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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgcatatgtttcaagcatagcatagactgttcaagccttttaaaagattgttatggcctgatttgagaaatgaaacttttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCAGAATTGGACACCTTGAGCGAGGAGTCATACAAGGACAGCACTCTGATTATGCAGCTG

Basic information

species Vitis vinifera
transcript Vv01s0011g00620.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g00620.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA01G07070.1 (Glycine max), 3'ss of exon 4
gtaatgcatatgtt-tcaagcatagcataga-ctgttcaagccttttaaaagattgttatggcctga-tttgagaaatgaaacttttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCAGAATTGGACACCTTGAGCGAGGAGTCATACAAGGACAGCACTCTGATTATGCAGCTG
||||   |   ||| ||       |||| || |  || ||   ||||    | | | | | | |||| | | |  | ||||||||  |||||||||||||||||||||||||||||||||||||||||||||| || ||||||||| |||| || ||||||||||||||||||||| |||| |||||||||
gtaagttactggttctctcattctgcatggatccatttaattgtttttgttgctagctcttgtctgaatatcattactgaaactt--acagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGACACCCTGAGTGAAGAGTCATACAAGGACAGCACTTTGATCATGCAGCTG

upper sequence: Vv01s0011g00620.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA02G12930.1 (Glycine max), 3'ss of exon 4
gtaatgcatatgtt-tcaagcatagcataga-ctgttcaagccttttaaaagattgttatggcctga-tttgagaaatgaaacttttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCAGAATTGGACACCTTGAGCGAGGAGTCATACAAGGACAGCACTCTGATTATGCAGCTG
||||   ||   || ||        | | || |  || ||   ||||    | | | | | | |||| | | |  | ||||||||  ||||||||||||||||||| |||||||||||||||||||||||||| || ||||||||| |||| || ||||||||||||||||||||| |||| |||||||||
gtaagttattgattctctcattcttcgtggatccatttaattgtttttgttgctagctcttgtctgaatatcattactgaaactt--acagGGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGACACCCTGAGTGAAGAGTCATACAAGGACAGCACTTTGATCATGCAGCTG

upper sequence: Vv01s0011g00620.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA20G03120.1 (Glycine max), 3'ss of exon 4
----------gtaatgcatatgttt-caagcatagcatagactgttcaagccttttaaaagattgttatggcctgatttgagaaatga-aacttttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCAGAATTGGACACCTTGAGCGAGGAGTCATACAAGGACAGCACTCTGATTATGCAGCTG
             ||  ||||| |     |||| |  |  | || | | |  | ||   || | |   |      ||||    | |   |||  |||||||||||| |||||||||||||||||||| ||||||||||||||||| || ||||||||||| || ||||||||||||||||||||| |||| |||||||||
tcccaacactcctatcaatatgatcatctgcattggttccattgcttaggtatgttgccagctggcgttaatgacatttacctattactaacacttacagGGCCTGTCATTTGGCTAAGCAAGCTTTCGATGAGGCAATTGCAGAGTTAGACACCTTGAGTGAAGAGTCATACAAGGACAGCACTTTGATCATGCAGCTG

upper sequence: Vv01s0011g00620.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA07G35240.1 (Glycine max), 3'ss of exon 4
----------------gtaatgc-atatg-tttcaagcatagcatagactgttcaagccttttaaaagattgttatggcctgatttgagaaatgaaacttttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCAGAATTGGACACCTTGAGCGAGGAGTCATACAAGGACAGCACTCTGATTATGCAGCTG
                  | | | ||||| |||| | ||   |   ||   |         |  ||    |  | |  | |  |||      ||||||||   ||||||||| |||||||||||||||||||| ||||||||||||||||| || ||||||||||| || ||||||||||||||||||||| |||| |||||||||
cctcatttcacttattacactcccatatggtttccaacacttctatgatcatctgcattggtccaattgcttatttcacttttttttc----tgaaactt--gcagGGCCTGTCATTTGGCTAAGCAAGCTTTCGATGAGGCAATTGCAGAGTTAGACACCTTGAGTGAAGAGTCATACAAGGACAGCACTTTGATCATGCAGCTG

upper sequence: Vv01s0011g00620.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S201_25V6.1 (Physcomitrella patens), 3'ss of exon 4
gtaatgcatatgtttcaagcatagcata------gactgttcaagccttttaaaaga--ttgttatggcctgatttgagaaatgaaacttttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCAGAATTGGACACCTTGAGCGAGGAGTCATACAAGGACAGCACTCTGATTATGCAGCTG
||||    |    || | |  | | ||       |   || |    |||||    |   | || |  | ||| |  ||   |        |   ||||| ||||||||||| |||||||| || || ||||||||||| ||||||||||| ||||| |||||||| ||||||||||||||  |||| ||||| || 
gtaagattttgagttgaggttttggatgcctgtgggacgtgcttttcttttggcggggttcgtaactgactg-tgcgattgactgcgtggtggtagGGCATGCCATTTGGCGAAGCAAGCATTCGACGAGGCAATTGCCGAATTGGACACATTGAGTGAGGAGTCGTACAAGGACAGCACATTGATCATGCAACTA

upper sequence: Vv01s0011g00620.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S67_176V6.1 (Physcomitrella patens), 3'ss of exon 4
----------------------------------------------------------------------gtaatgcatatgtttcaagcatagcatagactgttcaagccttttaaaagattgttatggcctgatttgagaaatgaaactt--ttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCAGAATTGGACACCTTGAGCGAGGAGTCATACAAGGACAGCACTCTGATTATGCAGCTG
                                                                       | ||  ||    ||   |  ||||||      ||   || | |     | |||    ||    | |   | | ||  |     ||||||||| ||||||||||| |||||||| ||||||||||| || || ||  |||| || ||||| || ||||| ||||||||||||||  |||| |||||| ||
gtaagattgtggtagttgattatgcggtgaagcagatgagagtgattgaaccgtctattggacggggccattgattgatgaagttttcg-gtagcatgctgaatttgtgcttatctgg-gtttgcaccggtaataatcaggtagtggtatggaattacagGGCATGCCATTTGGCGAAGCAAGCATTTGATGAGGCTATCGCTGAGCTGGATACGTTGAGTGAAGAGTCGTACAAGGACAGCACATTGATCATGCAGTTG

upper sequence: Vv01s0011g00620.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S46_127V6.1 (Physcomitrella patens), 3'ss of exon 4
----------------gtaatgcatatgtttcaagcatagcatagactgttcaagccttttaaaagattgt-tatggcctgatttgaga---aatga----aacttttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCAGAATTGGACACCTTGAGCGAGGAGTCATACAAGGACAGCACTCTGATTATGCAGCTG
                |||  |  |  | |    |       ||    ||       |||| |  |||||  |||        ||| ||   ||||      ||| |  |||||| ||||||||||| || ||||| ||||| ||||| ||||| || ||||| || || || |||||||| ||||||||||||||  |||| |||||||| 
gtatgaattttggtcagtagagacttagctgttggttggttttacggcgtgttttttttttcagggattgaatatattggagcttgtgactgaatgccattgactgtggcagGGCATGCCATTTGGCGAAACAAGCATTTGACGAGGCGATTGCTGAGTTGGATACGTTAAGTGAGGAGTCGTACAAGGACAGCACATTGATCATGCAGCTA

upper sequence: Vv01s0011g00620.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S348_15V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------------------------------------------------------------------------------gtaatgcatatgtttcaag-catagc--atagactgttcaagccttttaaaagattgttatggcctgatttgagaaatgaaacttttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCAGAATTGGACACCTTGAGCGAGGAGTCATACAAGGACAGCACTCTGATTATGCAGCTG
                                                                                     | |  |||| ||| |   | | | |   ||  |  |||   |   |    ||   ||  | ||  ||  | | |   ||| | ||   ||| || ||||||||||| |||||||| ||||||||||| || || ||  |||| || |||||||||||||| ||||||||||||||  |||| |||||||| 
gtaagagtggctgtgtggcatgcggcgaagcggttgagggtgattgtggaggcgtggatggaacgtgggcgtgggatggatgggtggatagcatgtgtgtgggggcgtggtggattcatggttgtggtggtccgcaatgctgaaacggggtg--tggtggtgtgagattt---cagAGCATGCCATTTGGCGAAGCAAGCGTTTGATGAGGCGATCGCGGAGCTGGATACGTTGAGCGAGGAGTCGTACAAGGACAGCACGTTGATCATGCAGCTA

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|349830763|gb|FQ417061.1|FQ417061
EST:     GCTCTCAACTTCTCTGTCTTCTACTATGAGATAATGAATTCTCCTGAAAG                         GGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCAGAATTGGA
genomic: GCTCTCAACTTCTCTGTCTTCTACTATGAGATAATGAATTCTCCTGAAAGgtaatgcata ... acttttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCAGAATTGGA
EST: gi|351012160|gb|FQ426882.1|FQ426882
EST:     GCTCTCAACTTCTCTGTCTTCTACTATGAGATAATGAATTCTCCTGAAAG                         GGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCAGAATTGGA
genomic: GCTCTCAACTTCTCTGTCTTCTACTATGAGATAATGAATTCTCCTGAAAGgtaatgcata ... acttttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCAGAATTGGA
EST: gi|110373768|gb|EC938103.1|EC938103
EST:     GCTCTCAACTTCTCTGTCTTCTACTATGAGATAATGAATTCTCCTGAAAG                         GGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCAGAATTGGA
genomic: GCTCTCAACTTCTCTGTCTTCTACTATGAGATAATGAATTCTCCTGAAAGgtaatgcata ... acttttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCAGAATTGGA
EST: gi|351033251|gb|FQ462023.1|FQ462023
EST:     GCTCTCAACTTCTCTGTCTTCTACTATGAGATAATGAATTCTCCTGAAAG                         GGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCAGAATTGGA
genomic: GCTCTCAACTTCTCTGTCTTCTACTATGAGATAATGAATTCTCCTGAAAGgtaatgcata ... acttttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCAGAATTGGA
EST: gi|352789764|gb|FQ478579.1|FQ478579
EST:     GCTCTCAACTTCTCTGTCTTCTACTATGAGATAATGAATTCTCCTGAAAG                         GGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCAGAATTGGA
genomic: GCTCTCAACTTCTCTGTCTTCTACTATGAGATAATGAATTCTCCTGAAAGgtaatgcata ... acttttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCAGAATTGGA
EST: gi|110386347|gb|EC950937.1|EC950937
EST:     GCTCTCAACTTCTCTGTCTTCTACTATGAGATAATGAATTCTCCTGAAAG                         GGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCAGAATTGGA
genomic: GCTCTCAACTTCTCTGTCTTCTACTATGAGATAATGAATTCTCCTGAAAGgtaatgcata ... acttttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCAGAATTGGA
EST: gi|351055188|gb|FQ440527.1|FQ440527
EST:     GCTCTCAACTTCTCTGTCTTCTACTATGAGATAATGAATTCTCCTGAAAG                         GGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCAGAATTGGA
genomic: GCTCTCAACTTCTCTGTCTTCTACTATGAGATAATGAATTCTCCTGAAAGgtaatgcata ... acttttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCAGAATTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcaagccttttaaaagattgttatggcctgatttgagaaatgaaacttttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCAGAATTGGACACCTTGAGCGAGGAGTCATACAAGGACAGCACTCTGATTATGCAGCTG
                          gcctgat  putative branch site (score: 4)
                                              cttttac  putative PPT
        ttttaaaagattgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgcatatgtttcaagcatagcatagactgttcaagccttttaaaagattgttatggcctgatttgagaaatgaaacttttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCAGAATTGGACACCTTGAGCGAGGAGTCATACAAGGACAGCACTCTGATTATGCAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG