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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgttaaatgtgatactagtggcagaggcatgtcatggggaaaaaaatctccattaaactaaggaacaaaacttacttttatttgctttctctcatgcagGGAAGTGCAAAGAGGCTGGTGAAAGCTGCTTTACAAGAAGCAGCAAAAAAGAGAGAAATGAGGTATTCAGACCTGAAGAAGATTGACCGAGGGGTTCGTC

Basic information

species Vitis vinifera
transcript Vv03s0038g02650.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g02650.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os06g50380.1 (Oryza sativa), 3'ss of exon 5
ctgttaaatgtgatactagtggcagaggcatgtcatggggaaaa-aaatctccattaaactaaggaacaaaacttacttttatttgctttctc-tcatgcagGGAAGTGCAAAGAGGCTGGTGAAAGCTGCTTTACAAGAAGCAGCAAAAAAGAGAGAAATGAGGTATTCAGACCTGAAGAAGATTGACCGAGGGGTTCGTC
    | | ||  |  | |   |||     |    ||||  |    || | |  |||     |||  | | ||  |  |  | | |||| | |  || | ||||||||||| | ||||||  | || || ||||| ||||||||||| || || |||||||||||||| ||||| || |||||||||||||| || ||||| |
gccctcagtggaaggcaacatgcatgaaaacaaaatggacacgctaagtgttgattgtg--aagtgaaagaatctgatgatttgtgctctttgatctttcagGGAAGTGCTAGGAGGCTCATAAAGGCAGCTTTGCAAGAAGCAGCCAAGAAAAGAGAAATGAGGTACTCAGATCTCAAGAAGATTGACCGTGGTGTTCGCC

upper sequence: Vv03s0038g02650.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G151254_T02 (Zea mays), 3'ss of exon 4
ctgttaaatgtgatactagtggcaga---ggcatgtcatggggaaaaaaatctccattaaactaaggaacaaaacttacttttatttgctttctctcatgcagGGAAGTGCAAAGAGGCTGGTGAAAGCTGCTTTACAAGAAGCAGCAAAAAAGAGAGAAATGAGGTATTCAGACCTGAAGAAGATTGACCGAGGGGTTCGTC
   |||||    |||  ||   || |   |  || || |  |   |    |    | |||    ||   | ||   | |   | | || ||  |||  |||||||  |||| | ||||||| | | ||| ||  | ||||| ||||| || || ||||| |||||||| || ||||| |||||||||||||| || ||||| |
-gtttaaacaaaatagaaggaacaaatatgaaatatcttctgtttagtgctaagtactaactgcagcgcctaatgctgcacatctctgtttgatct--tgcagGGCTGTGCTAGGAGGCTGATAAGAGCGGCACTGCAAGAGGCAGCCAAGAAAAGAGAGATGAGGTACTCGGACCTCAAGAAGATTGACCGCGGTGTTCGCC

upper sequence: Vv03s0038g02650.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G42910.1 (Glycine max), 3'ss of exon 4
ctgttaaatgtgatactagtggcagaggcatgtcatggggaaaaaaatctccattaaactaaggaac----------aaaacttact--tttatttgctttctctcatgcagGGAAGTGCAAAGAGGCTGGTGAAAGCTGCTTTACAAGAAGCAGCAAAAAAGAGAGAAATGAGGTATTCAGACCTGAAGAAGATTGACCGAGGGGTTCGTC
             |  |    | |||    |||  |||   | |||  || |  |  | |  | |||              |||  |  || || | |||||  || | |||||||| || | ||||||||| ||||||||  | |||||||| ||||| |||||||||||||| ||||||||  | ||||| ||||| || || |||||||
------------gttttgcatggagaaatttgttctggaatataaagccttcccttgatttggaaacctcttgttcagtggcttcatgtttcatcttctttccttctttcagGGAAGCGCTAGGAGGCTGGTAAAAGCTGCGCTTCAAGAAGCTGCAAAGAAGAGAGAAATGAGATATTCAGATTTAAAGAAAATTGATCGCGGAGTTCGTC

upper sequence: Vv03s0038g02650.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA20G24100.1 (Glycine max), 3'ss of exon 4
ctgttaaatgtgatactagtggcagaggcatgtcatggggaaaaaaatctccatt----aaactaaggaacaaaacttac-ttttatttgctttctctcatgcagGGAAGTGCAAAGAGGCTGGTGAAAGCTGCTTTACAAGAAGCAGCAAAAAAGAGAGAAATGAGGTATTCAGACCTGAAGAAGATTGACCGAGGGGTTCGTC
     |||       || | |   ||    | |        ||| |||||   ||     ||||  |  |    | | |  ||| || | || ||  || | |||||||| || | ||||||||| ||||||||  | |||||||| ||||| |||||||||||||| ||||||||  | ||||| ||||| || || |||||||
-----aaagccttcccttgagttggataactcttgcaaaacaaataatctgtttttggagaactctgtcagtggattcatgtttcatcttctatccttctttcagGGAAGCGCTAGGAGGCTGGTAAAAGCTGCGCTTCAAGAAGCTGCAAAGAAGAGAGAAATGAGATATTCAGATTTAAAGAAAATTGATCGCGGAGTTCGTC

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|83274406|gb|DV938503.1|DV938503
EST:     TCAGGA-GCAGTAGATA-TGTTCAAAG-CACCCTCGCAAT                         GGAAG-GCAAAGAGGCTGGTGAAAGCTGCTTTAC-AGAAGCAGCAAAAAAG
genomic: TCAGGAGGCAGTAGATATTGTTCAAAGTCACCCTCGCAATgtaagtcaac ... tctcatgcagGGAAGTGCAAAGAGGCTGGTGAAAGCTGCTTTACAAGAAGCAGCAAAAAAG
EST: gi|110422080|gb|EC988392.1|EC988392
EST:     ACCTTAGCAATCAGGAGGCAGTAGATATTGTTCAAAGTCACCCTCGCAAT                         GGAAGTGCAAAGAGGCTGGTGAAAGCTGCTTTACAAGAAGCAGCAAAAAAG
genomic: ACCTTAGCAATCAGGAGGCAGTAGATATTGTTCAAAGTCACCCTCGCAATgtaagtcaac ... tctcatgcagGGAAGTGCAAAGAGGCTGGTGAAAGCTGCTTTACAAGAAGCAGCAAAAAAG
EST: gi|34362373|gb|CF403958.1|CF403958
EST:     GTAGATATTGTTCAAAGTCACCCTCGCAAT                         GGAAGTGCAAAGAGGCTGGTGAAAGCTGCTTTACAAGAAGCAGCAAAAAAG
genomic: GTAGATATTGTTCAAAGTCACCCTCGCAATgtaagtcaac ... tctcatgcagGGAAGTGCAAAGAGGCTGGTGAAAGCTGCTTTACAAGAAGCAGCAAAAAAG
EST: gi|110375806|gb|EC940825.1|EC940825
EST:     ACCTTAGCAATCAGGAGGCAGTAGATATTGTTCAAAGTCACCCTCGCAAT                         GGAAGTGCAAAGAGGCTGGTGAAAGCTGCTTTACAAGAAGCAGCAAAAAAG
genomic: ACCTTAGCAATCAGGAGGCAGTAGATATTGTTCAAAGTCACCCTCGCAATgtaagtcaac ... tctcatgcagGGAAGTGCAAAGAGGCTGGTGAAAGCTGCTTTACAAGAAGCAGCAAAAAAG
EST: gi|110684850|gb|EE062597.1|EE062597
EST:     CTTTAACAACC-GGAGGCAGTAGATATTGTTTCAA-GTCACCCTCCCAAT                         GGAAGTGCTAAGAGGCTGGTGAAA
genomic: CTT-AGCAATCAGGAGGCAGTAGATATTGTT-CAAAGTCACCCTCGCAATgtaagtcaac ... tctcatgcagGGAAGTGCAAAGAGGCTGGTGAAA
EST: gi|45770466|gb|CN006318.1|CN006318
EST:     ACCTTAGCAATCAGGAGGCAGTAGATATTGTTCAAAGTCACCCTCGCAAT                         GGAAGTGCAAAGAGGCTGGTGAAAGCTGCTTTACAAGAAGCAGCNNNNNNN
genomic: ACCTTAGCAATCAGGAGGCAGTAGATATTGTTCAAAGTCACCCTCGCAATgtaagtcaac ... tctcatgcagGGAAGTGCAAAGAGGCTGGTGAAAGCTGCTTTACAAGAAGCAGC-AAAAAA
EST: gi|110358630|gb|EC922982.1|EC922982
EST:     ACCTTAGCAATCAGGAGGCAGTAGATATTGTTCAAAGTCACCCTCGCAAT                         GGAAGTGCAAAGAGGCTGGTGAAAGCTGCTTTACAAGAAGCAGCAAAAAAG
genomic: ACCTTAGCAATCAGGAGGCAGTAGATATTGTTCAAAGTCACCCTCGCAATgtaagtcaac ... tctcatgcagGGAAGTGCAAAGAGGCTGGTGAAAGCTGCTTTACAAGAAGCAGCAAAAAAG
EST: gi|110699642|gb|EE076817.1|EE076817
EST:     ACCTTAGCAATCAGGAGGCAGTAGATATTGTTCAAAGTCACCCTCGCAAT                         GGAAGTGCAAAGAGGCTGGTGAAAGCTGCTTTACAAGAAGCAGCNNNNNNN
genomic: ACCTTAGCAATCAGGAGGCAGTAGATATTGTTCAAAGTCACCCTCGCAATgtaagtcaac ... tctcatgcagGGAAGTGCAAAGAGGCTGGTGAAAGCTGCTTTACAAGAAGCAGCAAAAAA-
EST: gi|110358373|gb|EC922535.1|EC922535
EST:     ACCTTAGCAATCAGGAGGCAGTAGATATTGTTCAAAGTCACCCTCGCAAT                         GGAAGTGCAAAGAGGCTGGTGAAAGCTGCTTTACAAGAAGCAGCAAAAAAG
genomic: ACCTTAGCAATCAGGAGGCAGTAGATATTGTTCAAAGTCACCCTCGCAATgtaagtcaac ... tctcatgcagGGAAGTGCAAAGAGGCTGGTGAAAGCTGCTTTACAAGAAGCAGCAAAAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatctccattaaactaaggaacaaaacttacttttatttgctttctctcatgcagGGAAGTGCAAAGAGGCTGGTGAAAGCTGCTTTACAAGAAGCAGCAAAAAAGAGAGAAATGAGGTATTCAGACCTGAAGAAGATTGACCGAGGGGTTCGTC
                        aacttac  putative branch site (score: 2)
                          cttacttttatttgct  CT-rich tract
                      aaaacttacttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgttaaatgtgatactagtggcagaggcatgtcatggggaaaaaaatctccattaaactaaggaacaaaacttacttttatttgctttctctcatgcagGGAAGTGCAAAGAGGCTGGTGAAAGCTGCTTTACAAGAAGCAGCAAAAAAGAGAGAAATGAGGTATTCAGACCTGAAGAAGATTGACCGAGGGGTTCGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - -gcatgtc
- - - - - - - - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - -tctccat
- - - - - - - - - - - - - - - - - - - - - - - - - - - -aaactaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacaaaa