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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggttacctcaaaatgttgaagtctctgatcgttttctatttcaaaataagtaatatgccataaacttaagcatgtggctattattttttttctttggcagATTGTGTTCAGGGAGGATTTTGGAACTGAAGGTCGTGGTGGATATTTTGATGAATATGG

Basic information

species Vitis vinifera
transcript Vv14s0171g00490.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os04g40874.1 (Oryza sativa), 3'ss of exon 7
ggttacctcaaaatgttgaagtctctgatcgttttctatttcaa-aataagtaatatgccataaacttaagcat-gtggctattattttttttc-------tttggcagATTGTGTTCAGGGAGGATTTTGGAACTGAAGGTCGTGGTGGATATTTTGATGAATATGG
         ||||| | |   | | | ||  | | |||||| || | ||  |      | |||        ||| || |||   |||| |  ||       |   ||||||||| ||||||||||| ||||| ||||| || |||||||||||||||||| |||||||
--------aaaaatataggtatatttcatt-tgtactattttaacagtatattgccaacaatatggcatgccatagtagctgcaatttataatcaatacaatcctgcagATTGTATTCAGGGAGGACTTTGGGACTGACGGGCGTGGTGGATATTTTGATCAATATGG

upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G031107_T01 (Zea mays), 3'ss of exon 7
-------------------------------------------------------------------------------------------ggttacctcaaaatgt---tgaagtc----tctgatcgttttctatttcaaaataagtaatatgccataaacttaagcatgtggctattattttttttctttggcagATTGTGTTCAGGGAGGATTTTGGAACTGAAGGTCGTGGTGGATATTTTGATGAATATGG
                                                                                           | ||  || || |  |   | || |     ||  |  | | | | |||  |  ||| || | ||||  | |  |   | ||    || |   |   ||||   |||||| || || | |||||| |||||||||||||| ||||| |||||||||||| |||||||
gtaagatcctttcctaggtggttacagtattttttttatttctttataaatcatggttggctgttataagttgataacacatcttttgtcagtttgtctgaagaattaaataaaattgatgtcaaaaagctgtattttttcag-taattattgtgcctaacatatgttcttgcatgtaatgaatgaattct---gcagATCGTATTTAAGGAGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGG

upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G130230_T03 (Zea mays), 3'ss of exon 7
ggttacctcaaaatgttgaagtctctgatcgttt---tctatttcaaaataagtaatatgccataaacttaagcatgtggctattattttttttctttggcagATTGTGTTCAGGGAGGATTTTGGAACTGAAGGTCGTGGTGGATATTTTGATGAATATGG
  ||    |||     |  ||| |   ||   |       |    || |||| | | |    | |   | ||  |  |||| ||  |  ||  |     ||||||||| |||||||| || ||||| |||||||| ||||| |||||||||||  |||||||
tattgtaacaattgactacagtttgaaatgagtcaaactgaacctaagataactgaaag--tacagtatcaatgacatggc-atgctaattactacactgcagATTGTATTCAGGGAAGACTTTGGTACTGAAGGGCGTGGAGGATATTTTGACCAATATGG

upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA19G22690.1 (Glycine max), 3'ss of exon 7
ggttacctcaaaatgttgaagtctctgatcgttttctatttcaa-aataagtaatatgccataaacttaagcatgtggctattatt-ttttttctttggcagATTGTGTTCAGGGAGGATTTTGGAACTGAAGGTCGTGGTGGATATTTTGATGAATATGG
  ||   ||    ||||     ||    || | | ||   | |  ||  | | ||||||||||  ||||| | || |  | |   | ||||| ||||||||||| || ||||| ||  ||||||||||||||||||| ||||||||||||||  | |||||
aatttggtctgtctgttattaccta-attcatctactgcatgaccaaacatttatatgccatat-cttaaacttgagtttttggctgtttttactttggcagATCGTTTTCAGAGAAAATTTTGGAACTGAAGGTCGAGGTGGATATTTTGACCAGTATGG

upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA19G24250.1 (Glycine max), 3'ss of exon 7
ggttacctcaaaatgttgaagtctctgat-cgttttctatttcaaaataagtaatatgccataaacttaagcatgtggctattattttttttctttggcagATTGTGTTCAGGGAGGATTTTGGAACTGAAGGTCGTGGTGGATATTTTGATGAATATGG
  | ||   |   |||||   | ||| || |   | ||   | |   ||  | ||||| || |   |||| | ||  | | |  | |   |||| || ||||| || ||||| ||||||||||||||||| || |||||||||||||||||  |||||||
cttaacaatattttgttgccttatctaattcaactactgcattaccgtatttgatatggcacacttttaaacttg-agttttgctgtcaattctctgacagATAGTTTTCAGAGAGGATTTTGGAACTGATGGCCGTGGTGGATATTTTGACCAATATGG

upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA16G06850.1 (Glycine max), 3'ss of exon 7
ggttacctcaaaatgttgaagtctctgat-cgttttctatttcaaaataagtaatatgccataaacttaagcatgtggctattattttttttctttggcagATTGTGTTCAGGGAGGATTTTGGAACTGAAGGTCGTGGTGGATATTTTGATGAATATGG
  | ||       |||||   | ||| || |   | ||   |    | |  | ||||| || ||  |||| |  | |  |    | ||  |||| || ||||| || ||||| ||||||||||||||||| || |||||||||||||||||  | |||||
attaacaatcttttgttgccttatctaattcaactactgcattgccagagttgatatggcacaattttaaactagagtttggc-tgttaattctatgacagATAGTTTTCAGAGAGGATTTTGGAACTGATGGCCGTGGTGGATATTTTGACCAGTATGG

upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT5G40760.1 (Arabidopsis thaliana), 3'ss of exon 7
ggttacctcaaaatgttgaagtctctgatcgttttctatttcaaaataagtaatatgccataaacttaagcatgtggctattattt----tttttctttggcagATTGTGTTCAGGGAGGATTTTGGAACTGAAGGTCGTGGTGGATATTTTGATGAATATGG
                    ||    | |   |  |||   || ||  ||| | |     |    || ||  |      |   |||    |  || | | ||||||||| |||||||| ||||||||||||||||| ||||| ||||||||||| ||||||||
--------------------gtgagagctgcatagctaagacagaaatagtcagactgtttgttatttagagtcaattcacattttcaaatgcttttcttgcagATTGTTTTCAGGGAAGATTTTGGAACTGAAGGGCGTGGCGGATATTTTGACGAATATGG

upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT3G27300.1 (Arabidopsis thaliana), 3'ss of exon 7
ggttacctcaaaatgttgaagtctctgatcgttttctatttcaaaataagtaatatgccataaacttaagcatgtggctattattttttttctttggcagATTGTGTTCAGGGAGGATTTTGGAACTGAAGGTCGTGGTGGATATTTTGATGAATATGG
          | |  ||||  || || | |      |||||| |||    |     |   | ||   |  ||  |    ||   |  |||  ||| |||||| || ||||| || |||||||||||||||||||| |||||||||||||||||||| ||
-------gtgagagtttga--tcgcttagcacaaa-tatttctaaacttttgtatagagttgaatccatccacataa--atctctaatttctttttgcagATCGTTTTCAGAGAAGATTTTGGAACTGAAGGTCGCGGTGGATATTTTGATGAATACGG

upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: PP1S222_130V6.2 (Physcomitrella patens), 3'ss of exon 7
-ggttacctcaaaatgttgaagtctctgat--cgttttctatttcaaaataagtaatatgccataaacttaagcatgtggctattattttttttctttggcagATTGTGTTCAGGGAGGATTTTGGAACTGAAGGTCGTGGTGGATATTTTGATGAATATGG
  | || |    |    | | ||||  |||  |    | ||||||  |  |  | | |    |  | ||      ||  |   || ||  ||   | | ||||||||| || | |||||| ||||||||| |||| || ||||| ||||||||||| |||||
gagctagcatttatcaat-atgtcttcgattacaccatttatttctgatcacttcagaaa--agtagctgttctctgatgagtttgttagttacatctcgcagATTGTTTTTAAGGAGGACTTTGGAACTCAAGGACGAGGTGGTTATTTTGATGAGTATGG

upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: EFJ21593 (Selaginella moellendorffii), 3'ss of exon 6
ggttacctcaaaatgttgaagtctctgatcgttttctatttcaaaataagtaatatgccataaacttaagcatgtggctattattttttttctttggcagATTGTGTTCAGGGAGGATTTTGGAACTGAAGGTCGTGGTGGATATTTTGATGAATATGG
                                             ||  || | |    | |||     ||  |||  | | | |    | | |  |||||||||||||| |||| ||||||||||||| ||||| ||||| || ||||| ||||||||
-------------------------------------------gtatgggtgaca-atgacaaatcatcgctagtg-ttctaaatagcatacat--gcagATTGTGTTCAAGGAGAATTTTGGAACTGATGGTCGCGGTGGCTACTTTGACGAATATGG

upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: EFJ23968 (Selaginella moellendorffii), 3'ss of exon 6
ggttacctcaaaatgttgaagtctctgatcgttttctatttcaaaataagtaatatgccataaacttaagcatgtggctattattttttttctttggcagATTGTGTTCAGGGAGGATTTTGGAACTGAAGGTCGTGGTGGATATTTTGATGAATATGG
                                             ||  || | |    | |||     ||  |||  | | | |    | | |  ||||||||||||||||||| ||||||||||||| ||||| ||||| || ||||| ||||||||
-------------------------------------------gtatgggtgaca-atgacaaatcatcgctagtg-ttctaaatagcatacat--gcagATTGTGTTCAGGGAGAATTTTGGAACTGATGGTCGCGGTGGCTACTTTGACGAATATGG

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|30299156|gb|CB975950.1|CB975950
EST:     ATCGCATGTTTTTGCCCCTCTGGAACCGTGACAACATTGATAATGTACAG                         ATTGTGTTCAGGGAGGATTTTGGAACTGAAGGTCGTGGTGGATATTTTGAT
genomic: ATCGCATGTTTTTGCCCCTCTGGAACCGTGACAACATTGATAATGTACAGgttagattcc ... tctttggcagATTGTGTTCAGGGAGGATTTTGGAACTGAAGGTCGTGGTGGATATTTTGAT
EST: gi|110364929|gb|EC928538.1|EC928538
EST:     ATCGCATGTTTTTGCCCCTCTGGAACCGTGACAACATTGATAATGTACAG                         ATTGTGTTCAGGGAGGATTTTGGAACTGAAGGTCGTGGTGGATATTTTGAT
genomic: ATCGCATGTTTTTGCCCCTCTGGAACCGTGACAACATTGATAATGTACAGgttagattcc ... tctttggcagATTGTGTTCAGGGAGGATTTTGGAACTGAAGGTCGTGGTGGATATTTTGAT
EST: gi|110372969|gb|EC937167.1|EC937167
EST:     ATCGCATGTTTTTGCCCCTCTGGAACCGTGACAACATTGATAATGTACAG                         ATTGTGTTCAGGGAGGATTTTGGAACTGAAGGTCGTGGTGGATATTTTGAT
genomic: ATCGCATGTTTTTGCCCCTCTGGAACCGTGACAACATTGATAATGTACAGgttagattcc ... tctttggcagATTGTGTTCAGGGAGGATTTTGGAACTGAAGGTCGTGGTGGATATTTTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataagtaatatgccataaacttaagcatgtggctattattttttttctttggcagATTGTGTTCAGGGAGGATTTTGGAACTGAAGGTCGTGGTGGATATTTTGATGAATATGG
                                ctattattttttttct  CT-rich tract
                                 tattattttttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggttacctcaaaatgttgaagtctctgatcgttttctatttcaaaataagtaatatgccataaacttaagcatgtggctattattttttttctttggcagATTGTGTTCAGGGAGGATTTTGGAACTGAAGGTCGTGGTGGATATTTTGATGAATATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - -cctcaaa
- - - - - - - - tgaagtc
- - - - - - - - - - - - - - - - - - - - - aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - cataaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtgg