttttcttttttctttttctttcagGGATACTGCAGGACAGGAAAGGTTCAGGAGTCTGATCCCAAGTTACATTAGGGACTCCTCTGTTGCAGTCATTGTATATGATGTTGCAA
         |||   |  |   |  ||   |||  |   |  || |      |||         | |||     |  |   | |||| ||||  || |||||||||||| || |||||||| ||||||||| | || ||||| || ||||| ||||| || ||||| ||||||||||  ||||||||||
---------gtatggtgactactactg---cattcatagcctgtttgccccttgagatctatggactgttgaccttatgcatgttttattttctttgcagGGATACTGCTGGTCAGGAAAGATTCAGGAGTTTAATTCCAAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA

upper sequence: Vv15s0021g00640.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G075719_T01 (Zea mays), 3'ss of exon 2
aatatttttg-tacaatctcatgttttgaaacatcaaatccaagtctataatctgacgatggctaattgtctgtttcttttcttttttctttttctttcagGGATACTGCAGGACAGGAAAGGTTCAGGAGTCTGATCCCAAGTTACATTAGGGACTCCTCTGTTGCAGTCATTGTATATGATGTTGCAA
  |||  ||  ||| |   |||   ||      |     || |   | | ||||   ||  | | |   | ||  | | || |||| |       || ||||||||| || || |||||||||||||||||| | || ||||| || || || ||||| || ||||| ||||||||||  ||||||||||
-gtataattactactactgcatccgttagcctgtatggcccca--ttgtgatctacggaccgttgaccttatgcatgtgttgttttct-------ttgcagGGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA

upper sequence: Vv15s0021g00640.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA11G04330.1 (Glycine max), 3'ss of exon 2
aatatttttgtacaatctcatgttttgaaacatcaaatccaagtctataatctgacgatggctaattgtctgtttcttttcttttttc-tttttctttcagGGATACTGCAGGACAGGAAAGGTTCAGGAGTCTGATCCCAAGTTACATTAGGGACTCCTCTGTTGCAGTCATTGTATATGATGTTGCAA
    |||| || |||| | |||          |     |        |  | |     |  |    |||   |    ||  | ||||| | |||    ||||||||| || || |||||||| || || ||||| || ||||| |||||||||||||| ||||| || || |||||||||||||||||||
tgggttttagttcaat-taatgacacaccttcttttgactggtggagttttttttttttctcccggtgttcctaatgttcatcttttcatgttttcgacagGGATACAGCTGGCCAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAGGGACTCATCTGTAGCTGTTATTGTATATGATGTTGCAA

upper sequence: Vv15s0021g00640.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA01G41100.1 (Glycine max), 3'ss of exon 2
aatatttttgtacaatctcatgttttgaaacatcaaatccaagtctataatctgacgatggctaattgtctgtttcttttct----tttttctttttcttt-------cagGGATACTGCAGGACAGGAAAGGTTCAGGAGTCTGATCCCAAGTTACATTAGGGACTCCTCTGTTGCAGTCATTGTATATGATGTTGCAA
         || ||   |   ||||||   ||   |||   |  |  | || ||||  |||   | | | | ||||    ||    ||  ||||||  | |       ||||||||| || || |||||||| || || ||||| || ||||| ||||| |||||||| ||||| || || |||||||||||||||||||
---------gtgcatcgttgggttttggttcaattaatgacacccctttatttgac--tggtggagtttttttttcccccctaatattcatcttttcatgtgttatgacagGGATACAGCTGGGCAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATCAGGGACTCATCTGTAGCTGTTATTGTATATGATGTTGCAA

upper sequence: Vv15s0021g00640.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S346_29V6.1 (Physcomitrella patens), 3'ss of exon 3
----aatatttttgtacaatctcatgttttgaaacatcaaatccaagtctataatctgacgatggctaattgtctgtttcttttcttttttctttttctttcagGGATACTGCAGGACAGGAAAGGTTCAGGAGTCTGATCCCAAGTTACATTAGGGACTCCTCTGTTGCAGTCATTGTATATGATGTTGCAA
     |||      |  |   |    | |||   | | |  ||    | || || |  |  ||    |||   |    |  |||     |  | |    | ||||||||| || |||||||| |||||||||||| | || || ||||||||| |||| || || || |||||  |||| || |||||| |||
attagataacgagatggaggttgtcttcttgtttcttgacgtcttgttgtagaaacgaa--atactgaatc--catcataatttggggctgttatgaaatgcagGGATACCGCTGGACAGGAGAGGTTCAGGAGTTTAATTCCTAGTTACATTCGGGATTCGTCCGTGGCAGTGGTTGTGTACGATGTTTCAA

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|349831044|gb|FQ420714.1|FQ420714
EST:     CTATCAAAGACGATGTACCTTGAAGATCGGACGGTCCGTTTGCAACTCTG                         GGATACTGCAGGACAGGAAAGGTTCAGGAGTCTGATCCCAAGTTACATTAG
genomic: CTATCAAAGACGATGTACCTTGAAGATCGGACGGTCCGTTTGCAACTCTGgtgagatttt ... tttctttcagGGATACTGCAGGACAGGAAAGGTTCAGGAGTCTGATCCCAAGTTACATTAG
EST: gi|351023599|gb|FQ432982.1|FQ432982
EST:     CTATCAAAGACGATGTACCTTGAAGATCGGACGGTCCGTTTGCAACTCTG                         GGATACTGCAGGACAGGAAAGGTTCAGGAGTCTGATCCCAAGTTACATTAG
genomic: CTATCAAAGACGATGTACCTTGAAGATCGGACGGTCCGTTTGCAACTCTGgtgagatttt ... tttctttcagGGATACTGCAGGACAGGAAAGGTTCAGGAGTCTGATCCCAAGTTACATTAG
EST: gi|351034756|gb|FQ458113.1|FQ458113
EST:     CTATCAAAGACGATGTACCTTGAAGATCGGACGGTCCGTTTGCAACTCTG                         GGATACTGCAGGACAGGAAAGGTTCAGGAGTCTGATCCCAAGTTACATTAG
genomic: CTATCAAAGACGATGTACCTTGAAGATCGGACGGTCCGTTTGCAACTCTGgtgagatttt ... tttctttcagGGATACTGCAGGACAGGAAAGGTTCAGGAGTCTGATCCCAAGTTACATTAG
EST: gi|349828935|gb|FQ419268.1|FQ419268
EST:     CTATCAAAGACGATGTACCTTGAAGATCGGACGGTCCGTTTGCAACTCTG                         GGATACTGCAGGACAGGAAAGGTTCAGGAGTCTGATCCCAAGTTACATTAG
genomic: CTATCAAAGACGATGTACCTTGAAGATCGGACGGTCCGTTTGCAACTCTGgtgagatttt ... tttctttcagGGATACTGCAGGACAGGAAAGGTTCAGGAGTCTGATCCCAAGTTACATTAG
EST: gi|110700609|gb|EE077413.1|EE077413
EST:     CTATCAAAGACGATGTACCTTGAAGATCGGACGGTCCGTTTGCAACTCTG                         GGATACTGCAGGGCAGGAAAGGTTCAGGAGTCTGATCCCAAGTTACATTAG
genomic: CTATCAAAGACGATGTACCTTGAAGATCGGACGGTCCGTTTGCAACTCTGgtgagatttt ... tttctttcagGGATACTGCAGGACAGGAAAGGTTCAGGAGTCTGATCCCAAGTTACATTAG
EST: gi|349824858|gb|FQ414716.1|FQ414716
EST:     CTATCAAAGACGATGTACCTTGAAGATCGGACGGTCCGTTTGCAACTCTG                         GGATACTGCAGGACAGGAAAGGTTCAGGAGTCTGATCCCAAGTTACATTAG
genomic: CTATCAAAGACGATGTACCTTGAAGATCGGACGGTCCGTTTGCAACTCTGgtgagatttt ... tttctttcagGGATACTGCAGGACAGGAAAGGTTCAGGAGTCTGATCCCAAGTTACATTAG
EST: gi|110696285|gb|EE075270.1|EE075270
EST:     CTATCAAAGACGATGTACCTTGAAGATCGGACGGTCCGTTTGCAACTCTG                         GGATACTGCAGGACAGGAAAGGTTCAGGAGTCTGATCCCAAGTTACATTAG
genomic: CTATCAAAGACGATGTACCTTGAAGATCGGACGGTCCGTTTGCAACTCTGgtgagatttt ... tttctttcagGGATACTGCAGGACAGGAAAGGTTCAGGAGTCTGATCCCAAGTTACATTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tataatctgacgatggctaattgtctgtttcttttcttttttctttttctttcagGGATACTGCAGGACAGGAAAGGTTCAGGAGTCTGATCCCAAGTTACATTAGGGACTCCTCTGTTGCAGTCATTGTATATGATGTTGCAA
              ggctaat  putative branch site (score: 3)
                ctaattgtctgtttct  CT-rich tract
                           tttcttttcttttttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatatttttgtacaatctcatgttttgaaacatcaaatccaagtctataatctgacgatggctaattgtctgtttcttttcttttttctttttctttcagGGATACTGCAGGACAGGAAAGGTTCAGGAGTCTGATCCCAAGTTACATTAGGGACTCCTCTGTTGCAGTCATTGTATATGATGTTGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - caatctc
- - - - - - - - - - - - - gaaacat
- - - - - - - - - - - - - - - - - -aatccaa