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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaatagcaaatgtgtttcccttctttttttttttttaggcttgccggatcagcctctaatctgctttccttctcagGCTTTTCTGTTCAATGCTTTGTTCTGACCCTAAGCTGGATTCACACCGATTCAAGGATATTCTTGATGAGGCAATATCAGCAG

Basic information

species Vitis vinifera
transcript Vv08s0007g07960.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g07960.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G090689_T01 (Zea mays), 3'ss of exon 3
---------------------------------------------------gtacaatagcaaatgtgtttcccttctttttttttttttaggcttgccggatcagcctctaatctgctttccttctcagGCTTTTCTGTTCAATGCTTTGTTCTGACCCTAAGCTGGATTCACACCGATTCAAGGATATTCTTGATGAGGCAATATCAGCAG
                                                     | | |   |  |||       | |    |  || |||    || |   ||  || |    | | |  | ||  |||||||||||||  ||||| |||| || || || ||||| ||||| ||||| |||||||||||  |||||||||| ||    | ||
gtgatttctttgaattttaatttccttttatgcttgttcaaacctttatcctgaaagtgaaagctgtaaactggtccaacatgcttgttttaattt-ctatattggcat----tgttcccttctattcagGCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTTCAAGGATATAATTGATGAGGCGATTGGTGAAG

upper sequence: Vv08s0007g07960.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G006753_T01 (Zea mays), 3'ss of exon 3
---------------------------------------------gtacaatagcaaatgtgtttcccttctttttttttttttaggcttgccggatcagcctctaatctgctttccttctcagGCTTTTCTGTTCAATGCTTTGTTCTGACCCTAAGCTGGATTCACACCGATTCAAGGATATTCTTGATGAGGCAATATCAGCAG
                                              ||   |   |  |||       | |       || |||    || |   ||  || |    | | |  | ||  |||||||||||||  ||||| |||| || || || ||||| ||||| ||||| |||||||||||  |||||||||| ||    | ||
gtgatttctttgaattttaatttccttttatgcttgttcaaacctttatcctgaaagctgtaaactggtccaacaggcttgttttaattt-ctatattggcat----tgttcccttctattcagGCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTTCAAGGATATAATTGATGAGGCGATTGGTGAAG

upper sequence: Vv08s0007g07960.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA19G32480.1 (Glycine max), 3'ss of exon 5
-----gtacaatagcaaatgtgtttcccttctttttttttttttaggcttgccggatcagcctcta-atctgctttccttctcagGCTTTTCTGTTCAATGCTTTGTTCTGACCCTAAGCTGGATTCACACCGATTCAAGGATATTCTTGATGAGGCAATATCAGCAG
       |  || |  ||| ||     |   |      | ||| |         | |     ||   |  |   | ||||  ||||||||| ||||||||||||||||| || ||||| || |||||||||||||||||||||||||| |||||||| ||| |  |||
gtaagaaagcattgtgaatttgagatgcgcatgagccgtatttgaaaaggttgagcttgatatcaggagttatctccctttgcagGCTTTTTTGTTCAATGCTTTGTTCAGATCCTAAACTTGATTCACACCGATTCAAGGATATTCTCGATGAGGCTATAGCTTCAG

upper sequence: Vv08s0007g07960.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA10G12350.1 (Glycine max), 3'ss of exon 5
gtacaatagcaaatgtgtttcccttctttttttttttttaggcttgccggatcagcctctaatctgctttccttctcagGCTTTTCTGTTCAATGCTTTGTTCTGACCCTAAGCTGGATTCACACCGATTCAAGGATATTCTTGATGAGGCAATATCAGCAG
||| ||         ||        | |||| ||   | | |  |  | | |     || | |   ||| ||||  |||||| |||||||||||||||||||| || ||||| || || ||||||||||||||||||||| |||||||||  ||| | || |
gtaaaaacattgtgatgaggaagaaccttttgttggataaagaatttcagtttgatatcgagta-acttccctttgcagGCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCACACCGATTCAAGGATATTATTGATGAGGTTATAGCTGCTG

upper sequence: Vv08s0007g07960.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA02G31080.1 (Glycine max), 3'ss of exon 5
gtacaatagcaaatgtgtttcccttctttttttttttttaggcttgccggatcagcctctaatctgctttccttctcagGCTTTTCTGTTCAATGCTTTGTTCTGACCCTAAGCTGGATTCACACCGATTCAAGGATATTCTTGATGAGGCAATATCAGCAG
      ||  ||   |||              |||| || |   | | | ||     | | || |   | ||||  |||||| |||||||||||||||||||| || ||||| || || || |||||||||||||||||| |||||||||  ||| | || |
-----gtaaaaacattgtgatgaggaagaaccttttattgga--tacagaatttcagtttgatat---tccctttgcagGCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCTCACCGATTCAAGGATATTATTGATGAGGTTATAGCTGCTG

upper sequence: Vv08s0007g07960.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G06910.1 (Arabidopsis thaliana), 3'ss of exon 5
gtacaatagcaaatgtgtttcccttctttttttttttttaggcttgccggatcagcctctaatctgctttccttctcagGCTTTTCTGTTCAATGCTTTGTTCTGACCCTAAGCTGGATTCACACCGATTCAAGGATATTCTTGATGAGGCAATATCAGCAG
        | || |     ||| |||||||   | || | |   |   |  |     | ||      ||| |||| |||||| ||||| ||||||||||| || ||||| ||||| ||||||||||| ||||| || || ||||||||||| ||  ||||||
--------gtaattcatcatcctttcttttcgatattgttgaggttgtgagttgatttatatatatattttcttcccagGCTATTCTGCTCAATGCTTTGCTCGGACCCCAAGCTTGATTCACACCGTTTCAAAGACATGCTTGATGAGGCCATTGCAGCAG

upper sequence: Vv08s0007g07960.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT3G12170.1 (Arabidopsis thaliana), 3'ss of exon 5
gta--caatagcaaatgtgtttcccttctttttttttttttaggcttg---ccggatcagcct--ctaatctgctttccttctcagGCTTTTCTGTTCAATGCTTTGTTCTGACCCTAAGCTGGATTCACACCGATTCAAGGATATTCTTGATGAGGCAATATCAGCAG
|||   |||        ||||| | || || |    ||| |  | |       | || | | |   |  |    | ||  | ||||||||||||| ||||||||||| ||  |||| ||||| ||||| ||||| ||||| |||||| | |||||||| ||  |||| |
gtaattaatcatccccttgttttcattattgtcaagtttgtgagttgaagtttgtataaacattattggtactatatctctttcagGCTTTTCTGCTCAATGCTTTGCTCGAACCCCAAGCTTGATTCGCACCGTTTCAAAGATATTATCGATGAGGCCATTGCAGCGG

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|30297265|gb|CB974059.1|CB974059
EST:     AAGAATGATTTGATTGACCTGTACAAAAAGTGCAAGGGTAATATGAACAG                         GCTTTTCTGTTCAATGCTTTGTTCTGACCCTAAGCTGGATTCACCCCGATT
genomic: AAGAATGATTTGATTGACCTGTACAAAAAGTGCAAGGGTAATATGAACAGgtacaatagc ... tccttctcagGCTTTTCTGTTCAATGCTTTGTTCTGACCCTAAGCTGGATTCACACCGATT
EST: gi|351015510|gb|FQ447339.1|FQ447339
EST:     AAGAATGATTTGATTGACCTGTACAAAAAGTGCAAGGGTAATATGAACAG                         GCTTTTCTGTTCAATGCTTTGTTCTGACCCTAAGCTGGATTCACACCGATT
genomic: AAGAATGATTTGATTGACCTGTACAAAAAGTGCAAGGGTAATATGAACAGgtacaatagc ... tccttctcagGCTTTTCTGTTCAATGCTTTGTTCTGACCCTAAGCTGGATTCACACCGATT
EST: gi|349825564|gb|FQ419481.1|FQ419481
EST:     AAGAATGATTTGATTGACCTGTACAAAAAGTGCAAGGGTAATATGAACAG                         GCTTTTCTGTTCAATGCTTTGTTCTGACCCTAAGCTGGATTCACACCGATT
genomic: AAGAATGATTTGATTGACCTGTACAAAAAGTGCAAGGGTAATATGAACAGgtacaatagc ... tccttctcagGCTTTTCTGTTCAATGCTTTGTTCTGACCCTAAGCTGGATTCACACCGATT
EST: gi|30297223|gb|CB974017.1|CB974017
EST:     AAGAATGATTTGATTGACCTGTACAAAAAGTGCAAGGGTAATATGAACAG                         GCTTTTCTGTTCAATGCTTTGTTCTGACCCTAAGCTGGATTCACACCGATT
genomic: AAGAATGATTTGATTGACCTGTACAAAAAGTGCAAGGGTAATATGAACAGgtacaatagc ... tccttctcagGCTTTTCTGTTCAATGCTTTGTTCTGACCCTAAGCTGGATTCACACCGATT
EST: gi|352794289|gb|FQ479531.1|FQ479531
EST:     AAGAATGATTTGATTGACCTGTACAAAAAGTGCAAGGGTAATATGAACAG                         GCTTTTCTGTTCAATGCTTTGTTCTGACCCTAAGCTGGATTCACACCGATT
genomic: AAGAATGATTTGATTGACCTGTACAAAAAGTGCAAGGGTAATATGAACAGgtacaatagc ... tccttctcagGCTTTTCTGTTCAATGCTTTGTTCTGACCCTAAGCTGGATTCACACCGATT
EST: gi|351028672|gb|FQ446345.1|FQ446345
EST:     AAGAATGATTTGATTGACCTGTACAAAAAGTGCAAGGGTAATATGAACAG                         GCTTTTCTGTTCAATGCTTTGTTCTGACCCTAAGCTGGATTCACACCGATT
genomic: AAGAATGATTTGATTGACCTGTACAAAAAGTGCAAGGGTAATATGAACAGgtacaatagc ... tccttctcagGCTTTTCTGTTCAATGCTTTGTTCTGACCCTAAGCTGGATTCACACCGATT
EST: gi|351054628|gb|FQ456825.1|FQ456825
EST:     AAGAATGATTTGATTGACCTGTACAAAAAGTGCAAGGGTAATATGAACAG                         GCTTTTCTGTTCAATGCTTTGTTCTGACCCTAAGCTGGATTCACACCGATT
genomic: AAGAATGATTTGATTGACCTGTACAAAAAGTGCAAGGGTAATATGAACAGgtacaatagc ... tccttctcagGCTTTTCTGTTCAATGCTTTGTTCTGACCCTAAGCTGGATTCACACCGATT
EST: gi|110686833|gb|EE063714.1|EE063714
EST:     AAGAATGATTTGATTGACCTGTACAAAAAGTGCAAGGGTAATATGAACAG                         GCTTCTCTGTTCAATGCTTTGTTCTGACCCTAAGCTGGATTCACACCGATT
genomic: AAGAATGATTTGATTGACCTGTACAAAAAGTGCAAGGGTAATATGAACAGgtacaatagc ... tccttctcagGCTTTTCTGTTCAATGCTTTGTTCTGACCCTAAGCTGGATTCACACCGATT
EST: gi|349827514|gb|FQ422382.1|FQ422382
EST:     AAGAATGATTTGATTGACCTGTACAAAAAGTGCAAGGGTAATATGAACAG                         GCTTTTCTGTTCAATGCTTTGTTCTGACCCTAAGCTGGATTCACACCGATT
genomic: AAGAATGATTTGATTGACCTGTACAAAAAGTGCAAGGGTAATATGAACAGgtacaatagc ... tccttctcagGCTTTTCTGTTCAATGCTTTGTTCTGACCCTAAGCTGGATTCACACCGATT
EST: gi|110701183|gb|EE078491.1|EE078491
EST:     AAGAATGATTTGATTGAGCTGTACAAAAAGTGCAAGGGTAATATGAACAG                         GCTTTTTTGTTCAATGCTTTGTTCTGACCCTAAGCTGGATTCACACCGATT
genomic: AAGAATGATTTGATTGACCTGTACAAAAAGTGCAAGGGTAATATGAACAGgtacaatagc ... tccttctcagGCTTTTCTGTTCAATGCTTTGTTCTGACCCTAAGCTGGATTCACACCGATT
EST: gi|351048863|gb|FQ431528.1|FQ431528
EST:     AAGAATGATTTGATTGACCTGTACAAAAAGTGCAAGGGTAATATGAACAG                         GCTTTTCTGTTCAATGCTTTGTTCTGACCCTAAGCTGGATTCACACCGATT
genomic: AAGAATGATTTGATTGACCTGTACAAAAAGTGCAAGGGTAATATGAACAGgtacaatagc ... tccttctcagGCTTTTCTGTTCAATGCTTTGTTCTGACCCTAAGCTGGATTCACACCGATT
EST: gi|351023284|gb|FQ432667.1|FQ432667
EST:     AAGAATGATTTGATTGACCTGTACAAAAAGTGCAAGGGTAATATGAACAG                         GCTTTTCTGTTCAATGCTTTGTTCTGACCCTAAGCTGGATTCACACCGATT
genomic: AAGAATGATTTGATTGACCTGTACAAAAAGTGCAAGGGTAATATGAACAGgtacaatagc ... tccttctcagGCTTTTCTGTTCAATGCTTTGTTCTGACCCTAAGCTGGATTCACACCGATT
EST: gi|351040488|gb|FQ434621.1|FQ434621
EST:     AAGAATGATTTGATTGACCTGTACAAAAAGTGCAAGGGTAATATGAACAG                         GCTTTTCTGTTCAATGCTTTGTTCTGACCCTAAGCTGGATTCACACCGATT
genomic: AAGAATGATTTGATTGACCTGTACAAAAAGTGCAAGGGTAATATGAACAGgtacaatagc ... tccttctcagGCTTTTCTGTTCAATGCTTTGTTCTGACCCTAAGCTGGATTCACACCGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttttttttttttaggcttgccggatcagcctctaatctgctttccttctcagGCTTTTCTGTTCAATGCTTTGTTCTGACCCTAAGCTGGATTCACACCGATTCAAGGATATTCTTGATGAGGCAATATCAGCAG
                                ctctaat  putative branch site (score: 3)
                               cctctaatctgctttc  CT-rich tract
     tttttttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacaatagcaaatgtgtttcccttctttttttttttttaggcttgccggatcagcctctaatctgctttccttctcagGCTTTTCTGTTCAATGCTTTGTTCTGACCCTAAGCTGGATTCACACCGATTCAAGGATATTCTTGATGAGGCAATATCAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA