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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attatgatgtttgattttagagatacaattcacaaactactgcttaatatacatagactgcatattcttctatctaattcctcattttctatcttcttagGCCCTACAAAGAAGAAAAAGCTTGATTGGGAAACTCGTCTTCAGATTGCACTTGGAGCAGCTCAAGGGCTTGCTTACCTTCACCATGATTGTAGCCCTCG

Basic information

species Vitis vinifera
transcript Vv04s0008g01970.t01
intron # 25
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g01970.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: LOC_Os06g10230.1 (Oryza sativa), 3'ss of exon 25
--------------------------------------------------------------------------------attatgatgtttgattt-tagagatacaattc-acaaactac--tgcttaatatacata-gactgcatattcttctatctaattcctcattttc--tatcttcttagGCCCTACAAAGAAGAAAAAGCTTGATTGGGAAACTCGTCTTCAGATTGCACTTGGAGCAGCTCAAGGGCTTGCTTACCTTCACCATGATTGTAGCCCTCG
                                                                                |  ||||| |||||    | || ||    |||     | | |  | |  |||    | | |||  | | ||    | |  || || |  |||||  |||  |   ||| || || ||||||||||| |||||||||||||||||||| |  ||||| || || || || ||||| |||||||| ||||| ||||| ||||||||   
gtaagtgccgactgccaactcattgcacagtttgattgtcattgcaatttgcacagaagcaccaacatgccattctcaaaagcatgatatttgacacattgatatttgcttctgttgattgcaataccaaattgttacatgacatcttgttaccatgttaaaatcttttttttcattattctagAAGGTCCAACTAAGAAGAAAAAACTTGATTGGGAAACTCGTCTACGAATTGCTCTAGGTGCGGCCCAAGGCCTTGCTTATCTTCATCATGACTGTAGCCC---

upper sequence: Vv04s0008g01970.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: GRMZM5G809695_T03 (Zea mays), 3'ss of exon 24
attatgatgtttgattttagagatacaattcacaaactactgcttaatatacata-gactgcatattcttctatctaattcctcattt---tctatcttctt-----agGCCCTACAAAGAAGAAAAAGCTTGATTGGGAAACTCGTCTTCAGATTGCACTTGGAGCAGCTCAAGGGCTTGCTTACCTTCACCATGATTGTAGCCCTCG
     ||   ||||| ||   |  |    |  |  | |      | ||  | ||  | ||||| |||  | || | | ||||| ||||    ||||  ||||     |||| |  | |||||||| || ||||| ||||  ||||| || | ||| || ||||| ||||||||||| || ||||||||||||||||| || |||||   
----agacagttgatgttttggcgaaggcttgcttatttaatggtcatggatatttggctgca-atttctatacc-atttcctaatttaaacctattgtctttcagAAGGCTCATCCAAGAAGAACAAACTTGACTGGGTGACTCGCCTACGGATCGCTCTTGGTGCAGCTCAAGGCCTCGCTTACCTTCACCATGACTGCAGCCC---

upper sequence: Vv04s0008g01970.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: GLYMA06G05900.1 (Glycine max), 3'ss of exon 26
--attatgatgtttgattttagagatacaattcacaaactactgcttaatata--catagactgcatattcttctatctaat-tcctcattttctatcttcttagGCCCTACAAAGAAGAAAAAGCTTGATTGGGAAACTCGTCTTCAGATTGCACTTGGAGCAGCTCAAGGGCTTGCTTACCTTCACCATGATTGTAGCCCTCG
  |||      ||    | |     || |||  | | |    |  | |||  |  ||  || |  |||||| |   | | || |   ||||||     ||   ||| ||||| |||||||||||||||||||||||   ||||||  | || ||||| ||| |||| |||||||||||||| || ||||||||||| || || | 
taattgacgcattaacatctttcagtaaaatgtaaataaacattttcaatccaagcaatgattttatattcatgattttgatatgtacatttt-----tttgcagGACCTACCAAGAAGAAAAAGCTTGATTGGGATCTTCGTCTAAAAATAGCACTAGGATCAGCCCAAGGGCTTGCTTATCTACACCATGATTGCAGTCCACT

upper sequence: Vv04s0008g01970.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: GLYMA17G34380.2 (Glycine max), 3'ss of exon 24
----attatgatgtttgattttagagatacaattcacaaactactgcttaatatacatagactgcatattcttctatctaattcctcattttctatcttcttagGCCCTACAAAGAAGAAAAAGCTTGATTGGGAAACTCGTCTTCAGATTGCACTTGGAGCAGCTCAAGGGCTTGCTTACCTTCACCATGATTGTAGCCCTCG
     |        |  |||  | |    ||||| | |||     | |||  |  ||     || || || || | | |  ||      | |   | || | ||| ||||| ||||||||||||||||| |||||    |||||  | || |||||||||||||| |||||||||||||| || |||||||||||  | ||| |
attagtctaagcagtgcattggataacagcaatttagaaaac---gtttagaagccagcttatg-attttattatgtatggttttcttgtgttctttttttcagGACCTACCAAGAAGAAAAAGCTTGACTGGGAGCTGCGTCTAAAAATAGCACTTGGAGCAGCACAAGGGCTTGCTTATCTACACCATGATTGCTGTCCTAG

upper sequence: Vv04s0008g01970.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: GLYMA14G11220.1 (Glycine max), 3'ss of exon 25
attatgatgtttgattttagagatacaattcacaa-actactgcttaatatacatagactgcatattcttctatctaattcctcatt-ttctatcttcttagGCCCTACAAAGAAGAAAAAGCTTGATTGGGAAACTCGTCTTCAGATTGCACTTGGAGCAGCTCAAGGGCTTGCTTACCTTCACCATGATTGTAGCCCTCG
  |||  | || | | | ||  || || |  | || |  | |  ||   | ||||  |      |   |   ||   |||    ||  || | |  | | ||| ||||| ||||||||||||||||| |||||    |||||  | || |||||||||||||| ||||| |||||||| || |||||||||||  | ||| |
-gtattttattag-tctaagcaatgcattggataacagcaattttttgaaaacatttagaagccaacttatgattctattatgtatggttttcttgtgtcagGACCTACCAAGAAGAAAAAGCTTGACTGGGAGCTGCGTCTAAAAATAGCACTTGGAGCAGCACAAGGACTTGCTTATCTACACCATGATTGCTGTCCTAG

upper sequence: Vv04s0008g01970.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: GLYMA14G11220.2 (Glycine max), 3'ss of exon 25
attatgatgtttgattttagagatacaattcacaa-actactgcttaatatacatagactgcatattcttctatctaattcctcatt-ttctatcttcttagGCCCTACAAAGAAGAAAAAGCTTGATTGGGAAACTCGTCTTCAGATTGCACTTGGAGCAGCTCAAGGGCTTGCTTACCTTCACCATGATTGTAGCCCTCG-----------
              | | ||  || || |  | || |  | |  ||   | ||||  |      |   |   ||   |||    ||  || | |  | | ||| ||||| ||||||||||||||||| |||||    |||||  | || |||||||||||||| ||||| |||||||| || |||||||||||  | ||| |           
-------------gtctaagcaatgcattggataacagcaattttttgaaaacatttagaagccaacttatgattctattatgtatggttttcttgtgtcaggacctaccaagAAGAAAAAGCTTGACTGGGAGCTGCGTCTAAAAATAGCACTTGGAGCAGCACAAGGACTTGCTTATCTACACCATGATTGCTGTCCTAGAATCATCCACA

upper sequence: Vv04s0008g01970.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: GLYMA04G05910.1 (Glycine max), 3'ss of exon 17
-attatgatgtttgattttagagatacaattcacaaactactgcttaatatacatagactgcatattcttctatctaattcctcattttctatcttctt--agGCCCTACAAAGAAGAAAAAGCTTGATTGGGAAACTCGTCTTCAGATTGCACTTGGAGCAGCTCAAGGGCTTGCTTACCTTCACCATGATTGTAGCCCTCG
 |||   || ||| |    | |  |||||   | | || |||  | |  |  ||  || |  ||  | || |   | |||      | |  || || ||  ||| ||||| |||||||||||||||||||||||   ||||||  | || ||||||||| | || ||||| ||| |||| || ||||| ||||| || || ||
catttatatctttcagca-aaatgtacaaaaaaaacac-acttttaatcaagcaatgatta-atgattttattcatgattttgatatgtacatttttttgcagGACCTACCAAGAAGAAAAAGCTTGATTGGGATCTTCGTCTAAAAATAGCACTTGGATCGGCCCAAGGACTTTCTTATCTGCACCACGATTGCAGTCCACG

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|351032632|gb|FQ462346.1|FQ462346
EST:     ACTCTTCTATGACTACATGGAAAATGGCAGTCTCTGGGATCTACTTCATG                         GCCCTACAAAGAAGAAAAAGCTTGATTGGGAAACTCGTCTTCAGATTGCAC
genomic: ACTCTTCTATGACTACATGGAAAATGGCAGTCTCTGGGATCTACTTCATGgtaagtttaa ... atcttcttagGCCCTACAAAGAAGAAAAAGCTTGATTGGGAAACTCGTCTTCAGATTGCAC
EST: gi|352786698|gb|FQ479905.1|FQ479905
EST:     ACTCTTCTATGACTACATGGAAAATGGCAGTCTCTGGGATCTACTTCATG                         GCCCTACAAAGAAGAAAAAGCTTGATTGGGAAACTCGTCTTCAGATTGCAC
genomic: ACTCTTCTATGACTACATGGAAAATGGCAGTCTCTGGGATCTACTTCATGgtaagtttaa ... atcttcttagGCCCTACAAAGAAGAAAAAGCTTGATTGGGAAACTCGTCTTCAGATTGCAC
EST: gi|351043857|gb|FQ452651.1|FQ452651
EST:     ACTCTTCTATGACTACATGGAAAATGGCAGTCTCTGGGATCTACTTCATG                         GCCCTACAAAGAAGAAAAAGCTTGATTGGGAAACTCGTCTTCAGATTGCAC
genomic: ACTCTTCTATGACTACATGGAAAATGGCAGTCTCTGGGATCTACTTCATGgtaagtttaa ... atcttcttagGCCCTACAAAGAAGAAAAAGCTTGATTGGGAAACTCGTCTTCAGATTGCAC
EST: gi|351054408|gb|FQ450491.1|FQ450491
EST:     ACTCTTCTATGACTACATGGAAAATGGCAGTCTCTGGGATCTACTTCATG                         GCCCTACAAAGAAGAAAAAGCTTGATTGGGAAACTCGTCTTCAGATTGCAC
genomic: ACTCTTCTATGACTACATGGAAAATGGCAGTCTCTGGGATCTACTTCATGgtaagtttaa ... atcttcttagGCCCTACAAAGAAGAAAAAGCTTGATTGGGAAACTCGTCTTCAGATTGCAC
EST: gi|351047766|gb|FQ458986.1|FQ458986
EST:     ACTCTTCTATGACTACATGGAAAATGGCAGTCTCTGGGATCTACTTCATG                         GCCCTACAAAGAAGAAAAAGCTTGATTGGGAAACTCGTCTTCAGATTGCAC
genomic: ACTCTTCTATGACTACATGGAAAATGGCAGTCTCTGGGATCTACTTCATGgtaagtttaa ... atcttcttagGCCCTACAAAGAAGAAAAAGCTTGATTGGGAAACTCGTCTTCAGATTGCAC
EST: gi|351039249|gb|FQ457924.1|FQ457924
EST:     ACTCTTCTATGACTACATGGAAAATGGCAGTCTCTGGGATCTACTTCATG                         GCCCTACAAAGAAGAAAAAGCTTGATTGGGAAACTCGTCTTCAGATTGCAC
genomic: ACTCTTCTATGACTACATGGAAAATGGCAGTCTCTGGGATCTACTTCATGgtaagtttaa ... atcttcttagGCCCTACAAAGAAGAAAAAGCTTGATTGGGAAACTCGTCTTCAGATTGCAC
EST: gi|351048041|gb|FQ441213.1|FQ441213
EST:     ACTCTTCTATGACTACATGGAAAATGGCAGTCTCTGGGATCTACTTCATG                         GCCCTACAAAGAAGAAAAAGCTTGATTGGGAAACTCGTCTTCAGATTGCAC
genomic: ACTCTTCTATGACTACATGGAAAATGGCAGTCTCTGGGATCTACTTCATGgtaagtttaa ... atcttcttagGCCCTACAAAGAAGAAAAAGCTTGATTGGGAAACTCGTCTTCAGATTGCAC
EST: gi|351048270|gb|FQ442240.1|FQ442240
EST:     ACTCTTCTATGACTACATGGAAAATGGCAGTCTCTGGGATCTACTTCATG                         GCCCTACAAAGAAGAAAAAGCTTGATTGGGAAACTCGTCTTCAGATTGCAC
genomic: ACTCTTCTATGACTACATGGAAAATGGCAGTCTCTGGGATCTACTTCATGgtaagtttaa ... atcttcttagGCCCTACAAAGAAGAAAAAGCTTGATTGGGAAACTCGTCTTCAGATTGCAC
EST: gi|351045309|gb|FQ451757.1|FQ451757
EST:     ACTCTTCTATGACTACATGGAAAATGGCAGTCTCTGGGATCTACTTCATG                         GCCCTACAAAGAAGAAAAAGCTTGATTGGGAAACTCGTCTTCAGATTGCAC
genomic: ACTCTTCTATGACTACATGGAAAATGGCAGTCTCTGGGATCTACTTCATGgtaagtttaa ... atcttcttagGCCCTACAAAGAAGAAAAAGCTTGATTGGGAAACTCGTCTTCAGATTGCAC
EST: gi|352790304|gb|FQ481503.1|FQ481503
EST:     ACTCTTCTATGACTACATGGAAAATGGCAGTCTCTGGGATCTACTTCATG                         GCCCTACAAAGAAGAAAAAGCTTGATTGGGAAACTCGTCTTCAGATTGCAC
genomic: ACTCTTCTATGACTACATGGAAAATGGCAGTCTCTGGGATCTACTTCATGgtaagtttaa ... atcttcttagGCCCTACAAAGAAGAAAAAGCTTGATTGGGAAACTCGTCTTCAGATTGCAC
EST: gi|352798821|gb|FQ478456.1|FQ478456
EST:     ACTCTTCTATGACTACATGGAAAATGGCAGTCTCTGGGATCTACTTCATG                         GCCCTACAAAGAAGAAAAAGCTTGATTGGGAAACTCGTCTTCAGATTGCAC
genomic: ACTCTTCTATGACTACATGGAAAATGGCAGTCTCTGGGATCTACTTCATGgtaagtttaa ... atcttcttagGCCCTACAAAGAAGAAAAAGCTTGATTGGGAAACTCGTCTTCAGATTGCAC
EST: gi|351035908|gb|FQ463753.1|FQ463753
EST:     ACTCTTCTATGACTACATGGAAAATGGCAGTCTCTGGGATCCACTTCATG                         GCCCTACAAAGAAGAAAAAGTTTGATTGGGAAACTCGTCTTCAGATTGCAC
genomic: ACTCTTCTATGACTACATGGAAAATGGCAGTCTCTGGGATCTACTTCATGgtaagtttaa ... atcttcttagGCCCTACAAAGAAGAAAAAGCTTGATTGGGAAACTCGTCTTCAGATTGCAC
EST: gi|351048645|gb|FQ448919.1|FQ448919
EST:     ACTCTTCTATGACTACATGGAAAATGGCAGTCTCTGGGATCTACTTCATG                         GCCCTACAAAGAAGAAAAAGCTTGATTGGGAAACTCGTCTTCAGATTGCAC
genomic: ACTCTTCTATGACTACATGGAAAATGGCAGTCTCTGGGATCTACTTCATGgtaagtttaa ... atcttcttagGCCCTACAAAGAAGAAAAAGCTTGATTGGGAAACTCGTCTTCAGATTGCAC
EST: gi|352786929|gb|FQ481304.1|FQ481304
EST:     ACTCTTCTATGACTACATGGAAAATGGCAGTCTCTGGGATCTACTTCATG                         GCCCTACAAAGAAGAAAAAGCTTGATTGGGAAACTCGTCTTCAGATTGCAC
genomic: ACTCTTCTATGACTACATGGAAAATGGCAGTCTCTGGGATCTACTTCATGgtaagtttaa ... atcttcttagGCCCTACAAAGAAGAAAAAGCTTGATTGGGAAACTCGTCTTCAGATTGCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatatacatagactgcatattcttctatctaattcctcattttctatcttcttagGCCCTACAAAGAAGAAAAAGCTTGATTGGGAAACTCGTCTTCAGATTGCACTTGGAGCAGCTCAAGGGCTTGCTTACCTTCACCATGATTGTAGCCCTCG
                          atctaat  putative branch site (score: 3)
                   ttcttctatctaattc  CT-rich tract
                         tatctaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attatgatgtttgattttagagatacaattcacaaactactgcttaatatacatagactgcatattcttctatctaattcctcattttctatcttcttagGCCCTACAAAGAAGAAAAAGCTTGATTGGGAAACTCGTCTTCAGATTGCACTTGGAGCAGCTCAAGGGCTTGCTTACCTTCACCATGATTGTAGCCCTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - -gatacaa
- - - - - - - - - - - - - - - cacaaac
- - - - - - - - - - - - - - - - - - -tactgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - agactgc