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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcttctcctgtagtttgtgtttgttatgagaatgatcttatatggaagtggtggaaaaatagaataaatgatggagaattgatggtggttgaattgcagGGGAGTTGAAGAAGATGTTGTCAGGGCCAACAGGGCTTCACCACCAAGACCAGAAGCTGTTGTTCAAGGACAAGGAGAGGGACTCCAATGCCTACCTTGA

Basic information

species Vitis vinifera
transcript Vv16s0100g00470.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0100g00470.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os06g03640.1 (Oryza sativa), 3'ss of exon 1
gtcttctcctgtagtttgtgtttgttatgagaatgatcttatatggaagtggtggaaaaatagaataaatgatgga---gaattgatggtggttgaattgcagGGGAGTTGAAGAAGATGTTGTCAGGGCCAACAGGGCTTCACCACCAAGACCAGAAGCTGTTGTTCAAGGACAAGGAGAGGGACTCCAATGCCTACCTTGA
             ||  |||   |         |  || |    |     || | |      | ||    |        || ||  | |||| ||   |||||||||| ||||||||||| || | | || ||| ||||| || |   | ||||||||| || ||| |||||||||||||||||||||||| || | ||| ||
-------------gtcagtgcccgccgccgccgtcgtcgtcgtcgtcgacggcgaactcgatggatgggggccatgtctgatttcgttgtgggtgg--tgcagGGGAGCTGAAGAAGATGGTGGCGGCGCGAACGGGGCTGCATCCGGACGACCAGAAGGTGATGTACAAGGACAAGGAGAGGGACTCCAAGGCGTTCCTGGA

upper sequence: Vv16s0100g00470.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G017013_T01 (Zea mays), 3'ss of exon 1
gtcttctcctgtagtttgtgtttgttatgagaatgatcttatatggaagtggtggaaaaatagaataaatgatggagaattgatggtggttgaattgcagGGGAGTTGAAGAAGATGTTGTCAGGGCCAACAGGGCTTCACCACCAAGACCAGAAGCTGTTGTTCAAGGACAAGGAGAGGGACTCCAATGCCTACCTTGA
    |      || |       |   |    | |||  ||   ||| | |      |        | |  ||  ||     |  || | |     |||||| ||| ||||||||||| |||| | ||  || ||||| |||| | | |||||||||||| ||| ||||||||||||| |||||||||| || | ||| ||
---gtaagtaatactaataccatagcacaccagtgagattcc-tggcaattccacgagctgcttctgaccga--gatgggcgcgggcgatgctcctgcagGTGAGCTGAAGAAGATGCTGTCGGCGCGGACCGGGCTGCACCCCGAGGACCAGAAGCTGGTGTACAAGGACAAGGAGCGGGACTCCAAGGCGTTCCTGGA

upper sequence: Vv16s0100g00470.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G120305_T01 (Zea mays), 3'ss of exon 1
-----gtcttctcctgtagtttgtgtttgttatgag-aatgatcttatatggaagtggtgg----aaaaatagaataaatgatggagaattgatggtggttgaattgcagGGGAGTTGAAGAAGATGTTGTCAGGGCCAACAGGGCTTCACCACCAAGACCAGAAGCTGTTGTTCAAGGACAAGGAGAGGGACTCCAATGCCTACCTTGA
       |    || | ||  ||     ||   |      ||||  |   |    |  ||          |     | |||  || |    | |  |  |     |||||| ||| ||||||||||| |||| | ||  || ||||| |||| | | |||||||||||| | | ||||||||||||| |||||||||| || | ||| ||
gtaaatacagtaccagcagaatgcaccggtcccgtccggcgatcccacgagctgctcctgttcctgcttctgaccgagatggcggtgg--cgctcctcctcatcctgcagGTGAGCTGAAGAAGATGCTGTCGGTGCGGACGGGGCTGCACCCCGAGGACCAGAAGCTGGTATACAAGGACAAGGAGCGGGACTCCAAGGCGTTCCTGGA

upper sequence: Vv16s0100g00470.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G157481_T01 (Zea mays), 3'ss of exon 1
-----------gtcttctcctgtagtttgtgtttgt-tatgagaatgatcttatatggaagtggtggaaaaata--gaataaatgatggagaat-tgatggtggttgaattgcagGGGAGTTGAAGAAGATGTTGTCAGGGCCAACAGGGCTTCACCACCAAGACCAGAAGCTGTTGTTCAAGGACAAGGAGAGGGACTCCAATGCCTACCTTGA
           | |     |   | | | | | | | |||     |     | |||  |  |    || | |||  ||||  |    ||   || | |||   |    |  ||||| ||| |||||||| || |||| | |   || || || ||||   | ||||||||| || ||| |||||||||||||||||||||||| || | ||| ||
gtaatgccgccgccgctggcgccactatctatctatctatctatctatctatctatctatctacgcgatacatactgaatggagagcgggtgatgtcatgaacgaacgaacgcagGCGAGCTGAAGAAGCTGGTGTCGGAGAAGACGGGCCTGCACCCGGACGACCAGAAGGTGGTGTACAAGGACAAGGAGAGGGACTCCAAGGCGTTCCTGGA

upper sequence: Vv16s0100g00470.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G011281_T01 (Zea mays), 3'ss of exon 1
gtcttctcctgtagtttgtgtttgttatgagaatgatcttatatggaagtggtggaaaaatagaataaatgatggagaattgatggtggttgaattgcagGGGAGTTGAAGAAGATGTTGTCAGGGCCAACAGGGCTTCACCACCAAGACCAGAAGCTGTTGTTCAAGGACAAGGAGAGGGACTCCAATGCCTACCTTGA
      | | ||||     |  ||    |     |    |     ||  || |         ||   |  ||||| ||  || || |  |     |||||| ||| ||||||||||| |||| | |   || ||||| |||| | | |||||||||||| ||| ||||||||||||| |||||||||| || | ||| ||
-gtaaatacagtagcagcagaatgcaccggtcccggcgatcccacgagctgctcctgcttctgaccga--gatggcga--tggtgctcctcatcctgcagGTGAGCTGAAGAAGATGCTGTCGGCGAGGACGGGGCTGCACCCCGAGGACCAGAAGCTGGTGTACAAGGACAAGGAGCGGGACTCCAAGGCGTTCCTGGA

upper sequence: Vv16s0100g00470.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G035170_T01 (Zea mays), 3'ss of exon 1
-----gtcttctcctgtagtttgtgtttgttatgag-aatgatcttatatggaagtggtggaaaaatagaataaatgatggagaattgatggtggttgaattgcagGGGAGTTGAAGAAGATGTTGTCAGGGCCAACAGGGCTTCACCACCAAGACCAGAAGCTGTTGTTCAAGGACAAGGAGAGGGACTCCAATGCCTACCTTGA
       |    || | ||  ||     ||   |      ||||  |   |    |  ||      |     | |||  || |   || || |  |     |||||| ||| ||||||||||| |||| | ||  || ||||| ||||   | |||||||||||| ||| ||||||||||||| |||||||||| || | ||| ||
gtaaatacagtaccagcagaatgcaccggtcccggccggcgatcccacgagctgctcctgcttc--tgaccgagatggcggtgg--tggtgctcctcatcctgcagGTGAGCTGAAGAAGATGCTGTCGGCGCGGACGGGGCTGCACCCGGAGGACCAGAAGCTGGTGTACAAGGACAAGGAGCGGGACTCCAAGGCGTTCCTGGA

upper sequence: Vv16s0100g00470.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA16G32290.1 (Glycine max), 3'ss of exon 1
--gtcttctcctgtagtttgtgtttgttatgagaatgatcttatatggaagtggtggaaaaatagaataaatgatggagaattgatggtggttgaattgcagGGGAGTTGAAGAAGATGTTGTCAGGGCCAACAGGGCTTCACCACCAAGACCAGAAGCTGTTGTTCAAGGACAAGGAGAGGGACTCCAATGCCTACCTTGA
       |    | | |    |     | |   | |  | |  | |     |  |||  |  | |  ||     |      || ||  |  | |  ||||||||||||||||||| ||| |||| |||||||| ||| | |||||  |||| || |||||||| | ||| |||||||||||||| || || || |  |||||
acaataccaaaagcactcaaggaactgtgtctaagttttgtcctttcttgtttttggttatgtcggttattgtgtatgtgtttaat--ttctggggttgcagGGGAGTTGAAGAAAATGCTGTCTGGGCCAACTGGGTTACACCATGAAGATCAAAAGCTGTTATACAAAGACAAGGAGAGGGATTCAAAGGCTTTTCTTGA

upper sequence: Vv16s0100g00470.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA09G27070.1 (Glycine max), 3'ss of exon 1
gtcttctcctgtagtttgtgtttgt-tatgagaatgatcttatatggaagtggtggaaaaatagaataaatgatgg--agaattgatggtggttgaattgcagGGGAGTTGAAGAAGATGTTGTCAGGGCCAACAGGGCTTCACCACCAAGACCAGAAGCTGTTGTTCAAGGACAAGGAGAGGGACTCCAATGCCTACCTTGA
    |     | |     |   ||| | | ||  |  || | | |    ||  |||  | || || ||     ||     | ||     |  | |  |||||||||||||||| || ||| |||| |||||||| ||| | |||||  ||||||| |||||||| | ||| |||||||||||||| || || || |  |||||
---attaaaagcaaacaataactgtatctaagttttgtccttttttattgttttggttacattgattattgtgtgttttaacttttaactactggggttgcagGGGAGTTGAAAAAAATGCTGTCTGGGCCAACTGGGTTACACCATGAAGACCAAAAGCTGTTTTACAAAGACAAGGAGAGGGATTCAAAGGCTTTTCTTGA

upper sequence: Vv16s0100g00470.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA09G27100.1 (Glycine max), 3'ss of exon 1
---gtcttctcctgtagtttgtgtttgttatgagaatgatcttatatggaagtggtggaaaaatagaataaatgatggagaattgatggtggttgaattgcagGGGAGTTGAAGAAGATGTTGTCAGGGCCAACAGGGCTTCACCACCAAGACCAGAAGCTGTTGTTCAAGGACAAGGAGAGGGACTCCAATGCCTACCTTGA
        |      | |    |     | | ||  |  || | | | |   | ||   |      | |   || ||    ||| ||  |  | || ||||||||||||||||||| ||| ||||||||| ||| ||  | |||||  ||||||| |||||||| | ||| |||||||||||||| || || || |  |||||
aacaataccaaaaacactcaaagaactgtctaagttttgtcctttcttgttttcgttatatcggttattgtgtg-tgtgtgattaat--ttctggagttgcagGGGAGTTGAAGAAAATGCTGTCAGGGCTAACTGGTTTACACCATGAAGACCAAAAGCTGTTTTACAAAGACAAGGAGAGGGATTCAAAGGCTTTTCTTGA

upper sequence: Vv16s0100g00470.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA16G32280.1 (Glycine max), 3'ss of exon 1
----gtcttctcctgtagtttgtgtttgttatgagaatgatcttatatggaagtggtggaaaaatagaataaatgatggagaattgatggtggttgaattgcagGGGAGTTGAAGAAGATGTTGTCAGGGCCAACAGGGCTTCACCACCAAGACCAGAAGCTGTTGTTCAAGGACAAGGAGAGGGACTCCAATGCCTACCTTGA
      | |     | | | | |    ||| ||    |  |  | | |||      |||  |    |  |  ||| ||     || ||  |  | |  ||| ||||||||||||||| ||| |||| |||||||| ||| | |||||  |||| || |||||||| | ||| |||||||||||||| || || || |  |||||
caaaagcattcaaggaactgtatccaagttttgtccttttttgttt-tggttacattggttattgtgtgtttatg-tgtgtgtttaat--ttctggggttggagGGGAGTTGAAGAAAATGCTGTCTGGGCCAACTGGGTTACACCATGAAGATCAAAAGCTGTTATACAAAGACAAGGAGAGGGATTCAAAGGCTTTTCTTGA

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|349807921|gb|FQ402312.1|FQ402312
EST:     ATTCGGCTCCATCTATCACGAAATCTATATCAGTTCTCAAGCCACCTTCG                         GGGAGTTGAAGAAGATGTTGTCAGGGCCAACAGGGCTTCCCCACCA
genomic: ATTCGGCTCCATCTATCACGAAATCTATATCAGTTCTCAAGCCACCTTCGgtaattcttt ... tgaattgcagGGGAGTTGAAGAAGATGTTGTCAGGGCCAACAGGGCTTCACCACCA
EST: gi|161721184|gb|FC071041.1|FC071041
EST:     ATTCGGCTCCATCTATCACGAAATCTATATCAGTTCTCAAGCCACCTTCG                         GGGAGTTGAAGAAGATGTTGTCAGGGCCAACAGGGCTTCACCACCAAGACC
genomic: ATTCGGCTCCATCTATCACGAAATCTATATCAGTTCTCAAGCCACCTTCGgtaattcttt ... tgaattgcagGGGAGTTGAAGAAGATGTTGTCAGGGCCAACAGGGCTTCACCACCAAGACC
EST: gi|161715572|gb|FC069476.1|FC069476
EST:     ATTCGGCTCCATCTATCACGAAATCTATATCATTTCTCAAGCCACCTTCG                         GGGAGTTGAAGAAGATGTTGTCAGGGCCAACAGGGCTTCACCACCAAGACC
genomic: ATTCGGCTCCATCTATCACGAAATCTATATCAGTTCTCAAGCCACCTTCGgtaattcttt ... tgaattgcagGGGAGTTGAAGAAGATGTTGTCAGGGCCAACAGGGCTTCACCACCAAGACC
EST: gi|349831021|gb|FQ418305.1|FQ418305
EST:     ATTCGGCTCCATCTATCACGAAATCTATATCAGTTCTCAAGCCACCTTCG                         GGGAGTTGAAGAAGATGTTGTCAGGGCCAACAGGGCTTCAC-ACCAAGACC
genomic: ATTCGGCTCCATCTATCACGAAATCTATATCAGTTCTCAAGCCACCTTCGgtaattcttt ... tgaattgcagGGGAGTTGAAGAAGATGTTGTCAGGGCCAACAGGGCTTCACCACCAAGACC
EST: gi|37187703|gb|CF607056.1|CF607056
EST:     ATTCGGCTCCATCTATCACGAAATCTATATCAGTTCTCAAGCCACCTTCG                         GGGAGTTGAAGAAGATGTTGTCAGGGCCAACAGGGCTTCACCACCAAGACC
genomic: ATTCGGCTCCATCTATCACGAAATCTATATCAGTTCTCAAGCCACCTTCGgtaattcttt ... tgaattgcagGGGAGTTGAAGAAGATGTTGTCAGGGCCAACAGGGCTTCACCACCAAGACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagtggtggaaaaatagaataaatgatggagaattgatggtggttgaattgcagGGGAGTTGAAGAAGATGTTGTCAGGGCCAACAGGGCTTCACCACCAAGACCAGAAGCTGTTGTTCAAGGACAAGGAGAGGGACTCCAATGCCTACCTTGA
                                aattgat  putative branch site (score: 4)
          aaaaatagaataaatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcttctcctgtagtttgtgtttgttatgagaatgatcttatatggaagtggtggaaaaatagaataaatgatggagaattgatggtggttgaattgcagGGGAGTTGAAGAAGATGTTGTCAGGGCCAACAGGGCTTCACCACCAAGACCAGAAGCTGTTGTTCAAGGACAAGGAGAGGGACTCCAATGCCTACCTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- cttctcc
- - - - - - - - - - - - - - gagaatg
- - - - - - - - - - - - - - - - - - - - - - - - gtggtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatggtg