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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttttcttggtatgtcctcttgctgtagatcgatttatgctaaataagtgatgggtaaatcattataattgactttatatgtataaatatttcatgcagATTGATGGTGAATTTGCCAGATGCTTTAAATAGAGAGAAAATTCTGAGAGTTATTCTGGCCAAAGAAGAATTGGCACCTGATGTTGGTTTGGAAGCAGTT

Basic information

species Vitis vinifera
transcript Vv07s0005g00200.t01
intron # 23
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 23
lower sequence: LOC_Os07g47530.1 (Oryza sativa), 3'ss of exon 24
ctttttcttggtatgtcctcttgc--tgtagatcgatttatgctaaataagtgatgggtaaatcattataattgactttatatgtataaatatttcatgcagATTGATGGTGAATTTGCCAGATGCTTTAAATAGAGAGAAAATTCTGAGAGTTATTCTGGCCAAAGAAGAATTGGCACCTGATGTTGGTTTGGAAGCAGTT
          |||  |  | || |   |  |    |||  |  ||  |     |||   ||||  | ||  |||   ||   ||   | ||||   ||  || ||||||||||||||||||||||| |  |||||| | || ||||| || || || |||||||||||||| |||||   |||||| | | |||||||  | 
----------gtaactttttttacatcgctgtggtattccttttatttttacaatg---aaatgctaatggttg--cttgcctgatcacatatca-atttagGTTGATGGTGAATTTGCCAGATGCATCCAATAGAAAAAAGATTCTTAGCGTAATACTGGCCAAAGAAGATTTGGCTGATGATGTAGATCTGGAAGCTCTG

upper sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 23
lower sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 15
ctttttcttggtatgtcctcttgctgtagatcgatttatgctaaata-agtgatg---ggtaaatcattataattg--actttatatgtataaatatttcatgcagATTGATGGTGAATTTGCCAGATGCTTTAAATAGAGAGAAAATTCTGAGAGTTATTCTGGCCAAAGAAGAATTGGCACCTGATGTTGGTTTGGAAGCAGTT
 |    |||   || |||| || ||   | |       | |   ||   |||| |     ||      | ||||    | ||| ||  ||  | |||||||    | || ||||| || ||||| ||||| | |||||||||||||||||||| ||| ||| |||| ||||||||  ||| | | ||||||| | | ||  || ||
-tgggcctttagatctcct-ttactagggcttaggacctacctgatgtggtgaggcaacataggcggatttaatcaccattttttacttactattatttca----gGTTAATGGTAAACTTGCCTGATGCATCAAATAGAGAGAAAATTCTGAAAGTAATTTTGGCAAAAGAAGAGCTGGGATCGGATGTTGATCTCGACTCACTT

upper sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 23
lower sequence: GLYMA02G17400.1 (Glycine max), 3'ss of exon 20
ctttttcttggtatgtcc--tcttgctgtagatcgatttatgctaaataagtgatgggtaaatcattataattgactttatatgtataaatatttcatgcagATTGATGGTGAATTTGCCAGATGCTTTAAATAGAGAGAAAATTCTGAGAGTTATTCTGGCCAAAGAAGAATTGGCACCTGATGTTGGTTTGGAAGCAGTT
  |   || | |||||    | ||    |   |   ||  || |  | || |||      |   ||  |||||    || | |||  ||| || |  || ||||||||||| |||||||||||||||  ||||||||  |||||| | ||||||||| | || |||||||| |||||||||||||||| ||| |||||| | 
-gtaaactcgttatgtttgatgttaacttcttttatttcgtgttttacaaatga-----gatctatgctaattcgtgttctttgttgaaaaatat--tgtagATTGATGGTTAATTTGCCAGATGCTCCAAATAGAGGAAAAATTGTCAGAGTTATTTTAGCAAAAGAAGATTTGGCACCTGATGTTGATTTTGAAGCAATA

upper sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 23
lower sequence: GLYMA10G02410.1 (Glycine max), 3'ss of exon 20
-ctttttcttggtatgtcctcttgctgtagatcgatttatgctaaataagtgatgggtaaatcattataattgactttatatgtataaatatttcatgcagATTGATGGTGAATTTGCCAGATGCTTTAAATAGAGAGAAAATTCTGAGAGTTATTCTGGCCAAAGAAGAATTGGCACCTGATGTTGGTTTGGAAGCAGTT
      || |  | | |  | |     |   |   ||  || |  | || |||      |   ||  |||||    || | | |  ||| |  |  || ||||||||||| |||||||| ||||||  ||| ||||| |||||| | || |||||| | || ||||||||||||||||||||||||| ||| |||||| | 
gtaaactcattatgtttgatgtcagcttcttttatttcgtgtttcacaaatga-----gatctatgctaatttgtgttctttcttgaaaaaaat--tgtagATTGATGGTTAATTTGCCCGATGCTCCAAACAGAGAAAAAATTGTTAGTGTTATTTTAGCAAAAGAAGAATTGGCACCTGATGTTGATTTCGAAGCAATA

upper sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 23
lower sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 23
ctttttcttggtatgtcctcttgctgtagatcgatttatgctaaataagtgatgggtaaatcattataattgactttatatgtataaatatttcatgcagATTGATGGTGAATTTGCCAGATGCTTTAAATAGAGAGAAAATTCTGAGAGTTATTCTGGCCAAAGAAGAATTGGCACCTGATGTTGGTTTGGAAGCAGTT
  |   | || |||||    |         |   || ||| |  | |  |||      |   ||| ||||  |   | |   |  |  | |||  || ||||||||||| |||||||||||||||  ||| ||||| |||||||| ||||| ||| | |  |||||||| ||||||||||| |||| ||| |||||| | 
-gtgagcatgttatgtttaatgttaacttgtattttcatgttttacagatgac-----atctattctaatgcatggtctgacttcattttttttttgtagATTGATGGTTAATTTGCCAGATGCTCCAAACAGAGAAAAAATTCTCAGAGTCATTTTAGTGAAAGAAGATTTGGCACCTGACGTTGATTTTGAAGCAATA

upper sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 23
lower sequence: GLYMA02G17410.1 (Glycine max), 3'ss of exon 19
ctttttcttggtatgtcctcttgctgtagatcgatttatgctaaataagtgatgggtaaatcattataattgactttatatgtataaatatttcatgcagATTGATGGTGAATTTGCCAGATGCTTTAAATAGAGAGAAAATTCTGAGAGTTATTCTGGCCAAAGAAGAATTGGCACCTGATGTTGGTTTGGAAGCAGTT
  |   | || |||||    |         |   || ||| |  | |  |||      |   ||| ||||  |   | | | |  || | |||  || ||||| ||||| |||||||||||||||  ||| ||||| |||||||| || || ||| |||| |||||||| |||||||||||  ||| ||| |||||| | 
-gtgagcatgttatgtttaatgttaacttgtattttcatgttttacagatgac-----atctattctaatgcatggtctgtcttcaatttttttttgtagATTAATGGTTAATTTGCCAGATGCTCCAAACAGAGAAAAAATTCTCAGTGTCATTTTGGCGAAAGAAGATTTGGCACCTGACATTGATTTTGAAGCAATA

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|34547757|gb|CF515989.1|CF515989
EST:     AATAGGCCTTTTGACCTTGATGAGGCTGTTATTAGGAGGCTACCCAGGAG                         ATTGATGGTGAATTTGCCAGATGCTTTAAATAGAGAGAAAATTCTGAGAGT
genomic: AATAGGCCTTTTGACCTTGATGAGGCTGTTATTAGGAGGCTACCCAGGAGgtaaacatca ... tttcatgcagATTGATGGTGAATTTGCCAGATGCTTTAAATAGAGAGAAAATTCTGAGAGT
EST: gi|71854977|gb|DT004032.1|DT004032
EST:     AATAGGCCTTTTGACCTTGATGAGGCTGTTATTAGGAGGCTACCCAGGAG                         ATTGATGGTGAATTTGCCAGATGCTTTAAATAGAGAGAAAATTCTGAGAGT
genomic: AATAGGCCTTTTGACCTTGATGAGGCTGTTATTAGGAGGCTACCCAGGAGgtaaacatca ... tttcatgcagATTGATGGTGAATTTGCCAGATGCTTTAAATAGAGAGAAAATTCTGAGAGT
EST: gi|30300649|gb|CB977443.1|CB977443
EST:     AATAGGCCTTTTGACCTTGATGAGGCTGTTATTAGGAGGCTACCCAGGAG                         ATTGATGGTGAATTTGCCAGATGCTTTAAATAGAGAGAAAATTCTGAGAGT
genomic: AATAGGCCTTTTGACCTTGATGAGGCTGTTATTAGGAGGCTACCCAGGAGgtaaacatca ... tttcatgcagATTGATGGTGAATTTGCCAGATGCTTTAAATAGAGAGAAAATTCTGAGAGT
EST: gi|71881952|gb|DT031007.1|DT031007
EST:     AATAGGCCTTTTGACCTTGATGAGGCTGTTATTAGGAGGCTACCCAGGAG                         ATTGATGGTGAATTTGCCAGATGCTTTAAATAGAGAGAAAATTCTGAGAGT
genomic: AATAGGCCTTTTGACCTTGATGAGGCTGTTATTAGGAGGCTACCCAGGAGgtaaacatca ... tttcatgcagATTGATGGTGAATTTGCCAGATGCTTTAAATAGAGAGAAAATTCTGAGAGT
EST: gi|30300714|gb|CB977508.1|CB977508
EST:     AATAGGCCTTTTGACCTTGATGAGGCTGTTATTAGGAGGCTACCCAGGAG                         ATTGATGGTGAATTTGCCAGATGCTTTAAATAGAGAGAAAATTTTGAGAGT
genomic: AATAGGCCTTTTGACCTTGATGAGGCTGTTATTAGGAGGCTACCCAGGAGgtaaacatca ... tttcatgcagATTGATGGTGAATTTGCCAGATGCTTTAAATAGAGAGAAAATTCTGAGAGT
EST: gi|30134135|gb|CB919473.1|CB919473
EST:     AATAGGCCTTTTGACCTTGATGAGGCTGTTATTAGGAGGCTACCCAGGAG                         ATTGATGGTGAATTTGCCAGATGCTTTAAATAGAGAGAAAATTCTGAGAGT
genomic: AATAGGCCTTTTGACCTTGATGAGGCTGTTATTAGGAGGCTACCCAGGAGgtaaacatca ... tttcatgcagATTGATGGTGAATTTGCCAGATGCTTTAAATAGAGAGAAAATTCTGAGAGT
EST: gi|30130536|gb|CB915875.1|CB915875
EST:     AATAGGCCTTTTGACCTTGATGAGGCTGTTATTAGGAGGCTACCCAGGAG                         ATTGATGGTGAATTTGCCAGATGCTTTAAATAGAGAGAAAATTCTGAGAGT
genomic: AATAGGCCTTTTGACCTTGATGAGGCTGTTATTAGGAGGCTACCCAGGAGgtaaacatca ... tttcatgcagATTGATGGTGAATTTGCCAGATGCTTTAAATAGAGAGAAAATTCTGAGAGT
EST: gi|30125513|gb|CB910852.1|CB910852
EST:     AATAGGCCTTTTGACCTTGATGAGGCTGTTATTAGGAGGCTACCCAGGAG                         ATTGATGGTGAATTTGCCAGATGCTTTAAATAGAGAGAAAATTCTGAGAGT
genomic: AATAGGCCTTTTGACCTTGATGAGGCTGTTATTAGGAGGCTACCCAGGAGgtaaacatca ... tttcatgcagATTGATGGTGAATTTGCCAGATGCTTTAAATAGAGAGAAAATTCTGAGAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taagtgatgggtaaatcattataattgactttatatgtataaatatttcatgcagATTGATGGTGAATTTGCCAGATGCTTTAAATAGAGAGAAAATTCTGAGAGTTATTCTGGCCAAAGAAGAATTGGCACCTGATGTTGGTTTGGAAGCAGTT
                      aattgac  putative branch site (score: 3)
           taaatcattataattg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttttcttggtatgtcctcttgctgtagatcgatttatgctaaataagtgatgggtaaatcattataattgactttatatgtataaatatttcatgcagATTGATGGTGAATTTGCCAGATGCTTTAAATAGAGAGAAAATTCTGAGAGTTATTCTGGCCAAAGAAGAATTGGCACCTGATGTTGGTTTGGAAGCAGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - ttcttgg
- - - - - - -tgtcctc
- - - - - - - - - - -tgctgta
- - - - - - - - - - - - - - - - - - - - -taaataa
- - - - - - - - - - - - - - - - - - - - - - - - gtgatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaatcat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ataaata