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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttgttctcaagagttgtatcatgttgcagttctcttgaatttgcaaattcctgtattactcatagtttgtggccgtatattttttggtcatcttacattcttatttgttagGGTGGTGATCTTACTGAGATTGGTGAAAGGGGGGTGAATATTAGTGGTGGTCAAAAGCAACGAGTTTCCATGGCTAGGGCAGTATATTCCAATTCAGATG

Basic information

species Vitis vinifera
transcript Vv10s0003g04390.t01
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0003g04390.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GRMZM2G084181_T01 (Zea mays), 3'ss of exon 18
gtaagtttgttctcaagagttgtatcatgttgcagttctcttgaatttgcaaattcc--tgtattactcatagtttgtggccgtatattttttggt----catcttacattcttatttgttagGGTGGTGATCTTACTGAGATTGGTGAAAGGGGGGTGAATATTAGTGGTGGTCAAAAGCAACGAGTTTCCATGGCTAGGGCAGTATATTCCAATTCAGATG
                      | | ||   |   | |  ||| ||||   ||| |    | | |  |  ||  |||   | ||| |||      |    ||| |     |  | | | | |||| || ||||| || |||||||||||||| || || ||||||||||| || || |||||| ||||||| ||||| || || || |||||  |||||||||
----------------------tttaatccagtgatgcctttgtattttttaatactggcgcactgttt-taacttgctactgtacattaacaaataatgcatttggttatgctttctatcagGGAGGCGATCTGACAGAGATTGGTGAAAGAGGAGTTAATATTAGTGGAGGGCAGAAGCAAAGAGTTTCAATGGCAAGAGCTGTGTATTCTGATTCAGATG

upper sequence: Vv10s0003g04390.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA15G09900.1 (Glycine max), 3'ss of exon 18
gtaagtttgttctcaagagttgtatcatgtt-gcagttctcttgaatttgcaaattcctgtattactcatagtttgtggccgtatattttttggtcatcttacattcttatttgttagGGTGGTGATCTTACTGAGATTGGTGAAAGGGGGGTGAATATTAGTGGTGGTCAAAAGCAACGAGTTTCCATGGCTAGGGCAGTATATTCCAATTCAGATG
|| ||| | |      ||||| || ||| |  |    |    ||||| | ||| ||     |||| |     |||  |   |||    |||    | |||| |  ||||| |   |||||||||||||||||||| ||||||||||| ||||| || || || ||||| ||||||||  |||| ||||||||||| || || || |||||||| ||||
gtgagtgtat------gagttatagcatttaagtgcatacaatgaatgttcaattta----attattagatttttaagttggtaggcctttcttccttctttc--tcttaatgactagGGTGGTGATCTTACTGAAATTGGTGAAAGAGGGGTAAACATCAGCGGTGGCCAAAAGCAGAGAGTATCCATGGCTAGAGCTGTCTACTCCAATTCTGATG

upper sequence: Vv10s0003g04390.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA13G29180.1 (Glycine max), 3'ss of exon 18
gtaagtttgttctcaagagttgtatcatgttgcagt-tctcttgaatttgcaaattcctgtattactcatagtttgtggccgtatattttttggtcatcttacattcttatttgttagGGTGGTGATCTTACTGAGATTGGTGAAAGGGGGGTGAATATTAGTGGTGGTCAAAAGCAACGAGTTTCCATGGCTAGGGCAGTATATTCCAATTCAGATG
|| ||| | | ||    |||| || | | |    |  ||   ||||      ||||  |  |||  | |  |||||||| | |   ||  ||  |  ||| |||| |||| |   ||||||||||||| |||||| ||||||||||| ||||| || || |||||||| ||||||||  |||| ||||||||||| || || || || ||||| ||||
gtgagtgtatact----agttatagcgtttaagtgcatccaatgaacaatttaattgttagatttttaa--gtttgtgggccttgcttccttctttctctcacatacttaatgactagGGTGGTGATCATACTGAAATTGGTGAAAGAGGGGTAAACATCAGTGGTGGCCAAAAGCAGAGAGTATCCATGGCTAGAGCTGTCTACTCAAATTCTGATG

upper sequence: Vv10s0003g04390.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: AT2G34660.1 (Arabidopsis thaliana), 3'ss of exon 18
gtaagtttgttctcaagagttgtatcatgttgcagttctcttgaatttgcaaattcctgtattactcatagtttgtggccgtatattttttggtcatcttacattcttatttgttagGGTGGTGATCTTACTGAGATTGGTGAAAGGGGGGTGAATATTAGTGGTGGTCAAAAGCAACGAGTTTCCATGGCTAGGGCAGTATATTCCAATTCAGATG
    ||  ||| | | |||  |  || ||  |  | |  |  | |||||     || ||   |  ||      ||| ||    | | |||    |   ||    ||||  ||  |||||||||||||| || |||||||| ||||| || || ||||| ||||| || || |||||  | ||||||||||||||||| || || || ||||||||||
----gtaagttttgaggaga-gcttcgtggagttgataacaaggatttg-----tcttgc-ctgttctcg---tgttgctaagtttgtttcaacctcttt---ctcttgcttaatagGGTGGTGATCTCACGGAGATTGGAGAAAGAGGTGTTAATATCAGTGGAGGACAGAAGCAGAGGGTTTCCATGGCTAGGGCCGTTTACTCAAATTCAGATG

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|30304105|gb|CB980899.1|CB980899
EST:     AGAAAGCAATAGATGTGACTGCATTGCAGCATGACCTTGACTTACTGCCT                         GGTGGTGATCTTACTGAGATTGGTGAAAGGGGGGTGAATATTAGTGGTGGT
genomic: AGAAAGCAATAGATGTGACTGCATTGCAGCATGACCTTGACTTACTGCCTgtaagtttgt ... tatttgttagGGTGGTGATCTTACTGAGATTGGTGAAAGGGGGGTGAATATTAGTGGTGGT
EST: gi|30304042|gb|CB980836.1|CB980836
EST:     AGAAAGCAATAGATGTGACTGCATTGCAGCATGACCTTGACTTACTGCCT                         GGTGGTGATCTTACTGAGATTGGTGAAAGGGGGGTGAATATTAGTGGTGGT
genomic: AGAAAGCAATAGATGTGACTGCATTGCAGCATGACCTTGACTTACTGCCTgtaagtttgt ... tatttgttagGGTGGTGATCTTACTGAGATTGGTGAAAGGGGGGTGAATATTAGTGGTGGT
EST: gi|34549912|gb|CF518144.1|CF518144
EST:     AGAAAGCAATAGATGTGACTGCATTGCAGCATGACCTTGACTTACTGCCT                         GGTGGTGATCTTACTGAGATTGGTGAAAGGGGGGTGAATATTAGTGGTGGT
genomic: AGAAAGCAATAGATGTGACTGCATTGCAGCATGACCTTGACTTACTGCCTgtaagtttgt ... tatttgttagGGTGGTGATCTTACTGAGATTGGTGAAAGGGGGGTGAATATTAGTGGTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactcatagtttgtggccgtatattttttggtcatcttacattcttatttgttagGGTGGTGATCTTACTGAGATTGGTGAAAGGGGGGTGAATATTAGTGGTGGTCAAAAGCAACGAGTTTCCATGGCTAGGGCAGTATATTCCAATTCAGATG
                                 atcttac  putative branch site (score: 3)
                                         ttcttattt  CT-rich tract
                                    ttacattcttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttgttctcaagagttgtatcatgttgcagttctcttgaatttgcaaattcctgtattactcatagtttgtggccgtatattttttggtcatcttacattcttatttgttagGGTGGTGATCTTACTGAGATTGGTGAAAGGGGGGTGAATATTAGTGGTGGTCAAAAGCAACGAGTTTCCATGGCTAGGGCAGTATATTCCAATTCAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG