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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcttaaactaatttcacttttcccccccaaaccatggcttttgatgatttgatcattagtgtacctctctctttctctcatcctgtttgtttattgtagGACTTCCGTCAGCTTCTTGATGACAACCTAGGACTGCTGGTGAAACTGAGAGACTTCATTATTGATTGGGTTCAAGAAGGATTTCAAGACTTTTTCGGAA

Basic information

species Vitis vinifera
transcript Vv07s0005g01440.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g01440.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os03g52770.1 (Oryza sativa), 3'ss of exon 13
--------------------------------tgcttaaactaatttcacttttcccccccaaaccat-----ggcttttgatgatttgatcattagtgtacctct-ctctttctctcatcctgtt-tgtttattgtagGACTTCCGTCAGCTTCTTGATGACAACCTAGGACTGCTGGTGAAACTGAGAGACTTCATTATTGATTGGGTTCAAGAAGGATTTCAAGACTTTTTCGGAA
                                ||   |||  |  | || || |    |  |||| |       || | || |    | |       | | ||  |  |||   | |  |  |  | ||||  || ||||| || | ||| ||| | |||| |||   ||   | || || ||||||||||| ||  ||||||||||||| |||||||| |||||||| || ||    |
gtatatattgtggataatctgcggcataatattgtccaaataacatgcagttcttttac--aaactactagtaagcctatgcttgcataagagcatatattccaatgttctcattttttttttactatgttgtttctagGAATTTCATCATCTTATAGATGGCAATACAGAGTTACTTGTAAAACTGAGAGATTTGGTTATTGATTGGGTACAAGAAGGTTTTCAAGATTTCTTTCAGA

upper sequence: Vv07s0005g01440.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G023858_T03 (Zea mays), 3'ss of exon 13
-------------------------------tgcttaaactaatttcacttttcccccccaaaccatggcttttgatgatttga--tcattagtgtacctctctct-ttctctcatcctgttt--------gtttattgtagGACTTCCGTCAGCTTCTTGATGACAACCTAGGACTGCTGGTGAAACTGAGAGACTTCATTATTGATTGGGTTCAAGAAGGATTTCAAGACTTTTTCGGAA
                                 || |  |   ||    | ||  |   |||   ||   || |    ||   |  |||| | | |  |   |||| || |    | ||||||        |||  ||  |||| || | ||| ||  | |||| |||  |||   |||| || || ||||| || || |||||||||||||| |||||||| |||||||| ||||||   |
gtacatacttggaagcttcagaacttctgaacactcatccattttgtcatgttgtcaggcaacatatatgttatacgcatcaaaattcatgaatttctcatgctctgttttagtgttctgtttctggctatgttgcttccagGAATTTCATCATCTGGTAGATGGCAATATAGAGTTGCTTGTTAAGCTGAGGGATTTGATTATTGATTGGGTACAAGAAGGTTTTCAAGAGTTTTTCCAGA

upper sequence: Vv07s0005g01440.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA02G01610.1 (Glycine max), 3'ss of exon 14
-------------------------tgcttaaactaattt---cacttttcccccccaaaccatggcttttgatga----tttgatcattagtgtacctctctctttctct--catcctgtttgtttattgtagGACTTCCGTCAGCTTCTTGATGACAACCTAGGACTGCTGGTGAAACTGAGAGACTTCATTATTGATTGGGTTCAAGAAGGATTTCAAGACTTTTTCGGAA
                             || || |  ||     |  ||        |   || ||| ||| | |    ||   | ||| ||||   |     ||||  |  |||    | | | |  |  ||||||||||  |  || | |||||  ||   ||  | || || | | | ||||| || |||| ||||||||||||||||||| |||||||||||||  |  
gtaagcatgtttgtatgcttagattcatctatacaaggttatatgcaattatgtgtgcatgtattgctattgttaagattttctgttatttgtgttttttgtcatttcatttacatttaatctctctccttcagGACTTCCGCAAAGTTTTAGATGATGACTCTGGGATCCTAGTTAGATTAAGAGAGTTAATTACTGATTGGGTTCAAGAAGGACTTCAAGACTTTTTTAGGC

upper sequence: Vv07s0005g01440.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA10G01660.1 (Glycine max), 3'ss of exon 14
---------------tgcttaaactaattt-cacttttcccccccaaaccatggcttttgatgatttgatcattagtgtacctctctctttctctcat------cctgtttgtttattgtagGACTTCCGTCAGCTTCTTGATGACAACCTAGGACTGCTGGTGAAACTGAGAGACTTCATTATTGATTGGGTTCAAGAAGGATTTCAAGACTTTTTCGGAA
               |||||| | | || |  ||            ||  |||  |     |  |   ||  |||   |     | | ||| | ||||          ||| | |  |  ||||||| ||  |  || | |||||  ||   ||  | || || | | | ||||| || || ||||||||||||||||||||| ||||||| |||||  |  
gtaagcatgtttgtatgcttagattcatctatacaaggttatattcaattatgtatgcatgtattgctattgttaagattttgttatttttgtttcatttacatttaatttctctccttcagGACTTTCGCAAAATTTTAGATGATGACTCTGGGATCCTAGTTAGATTAAGAGAGTTAATCATTGATTGGGTTCAAGAAGGACTTCAAGAATTTTTTAGGC

upper sequence: Vv07s0005g01440.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AT4G02030.2 (Arabidopsis thaliana), 3'ss of exon 15
tgcttaaactaatttcacttttcccccccaaaccatggcttttg-atgatttgatcattagtgtacctctctctttctctcat-cctgtttgtttattgtagGACTTCCGTCAGCTTCTTGATGACAACCTAGGACTGCTGGTGAAACTGAGAGACTTCATTATTGATTGGGTTCAAGAAGGATTTCAAGACTTTTTCGGAA
     | | |  ||   || ||       | |   ||||| ||  || || ||   || | |      |||     | || ||    |||   | | |  ||||||||||||||||||||||||| ||    ||| |  |  | ||  |||  || || || | || |||| ||||  |||||| ||||||||| ||| |  
---gcacattccttcttctgttatttattatattttggctgttatatcatctg--tatgaattccatgctcaaaaacgcttatattcgttctatcacttcagGACTTCCGTCAGCTTCTTGATGAAAAAACTGGAATATTTATAAAGATGAAGGATTTAATCAGTGGTTGGATTCAGAAAGGATCTCAAGACTTCTTCAGGT

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|27579832|gb|CB002527.1|CB002527
EST:     GCAGTAATTCAAGGCAGCATGGCCATCTTACTG                         GACTTCCGTCAGCTTCTTGATGACAACCTAGGACTGCTGGTGAAACTGAGA
genomic: GCAGTAATTCAAGGCAGCATGGCCATCTTACTGgtaaaaatat ... tttattgtagGACTTCCGTCAGCTTCTTGATGACAACCTAGGACTGCTGGTGAAACTGAGA
EST: gi|161707865|gb|FC055661.1|FC055661
EST:     TGGAGGGAAGCAAGAAGGCAGTAATTCAAGGCAGCATGGCCATCTTACTG                         GACTTCCGTCAGCTTCTTGATGACAACCTAGGACTGCTGGTGAAACTGAGA
genomic: TGGAGGGAAGCAAGAAGGCAGTAATTCAAGGCAGCATGGCCATCTTACTGgtaaaaatat ... tttattgtagGACTTCCGTCAGCTTCTTGATGACAACCTAGGACTGCTGGTGAAACTGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatttgatcattagtgtacctctctctttctctcatcctgtttgtttattgtagGACTTCCGTCAGCTTCTTGATGACAACCTAGGACTGCTGGTGAAACTGAGAGACTTCATTATTGATTGGGTTCAAGAAGGATTTCAAGACTTTTTCGGAA
  atttgat  putative branch site (score: 5)
                 tacctctctctttctc  putative PPT
                                         tttgtttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcttaaactaatttcacttttcccccccaaaccatggcttttgatgatttgatcattagtgtacctctctctttctctcatcctgtttgtttattgtagGACTTCCGTCAGCTTCTTGATGACAACCTAGGACTGCTGGTGAAACTGAGAGACTTCATTATTGATTGGGTTCAAGAAGGATTTCAAGACTTTTTCGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - -aaactaa
- - - - - - - - - - - ccccccc
- - - - - - - - - - - - - - -aaaccat