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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcagacaactatgagcatcattgttgaatttaacctatttggagaaatttcacgaatcaaacgtgactgatccatcacctttttgtgctctaaactccagGTTTGCTATTACTGATGAGGGTTATAGCTGTGACATTCTGTGTGACTCTAGCTGCATCTTTAGCTGCACGCCAGGGACCAACATCCATGGCTGCATTCCA

Basic information

species Vitis vinifera
transcript Vv06s0004g02140.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g02140.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA13G41460.1 (Glycine max), 3'ss of exon 7
tcagacaactatgagcatcattgttgaatttaacctatttggagaaatttcacgaatcaaacgtgac-tgatccatcaccttt----ttgtgctctaaac-tccagGTTTGCTATTACTGATGAGGGTTATAGCTGTGACATTCTGTGTGACTCTAGCTGCATCTTTAGCTGCACGCCAGGGACCAACATCCATGGCTGCATTCCA
      ||   |  || | ||| ||    |  |    |||    | | || |  | | | || ||||   |||  |  |||||    |  || | |   | ||||||||| |||||| | ||||| || || ||||| |||||||||||||| || |||||||| ||||||||||| |||||||||||||| ||||| ||||| ||
------aatcttatgctttattttttttctgtataggtttactaacactttagtattgagacttgacaccatctttgtcctttcctatattgttgttgtcatccagGTTTTCTATTATTAATGAGAGTCATCGCTGTAACATTCTGTGTGACGCTGGCTGCATCATTAGCTGCACGGCAGGGACCAACATCTATGGCCGCATTTCA

upper sequence: Vv06s0004g02140.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA15G03930.1 (Glycine max), 3'ss of exon 7
tcagacaactatgagcatcattgttgaatttaacctatttggaga--aatttcacgaatcaa-acgtgactgatccatcacctttttgtgctctaaactccagGTTTGCTATTACTGATGAGGGTTATAGCTGTGACATTCTGTGTGACTCTAGCTGCATCTTTAGCTGCACGCCAGGGACCAACATCCATGGCTGCATTCCA
  |  |  |||      |  || |    ||     || |   |    | | |   || |  | ||     |  ||| || |  | ||||  |    | || |||||| |||||| | ||||| || || ||||| |||||||||||||| || ||||||||  |||||||||| |||||||||||||| ||||||||||| ||
--aatcttctactcttttttttttctgtttaggtttactaacactttagtattgagacttgacaccatctttgtccttccctatattgttgttgtca-tctagGTTTTCTATTATTAATGAGAGTCATCGCTGTAACATTCTGTGTGACACTGGCTGCATCACTAGCTGCACGGCAGGGACCAACATCTATGGCTGCATTTCA

upper sequence: Vv06s0004g02140.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA12G14270.1 (Glycine max), 3'ss of exon 4
tcagacaactatgagcatcattgttgaatttaacctatttggagaaatttcacgaatcaaacgtgactgatccatcacctttttgt---gctctaaactccagGTTTGCTATTACTGATGAGGGTTATAGCTGTGACATTCTGTGTGACT-CTAGCTGCATCTTTAGCTGCACGCCAGGGACCAACATCCATGGCTGCATTCCA
  |   |    ||| || |||  |||   ||  ||||| | |     | |    |  ||    || |||   ||  |  |    |    |  | ||  || | |  ||| ||| |   | | |  | ||| |  |     | ||||  || || || |    | | ||||   ||  || |                       
gtattgagacttga-caccatctttgtccttc-cctatattgt----tgttgtcatccaggtatgtctgcatcactagTTGCACGGCAGGGACCAACATCTATGGCTGC-ATTTCAAGT-ATGTCTGTAGGTTCGGTTGGCAGTGTCTCTTCTTGCGGATGGTCTGGCTGT-TGCTGGGCA-----------------------

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|110699707|gb|EE076951.1|EE076951
EST:     CTTACCTCCAAGTACCAAAGTTCTGCGATTTGGTCGATTTCTGAAAAATG                         GTTTGCTATTACTGATGAGGGTTATAGCTGTGACATTCTGTGTGACTCTAG
genomic: CTTACCTCCAAGTACCAAAGTTCTGCGATTTGGTCGATTTCTGAAAAATGgtgaggattt ... taaactccagGTTTGCTATTACTGATGAGGGTTATAGCTGTGACATTCTGTGTGACTCTAG
EST: gi|294967324|gb|GW836678.1|GW836678
EST:     CTTACCTCCAAGTACCAAAGTTCTGCGATTTGGTCGATTTCTGAAAAATG                         GTTTCCTATTATTGATGAGGGTTATAGCTGTGACATTCTGTGTGACTCTAG
genomic: CTTACCTCCAAGTACCAAAGTTCTGCGATTTGGTCGATTTCTGAAAAATGgtgaggattt ... taaactccagGTTTGCTATTACTGATGAGGGTTATAGCTGTGACATTCTGTGTGACTCTAG
EST: gi|110698510|gb|EE076088.1|EE076088
EST:     CTTACCTCCAAGTACCAAAGTTCTGCGATTTGGTCGATTTCTGAAAAATG                         GTTTGCTATTACTGATGAGGGTTATAGCTGTGACATTCTGTGTGACTCTAG
genomic: CTTACCTCCAAGTACCAAAGTTCTGCGATTTGGTCGATTTCTGAAAAATGgtgaggattt ... taaactccagGTTTGCTATTACTGATGAGGGTTATAGCTGTGACATTCTGTGTGACTCTAG
EST: gi|33405457|gb|CF211084.1|CF211084
EST:     CTTACCTCCAAGTACCAAAGTTCTGCGATTTGGTCGATTTCTGAAAAATG                         GTTTCCTATTACTGATGAGGGTTATAGCTGTGACATTCTGTGTGACTCTAG
genomic: CTTACCTCCAAGTACCAAAGTTCTGCGATTTGGTCGATTTCTGAAAAATGgtgaggattt ... taaactccagGTTTGCTATTACTGATGAGGGTTATAGCTGTGACATTCTGTGTGACTCTAG
EST: gi|294965646|gb|GW837245.1|GW837245
EST:     CTTACCTCCAAGTACCAAAGTTCTGCGATTTGGTCGATTTCTGAAAAATG                         GTTTGCTATTACTGATGAGGGTTATAGCTGTGACATTCTGTGTGACTCTAG
genomic: CTTACCTCCAAGTACCAAAGTTCTGCGATTTGGTCGATTTCTGAAAAATGgtgaggattt ... taaactccagGTTTGCTATTACTGATGAGGGTTATAGCTGTGACATTCTGTGTGACTCTAG
EST: gi|30300493|gb|CB977287.1|CB977287
EST:     CTTACCTCCAAGTACCAAAGTTCTGCGATTTGGTCGATTTCTGAAAAATG                         GTTTCCTATTACTGATGAGGGATATAGC
genomic: CTTACCTCCAAGTACCAAAGTTCTGCGATTTGGTCGATTTCTGAAAAATGgtgaggattt ... taaactccagGTTTGCTATTACTGATGAGGGTTATAGC
EST: gi|30301245|gb|CB978039.1|CB978039
EST:     CTTACCTCCAAGTACCAAAGTTCTGCGATTTGGTCGATTTCTGAAAAATG                         GTTTCCTATTACTGATGAGGGTTATAGCTGTGACATTCTGTGTGACTCTAG
genomic: CTTACCTCCAAGTACCAAAGTTCTGCGATTTGGTCGATTTCTGAAAAATGgtgaggattt ... taaactccagGTTTGCTATTACTGATGAGGGTTATAGCTGTGACATTCTGTGTGACTCTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttcacgaatcaaacgtgactgatccatcacctttttgtgctctaaactccagGTTTGCTATTACTGATGAGGGTTATAGCTGTGACATTCTGTGTGACTCTAGCTGCATCTTTAGCTGCACGCCAGGGACCAACATCCATGGCTGCATTCCA
                                          ctctaaa  putative branch site (score: 3)
                                cctttttgtgctct  CT-rich tract
         aatcaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcagacaactatgagcatcattgttgaatttaacctatttggagaaatttcacgaatcaaacgtgactgatccatcacctttttgtgctctaaactccagGTTTGCTATTACTGATGAGGGTTATAGCTGTGACATTCTGTGTGACTCTAGCTGCATCTTTAGCTGCACGCCAGGGACCAACATCCATGGCTGCATTCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- agacaac
- - - - - - -agcatca
- - - - - - - - - - - - - - - - - - - - ggagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - aatcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgactga