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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgaaacaggaccaccttgtaatttttgttgtagattcttttatatttataagtgattcattggttttgattttttgatgtgcgttacttttcttgcagAGAGATGATCCAGCACAGGCCATACACTCAGAAGGTAGATGTCTACAGCTTTGGAATTGTCCTGTGGGAGCTCATCACAGGCTTGCTTCCCTTCCAGAAC

Basic information

species Vitis vinifera
transcript Vv04s0008g03020.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g03020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os06g45300.1 (Oryza sativa), 3'ss of exon 2
catgaaacaggaccaccttgtaatttttgttgtagattcttttatatttataagtgattcattggttttgattttttgatgtgcgttacttttcttgcagAGAGATGATCCAGCACAGGCCATACACTCAGAAGGTAGATGTCTACAGCTTTGGAATTGTCCTGTGGGAGCTCATCACAGGCTTGCTTCCCTTCCAGAAC
  | |  ||  | |||    | |   |  |||   | | ||| |  ||| ||| |  |   |    | || || | |    |||        || ||||| |||||||||||||||||||| ||   ||| || |||||||| ||||||||||| |||||| |||||||||| || || ||| |||| ||||||   |||
-gtaagtcataatcacgcattcacgctcattgcctactgttt-acctttttaaatc-tctgtcaaatatgcttatct----tgc------catcatgcagGGAGATGATCCAGCACAGGCCTTATGATCATAAAGTAGATGTTTACAGCTTTGGGATTGTCTTGTGGGAGCTTATAACCGGCATGCTCCCCTTCACAAAC

upper sequence: Vv04s0008g03020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os04g51950.1 (Oryza sativa), 3'ss of exon 2
catgaaacaggaccaccttgtaatttttg-ttgtagattcttttatatttataagtgattca-ttggttttgattttttgatgtgcgttacttt--tcttgcagAGAGATGATCCAGCACAGGCCATACACTCAGAAGGTAGATGTCTACAGCTTTGGAATTGTCCTGTGGGAGCTCATCACAGGCTTGCTTCCCTTCCAGAAC
   ||        |   ||    |||    |||||  |  ||  |||  |  |  | ||| | ||||||     | | |||   ||  || |||  || |||||||| ||||| ||||||||||||||    ||||| ||||||||||| |||||||| ||||| || ||||||||||| || ||| |||| || |||   |||
---gagttgttttctatttactgtttcaaattgtaattcgttcaatacattcatcttattaacttggttcctgatgtctgactcgc-ctattttgatcctgcagAGAAATGATTCAGCACAGGCCATATGACCAGAAAGTAGATGTCTATAGCTTTGGCATTGTTCTATGGGAGCTCATTACTGGCATGCTCCCTTTCGCTAAC

upper sequence: Vv04s0008g03020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os08g12750.1 (Oryza sativa), 3'ss of exon 2
-catgaaacaggaccaccttgtaatttttgttgtagattcttttatatt-tataagtgattcattggttttgattttttgatgtgcgttacttttcttgcagAGAGATGATCCAGCACAGGCCATACACTCAGAAGGTAGATGTCTACAGCTTTGGAATTGTCCTGTGGGAGCTCATCACAGGCTTGCTTCCCTTCCAGAAC
     | | ||  |    |  ||   || |   |  ||| ||    ||| | |   |  |||||||||| |  |  |   |  |   |   ||  ||||||| ||| ||||||||||||| |||||    || || || ||||||||||| ||||| || ||||||||||||||  | || ||    ||||| ||    |||
ttcaaatatagtgcagtatgctagaattgg--atcaattattgctcattgtgtttttttttcattggttctagtcatgataactttttattttgacttgcagTGAGGTGATCCAGCACAGACCATATGACCAAAAAGTCGATGTCTACAGTTTTGGCATCGTCCTGTGGGAGCTAGTAACTGGGAACCTTCCTTTTGCAAAC

upper sequence: Vv04s0008g03020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G156013_T01 (Zea mays), 3'ss of exon 2
---catgaaacaggaccaccttgtaatttttgt-tgtagattcttttatatttataagtgattcattggttttgattttttgatgtgcgttacttttcttgcagAGAGATGATCCAGCACAGGCCATACACTCAGAAGGTAGATGTCTACAGCTTTGGAATTGTCCTGTGGGAGCTCATCACAGGCTTGCTTCCCTTCCAGAAC
     |       ||   |   || |||  |   |  | |||     |   ||||||  |    ||||     ||| |||  || |   ||  |  ||||||||||||||||| ||||| ||||||||    ||||| || ||||||||||||||||| ||||| |||||||||||||| || ||| |||| || ||    |||
ttttttcttgtttgaat-ctgagtcattcatacatacacatttgacaaaggttataaaaggaggattgaa---gatgtttacatattgttttttaatcttgcagAGAGATGATTCAGCATAGGCCATATGACCAGAAAGTTGATGTCTACAGCTTTGGCATTGTGCTGTGGGAGCTCATAACTGGCATGCTCCCTTTTGCTAAC

upper sequence: Vv04s0008g03020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G102088_T02 (Zea mays), 3'ss of exon 2
catgaaacaggaccaccttgtaatttttgttgtagattcttttatattt-ataagtgattcattggtttt-gattttttgatgt-gcgttacttttcttgcagAGAGATGATCCAGCACAGGCCATACACTCAGAAGGTAGATGTCTACAGCTTTGGAATTGTCCTGTGGGAGCTCATCACAGGCTTGCTTCCCTTCCAGAAC
     ||      |   ||  ||  |  ||     || | |  | | || | ||||  |  |  |  |   ||| |||  || | |  ||  |  ||||||||||||||||| ||||||||||||||    || || || ||||||||||||||||| ||||| |||||||||||||| || ||| |||| || ||    || 
---cgaatgttttcttgtttgaagctaagtcagtcatgcatacacaattgacaagttgtaaaaggactgaagatgtttacatattgtttttttaatcttgcagAGAGATGATTCAGCACAGGCCATATGACCAAAAAGTTGATGTCTACAGCTTTGGCATTGTGCTGTGGGAGCTCATAACTGGCATGCTCCCTTTTGCTAAT

upper sequence: Vv04s0008g03020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G140612_T03 (Zea mays), 3'ss of exon 2
catgaaacaggaccac-cttgtaatttttgttgtagattctttta-tatttataag----tgattcattggtttt-gattttttgatgtgc-gttacttttcttgcagAGAGATGATCCAGCACAGGCCATACACTCAGAAGGTAGATGTCTACAGCTTTGGAATTGTCCTGTGGGAGCTCATCACAGGCTTGCTTCCCTTCCAGAAC
           || |  |||  |||    ||| | |||  |||||  |||||  |     || ||  || ||||   || |  | |  |||  ||  |   || |||| || ||||||||||| ||||||||||  ||||| || ||||||||||| ||||  ||||||||||||||| |  | || ||     | |||||    |||
--------tttactattcttagaatacccgttatggatgtttttaacatttaccaagttctgttttgtttgtttccaatgtgataagttgctatttttccactcgcagTGAAATGATCCAGCATAGGCCATACAACCAGAAAGTTGATGTCTACAGTTTTGCCATTGTCCTGTGGGAGTTAGTGACTGGGAATGTCCCCTTTGCAAAC

upper sequence: Vv04s0008g03020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ13809 (Selaginella moellendorffii), 3'ss of exon 1
catgaaacaggaccaccttgtaatttttgttgtagattcttttatatttataagtgattcattggttttgattttttgatgtgcgttacttttcttgcagAGAGATGATCCAGCACAGGCCATACACTCAGAAGGTAGATGTCTACAGCTTTGGAATTGTCCTGTGGGAGCTCATCACAGGCTTGCTTCCCTTCCAGAAC
        | |  ||  |     ||  |  | |      |||  | ||  |     ||   | |  ||  |    |   |   |||| | ||  ||||||||||||||||||||||||||  ||||| || ||||| || || ||||||||||| ||||| |||||||||||||||||||| ||||| || |||||||||
------gtaagcgcatttctctcttcgttctcttcgcgttttcgtgttcttcctccatagctagacttcaaagcctcactaaccgtttcattcattgcagAGAGATGATCCAGCACAGGCTTTACACGCACAAGGTGGACGTTTACAGCTTTGGCATTGTGCTGTGGGAGCTCATCACAGGATTGCTACCGTTCCAGAAC

upper sequence: Vv04s0008g03020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ28993 (Selaginella moellendorffii), 3'ss of exon 1
catgaaacaggaccaccttgtaatttttgttgtagattcttttatatttataagtgattcattggttttgattttttgatgtgcgttacttttcttgcagAGAGATGATCCAGCACAGGCCATACACTCAGAAGGTAGATGTCTACAGCTTTGGAATTGTCCTGTGGGAGCTCATCACAGGCTTGCTTCCCTTCCAGAAC
        | |  ||  |     ||  |  | |      |||  | ||  |     ||   | |  ||  |    |   |   |||| | ||  ||||||||||||||||||||||||||  ||||| || ||||| || || ||||||||||| |||||||||||||||||||||||||| ||||| || |||||||||
------gtaagcgcatttctctcttcgttctcttcgcgttttcgtgttcttcctccatagctagacttcaaagcctcactaaccgtttcattcattgcagAGAGATGATCCAGCACAGGCTTTACACACACAAGGTGGACGTTTACAGCTTTGGCATTGTCCTGTGGGAGCTCATCACAGGATTGCTACCGTTCCAGAAC

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|34362954|gb|CF404539.1|CF404539
EST:     CAAACCGAAGGAATGACACCAGAGACAGGGACGTATCGCTGGATGGCCCC                         AGAGATGATCCAGCACAGGCCATACACTCAGAAGGTAGATGTCTACAGCTT
genomic: CAAACCGAAGGAATGACACCAGAGACAGGGACGTATCGCTGGATGGCCCCgtaagcattt ... tttcttgcagAGAGATGATCCAGCACAGGCCATACACTCAGAAGGTAGATGTCTACAGCTT
EST: gi|37188490|gb|CF607839.1|CF607839
EST:     CAAACCGAAGGAATGACACCAGAGACAGGGACGTATCGCTGGATGGCCCC                         AGAGATGATCCAGCACAGGCCATACACTCAGAAGGTAGATGTCTACAGCTT
genomic: CAAACCGAAGGAATGACACCAGAGACAGGGACGTATCGCTGGATGGCCCCgtaagcattt ... tttcttgcagAGAGATGATCCAGCACAGGCCATACACTCAGAAGGTAGATGTCTACAGCTT
EST: gi|83275443|gb|DV939451.1|DV939451
EST:     CAAACCGAAGGAATGACACCAGAGACAGGGACGTATCGCTGGATGGCCCC                         AGAGATGATCCAGCACAGGCCATACACTCAGAAGGTAGATGTCTACAGCTT
genomic: CAAACCGAAGGAATGACACCAGAGACAGGGACGTATCGCTGGATGGCCCCgtaagcattt ... tttcttgcagAGAGATGATCCAGCACAGGCCATACACTCAGAAGGTAGATGTCTACAGCTT
EST: gi|22011632|gb|BQ796666.1|BQ796666
EST:     CAAACCGAAGGAATGACACCAGAGACAGGGACGTATCGCTGGATGGCCCC                         AGAGATGATCCAGCACAGGCCATACACTCAGAAGGTAGATGTCTACAGCTT
genomic: CAAACCGAAGGAATGACACCAGAGACAGGGACGTATCGCTGGATGGCCCCgtaagcattt ... tttcttgcagAGAGATGATCCAGCACAGGCCATACACTCAGAAGGTAGATGTCTACAGCTT
EST: gi|110383332|gb|EC947698.1|EC947698
EST:     CAAACCGAAGGAATGACACCAGAGACAGGGACGTATCGCTGGATGGCCCC                         AGAGATGATCCAGCACAGGCCATACACTCAGAAGGTAGATGTCTACAGCTT
genomic: CAAACCGAAGGAATGACACCAGAGACAGGGACGTATCGCTGGATGGCCCCgtaagcattt ... tttcttgcagAGAGATGATCCAGCACAGGCCATACACTCAGAAGGTAGATGTCTACAGCTT
EST: gi|26266401|gb|CA817464.1|CA817464
EST:     CAAACCGAAGGAATGACCCCAGAGACAGGGACGTATCGCTGGATGGCCCC                         AGAGATGATCCAGCACAGGCCATACACTCAGAAGGTAGATGTTTACAGCTT
genomic: CAAACCGAAGGAATGACACCAGAGACAGGGACGTATCGCTGGATGGCCCCgtaagcattt ... tttcttgcagAGAGATGATCCAGCACAGGCCATACACTCAGAAGGTAGATGTCTACAGCTT
EST: gi|33406656|gb|CF212283.1|CF212283
EST:     CAAACCGAAGGAATGACACCAGAGACAGGGACGTATCGCTGGATGGCCCC                         AGAGATGATCCAGCACAGGCCATACACTCAGAAGGTAGATGTCTACAGCTT
genomic: CAAACCGAAGGAATGACACCAGAGACAGGGACGTATCGCTGGATGGCCCCgtaagcattt ... tttcttgcagAGAGATGATCCAGCACAGGCCATACACTCAGAAGGTAGATGTCTACAGCTT
EST: gi|34364201|gb|CF405786.1|CF405786
EST:     CAAACCGAAGGAATGACACCAGAGACAGGGACGTATCGCTGGATGGCCCC                         AGAGATGATCCAGCACAGGCCATCCACTCAGAAGGTAGATGTCTACAGCTT
genomic: CAAACCGAAGGAATGACACCAGAGACAGGGACGTATCGCTGGATGGCCCCgtaagcattt ... tttcttgcagAGAGATGATCCAGCACAGGCCATACACTCAGAAGGTAGATGTCTACAGCTT
EST: gi|110718320|gb|EE095017.1|EE095017
EST:     CAAACCGAAGGAATGACACCAGAGACAGGGACATATCGCTGGATGGCCCC                         AGAGATGATCCAGCACAGGCCATACACTC
genomic: CAAACCGAAGGAATGACACCAGAGACAGGGACGTATCGCTGGATGGCCCCgtaagcattt ... tttcttgcagAGAGATGATCCAGCACAGGCCATACACTC
EST: gi|110718934|gb|EE096335.1|EE096335
EST:     CAAACCGAAGGAATGACACCAGAGACAGGGTCGTATCGCTGGATGGCCCC                         AAAGATGATTCAGCACAGGCCATACACTCAGAAAGTAGATGTCTAC
genomic: CAAACCGAAGGAATGACACCAGAGACAGGGACGTATCGCTGGATGGCCCCgtaagcattt ... tttcttgcagAGAGATGATCCAGCACAGGCCATACACTCAGAAGGTAGATGTCTAC
EST: gi|26267451|gb|CA818514.1|CA818514
EST:     CAAACCGAAGGAATGACACCAGAGACAGGGACGTATCGCTGGATGGCCCC                         AGAGATGATCCAGCACAGGCCATACACTCAGAAGGTAGATGTTTACAGCTT
genomic: CAAACCGAAGGAATGACACCAGAGACAGGGACGTATCGCTGGATGGCCCCgtaagcattt ... tttcttgcagAGAGATGATCCAGCACAGGCCATACACTCAGAAGGTAGATGTCTACAGCTT
EST: gi|22015406|gb|BQ800440.1|BQ800440
EST:     CAAACCGAAGGAATGACACCAGAGACAGGGACGTATCGCTGGATGGCCCC                         AGAGATGATCCAGCACAGGCCATACACTCAGAAGGTAGATGTCTACAGCTT
genomic: CAAACCGAAGGAATGACACCAGAGACAGGGACGTATCGCTGGATGGCCCCgtaagcattt ... tttcttgcagAGAGATGATCCAGCACAGGCCATACACTCAGAAGGTAGATGTCTACAGCTT
EST: gi|33406569|gb|CF212196.1|CF212196
EST:     CAAACCGAAGGAATGACACCAGAGACAGGGACGTATCGCTGGATGGCCCC                         AGAGATGATCCAGCACAGGCCATACACTCAGAAGGTAGATGTCTACAGCTT
genomic: CAAACCGAAGGAATGACACCAGAGACAGGGACGTATCGCTGGATGGCCCCgtaagcattt ... tttcttgcagAGAGATGATCCAGCACAGGCCATACACTCAGAAGGTAGATGTCTACAGCTT
EST: gi|110409370|gb|EC975031.1|EC975031
EST:     CAAACCGAAGGAATGACACCAGAGACAGGGACGTATCGCTGGATGGCCCC                         AGAGATGATCCAGCACAGGCCATACACTCAGAAGGTAGATGTCTACAGCTT
genomic: CAAACCGAAGGAATGACACCAGAGACAGGGACGTATCGCTGGATGGCCCCgtaagcattt ... tttcttgcagAGAGATGATCCAGCACAGGCCATACACTCAGAAGGTAGATGTCTACAGCTT
EST: gi|110719491|gb|EE094664.1|EE094664
EST:     CAAACCGA-GGAATGACACCAGAGACAGGGACATATCGCTGGATGGCCC-                         AGAGATGATCCAGCACAAGCCATACACTCAAAAAGTAGATGTCTACAGCTT
genomic: CAAACCGAAGGAATGACACCAGAGACAGGGACGTATCGCTGGATGGCCCCgtaagcattt ... tttcttgcagAGAGATGATCCAGCACAGGCCATACACTCAGAAGGTAGATGTCTACAGCTT
EST: gi|110718315|gb|EE095004.1|EE095004
EST:     CAAACCGAAGGAATGACACCAGAGACAGGGACATATCGCTGGATGGCCCC                         ANAGATGATCCCGCACAAGCCATACACTCCAAAAG-TAAATGTCTACAGCT
genomic: CAAACCGAAGGAATGACACCAGAGACAGGGACGTATCGCTGGATGGCCCCgtaagcattt ... tttcttgcagAGAGATGATCCAGCACAGGCCATACACTC-AGAAGGTAGATGTCTACAGCT
EST: gi|110392535|gb|EC958023.1|EC958023
EST:     CAAACCGAAGGAATGACACCAGAGACAGGGACGTATCGCTGGATGGCCCC                         AGAGATGATCCAGCACAGGCCATACACTCAGAAGGTAGATGTCTACAGCTT
genomic: CAAACCGAAGGAATGACACCAGAGACAGGGACGTATCGCTGGATGGCCCCgtaagcattt ... tttcttgcagAGAGATGATCCAGCACAGGCCATACACTCAGAAGGTAGATGTCTACAGCTT
EST: gi|110720113|gb|EE095761.1|EE095761
EST:     CAAACCGAAGGGATGACACCAGAAACAGGGACGTATCGCTGGATGGCCCC                         AGAGAAGATCCAGCACAGGCCATACACTCGGAAGGTAGATGTCTACGGCTT
genomic: CAAACCGAAGGAATGACACCAGAGACAGGGACGTATCGCTGGATGGCCCCgtaagcattt ... tttcttgcagAGAGATGATCCAGCACAGGCCATACACTCAGAAGGTAGATGTCTACAGCTT
EST: gi|110719557|gb|EE094787.1|EE094787
EST:     CAAACCGAAGGAATGACACCAGAGACAGGGACATATCGCTGGATGGCCCC                         AAAGATGATCCAGCACANGCCATACACTCAAAAGGTAAATGT
genomic: CAAACCGAAGGAATGACACCAGAGACAGGGACGTATCGCTGGATGGCCCCgtaagcattt ... tttcttgcagAGAGATGATCCAGCACAGGCCATACACTCAGAAGGTAGATGT
EST: gi|22011570|gb|BQ796604.1|BQ796604
EST:     CAAACCGAAGGAATGACACCAGAGACAGGGACGTATCGCTGGATGGCCCC                         AGAGATGATCCAGCACAGGCCATACACTCAGAAGGTAGATGTCTACAGCTT
genomic: CAAACCGAAGGAATGACACCAGAGACAGGGACGTATCGCTGGATGGCCCCgtaagcattt ... tttcttgcagAGAGATGATCCAGCACAGGCCATACACTCAGAAGGTAGATGTCTACAGCTT
EST: gi|26265916|gb|CA816979.1|CA816979
EST:     CAAACCGAAGGAATGACACCAGAGACAGGGACGTATCGCTGGATGGCCCC                         AGAGATGATCCAGCACAGGCCATACACTCAGAAGGTAGATGTCTACAGCTT
genomic: CAAACCGAAGGAATGACACCAGAGACAGGGACGTATCGCTGGATGGCCCCgtaagcattt ... tttcttgcagAGAGATGATCCAGCACAGGCCATACACTCAGAAGGTAGATGTCTACAGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttataagtgattcattggttttgattttttgatgtgcgttacttttcttgcagAGAGATGATCCAGCACAGGCCATACACTCAGAAGGTAGATGTCTACAGCTTTGGAATTGTCCTGTGGGAGCTCATCACAGGCTTGCTTCCCTTCCAGAAC
                            ttttgat  putative branch site (score: 4)
                                        ttacttttctt  putative PPT
                    ttttgattttttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catgaaacaggaccaccttgtaatttttgttgtagattcttttatatttataagtgattcattggttttgattttttgatgtgcgttacttttcttgcagAGAGATGATCCAGCACAGGCCATACACTCAGAAGGTAGATGTCTACAGCTTTGGAATTGTCCTGTGGGAGCTCATCACAGGCTTGCTTCCCTTCCAGAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- -gaaacag
- - - - - - ccacctt