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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactgcaatcaaaacaatcatacatctgagtttcttttttttctctttttttggtttgacctcatttgatggtctggaaagtccaagttacatttttaaagtatttgacagGTTTGTGACAAGCAGAAAGCTATCTTGTTGGCAGATATGGCACATATTAGTGGGTTGGTTGCGGCTGGTGTTATCCCATCGCCATTTGAGTATGCAGATA

Basic information

species Vitis vinifera
transcript Vv00s0211g00120.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0211g00120.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 8
gtaactgcaatcaaaacaatcatacatctgagtttcttttttttctctttttttggtttgacctcatttgatggtctggaaagtccaa-gttacatttttaaagtatttgacagGTTTGTGACAAGCAGAAAGCTATCTTGTTGGCAGATATGGCACATATTAGTGGGTTGGTTGCGGCTGGTGTTATCCCATCGCCATTTGAGTATGCAGATA
                               ||   ||||  | |||  |  |   |      || |    |  | |    |||| ||   | || || | | | | |   |||||||||||||||||||| || ||  |  | ||||||||||||||||| |||||| | || || ||||||||| | ||||| || ||||| ||||||||| 
-------------------------------gtgaattttactgctcaatagtgcatgctgaatcttcaccttctgtaatcagtcaaataattcacttgttatgcaatctgcagGTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGTGGGCTTGTCGCAGCTGGTGTTGTTCCATCTCCTTTTGATTATGCAGATG

upper sequence: Vv00s0211g00120.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G135283_T03 (Zea mays), 3'ss of exon 8
---------------------gtaactgcaatcaaaacaatcatacatctgagtttctttttttt--------ctctttttttggtttgacctc-atttgatggtctggaaagtccaagttacatttttaaagtat---ttgacagGTTTGTGACAAGCAGAAAGCTATCTTGTTGGCAGATATGGCACATATTAGTGGGTTGGTTGCGGCTGGTGTTATCCCATCGCCATTTGAGTATGCAGATA
                     |||  |    || ||      |   | |||    |  || | ||        || |        ||  ||| | || |  |  | |  |     ||| | |     | |   |||   | ||||| | ||  |||||||||| || ||  |  | ||||| |||||||||||||||||| | ||||| ||||||||| | ||||| || ||||| ||||||||| 
gcaaggtttctttccacgatagtattttttctccaagatgcaagggagctgcacattattatattacagagaactatacagaacattgaaccgcgatctttttttttttatcaatcaaataattccataatgttatgtgtcgacagATATGCAACAAGCAGAAGGCAATACTTCTAGCAGACATGGCACATATTAGTGGGCTTGTTGCAGCTGGTGTTGTTCCATCTCCTTTTGATTATGCAGATG

upper sequence: Vv00s0211g00120.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA18G27710.1 (Glycine max), 3'ss of exon 9
gtaactgcaatcaaaacaatcatacatctgagtttcttttttttctctttttttggtttgacctcatttgatggtctggaaagtccaag-ttacatttttaaagtatttgacagGTTTGTGACAAGCAGAAAGCTATCTTGTTGGCAGATATGGCACATATTAGTGGGTTGGTTGCGGCTGGTGTTATCCCATCGCCATTTGAGTATGCAGATA
       |  |            |    | ||  | || || || |   ||||       || |    ||||  | |||||   ||||| ||| |||| | ||| || | |||||||||||| || ||||||||||| || ||||||||||||||||| || ||||| |||||||| |||||||| |||||||| || ||||| ||||||||| 
-------ctttttttcttggtgaagggataaggctgttgttgttgtacctttt-------actttgaatgatactatggaagtcccaaggttaaatttgtgaagcatgttacagGTTTGTGATAAACAGAAAGCTATATTATTGGCAGATATGGCACACATCAGTGGATTGGTTGCAGCTGGTGTCATCCCATCACCTTTTGATTATGCAGATG

upper sequence: Vv00s0211g00120.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA09G33480.1 (Glycine max), 3'ss of exon 8
gtaactg------caatcaaaacaatc------atacatctgagtttc--ttttttttctctttttttggtttgacctcatttgatggtctggaaagtccaag-ttacatttttaaagtatttgacagGTTTGTGACAAGCAGAAAGCTATCTTGTTGGCAGATATGGCACATATTAGTGGGTTGGTTGCGGCTGGTGTTATCCCATCGCCATTTGAGTATGCAGATA
||||||        |  |||||  ||       ||| |  | | | |    || | ||    ||| | | ||| |  |    || |  | |||||   | ||| ||  | || | ||| || | |||||| ||||| || ||||||||| |  ||||||||||||||||||| || ||||| || ||||| |||||||||||||| || || ||||| ||||||||| 
gtaacttgttgattatacaaaatgattttttaaatatagataaatattaaattgtcttggaatttgtggttttaaatttgaatggttatttggaacaccaaaggttgaacttgtgaagcatgttacagGTGTGTGATAAACAGAAAGCTGTGCTGTTGGCAGATATGGCACACATCAGTGGATTAGTTGCAGCTGGTGTTATCCCTTCACCTTTTGATTATGCAGATG

upper sequence: Vv00s0211g00120.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA08G37270.1 (Glycine max), 3'ss of exon 8
gtaactgcaatcaaaacaatcatacatctgagtttcttttttttctctttttttggtttgacctcatttgatggtctggaaagtccaag-ttacatttttaaagtatttgacagGTTTGTGACAAGCAGAAAGCTATCTTGTTGGCAGATATGGCACATATTAGTGGGTTGGTTGCGGCTGGTGTTATCCCATCGCCATTTGAGTATGCAGATA
    ||    |            |    | ||  | || || | |  |||          || |    ||||  | |||||   ||||| |||  ||| | ||  || | ||||||||| || || |||||||||||  | ||||||||||||||||| || ||||| |||||||| |||||||| |||||||| || ||||| ||||| ||| 
----cttttttagtttttggtgaagggataaggctgttgttgtacctttt----------actttgaatgatactatggaagtcccaaggttaattttgtgaaacatgttacagGTTTGCGATAAACAGAAAGCTATACTATTGGCAGATATGGCACACATCAGTGGATTGGTTGCAGCTGGTGTCATCCCATCACCTTTTGATTATGCTGATG

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|33407197|gb|CF212824.1|CF212824
EST:     CGTATTCGCAAG                         GTTTGTGACAAGCAGAAAGCTATCTTGTTGGCAGATATGGCACATATTAGT
genomic: CGTATTCGCAAGgtaactgcaa ... tatttgacagGTTTGTGACAAGCAGAAAGCTATCTTGTTGGCAGATATGGCACATATTAGT
EST: gi|27579405|gb|CB002100.1|CB002100
EST:     CTGGTGCTAGTGCTTATGCCCGTCTCTATGATTATGCACGTATTCGCAAG                         GTTTGTGACAAGCAGAAAGCTATCTTGTTGGCAGATATGGCACATATTAGT
genomic: CTGGTGCTAGTGCTTATGCCCGTCTCTATGATTATGCACGTATTCGCAAGgtaactgcaa ... tatttgacagGTTTGTGACAAGCAGAAAGCTATCTTGTTGGCAGATATGGCACATATTAGT
EST: gi|352781312|gb|FQ467758.1|FQ467758
EST:     CTGGTGCTAGTGCTTATGCCCGTCTCTATGATTATGCACGTATTCCCAAG                         GGTTGTGACCAGCAGA
genomic: CTGGTGCTAGTGCTTATGCCCGTCTCTATGATTATGCACGTATTCGCAAGgtaactgcaa ... tatttgacagGTTTGTGACAAGCAGA
EST: gi|352769306|gb|FQ471455.1|FQ471455
EST:     CTGGTGCTAGTGCTTATGCCCGTCTCTATGATTATGCACGTATTCGCAAG                         GTTTGTGACAAGCAAAAAGCTATCTTGTTGG
genomic: CTGGTGCTAGTGCTTATGCCCGTCTCTATGATTATGCACGTATTCGCAAGgtaactgcaa ... tatttgacagGTTTGTGACAAGCAGAAAGCTATCTTGTTGG
EST: gi|294966171|gb|GW839394.1|GW839394
EST:     CTGGTGCTAGTGCTTATGCCCGTCTCTATGATTATGCACGTATTCGCAAG                         GTTTGTGACAAGCAGAAAGCTATCTTGTTGGCAGATATGGCACATATTAGT
genomic: CTGGTGCTAGTGCTTATGCCCGTCTCTATGATTATGCACGTATTCGCAAGgtaactgcaa ... tatttgacagGTTTGTGACAAGCAGAAAGCTATCTTGTTGGCAGATATGGCACATATTAGT
EST: gi|351016424|gb|FQ423851.1|FQ423851
EST:     CTGGTGCTAGTGCTTATGCCCGTCTCTATGATTATGCACGTATTCGCAAG                         GTTTGTGACAAGCAGAAAGCTATCTTGTTGGCAGATATGGCACATATTAGT
genomic: CTGGTGCTAGTGCTTATGCCCGTCTCTATGATTATGCACGTATTCGCAAGgtaactgcaa ... tatttgacagGTTTGTGACAAGCAGAAAGCTATCTTGTTGGCAGATATGGCACATATTAGT
EST: gi|110373188|gb|EC937406.1|EC937406
EST:     CTGGTGCTAGTGCTTATGCCCGTCTCTATGATTATGCACGTATTCGCAAG                         GTTTGTGACAAGCAGAAAGCTATCTTGTTGGCAGATATGGCACATATTAGT
genomic: CTGGTGCTAGTGCTTATGCCCGTCTCTATGATTATGCACGTATTCGCAAGgtaactgcaa ... tatttgacagGTTTGTGACAAGCAGAAAGCTATCTTGTTGGCAGATATGGCACATATTAGT
EST: gi|32250119|gb|CD715938.1|CD715938
EST:     CTGGTGCTAGTGCTTATGCCCGTCTCTATGATTATGCACGTATTCGCAAG                         GTTTGTGACAAGCAGAAAGCTATCTTGTTGGCAGATATGGCACATATTAGT
genomic: CTGGTGCTAGTGCTTATGCCCGTCTCTATGATTATGCACGTATTCGCAAGgtaactgcaa ... tatttgacagGTTTGTGACAAGCAGAAAGCTATCTTGTTGGCAGATATGGCACATATTAGT
EST: gi|37184833|gb|CF604187.1|CF604187
EST:     CTGGTGCTAGTGCCTATGCCCGTCTCTATGATTATGCACGTATTCGCAAG                         GTTTGTGACAAGCAGAAAGCTATCTTGTTGGCAGATATGGCACATATTAGT
genomic: CTGGTGCTAGTGCTTATGCCCGTCTCTATGATTATGCACGTATTCGCAAGgtaactgcaa ... tatttgacagGTTTGTGACAAGCAGAAAGCTATCTTGTTGGCAGATATGGCACATATTAGT
EST: gi|351053957|gb|FQ441723.1|FQ441723
EST:     CTGGTGCTAGTGCTTATGCCCGTCTCTATGATTATGCACGTATTCGCAAG                         GTTTGTGACAAGCAGAAAGCTATCTTGTTGGCAGATATGGCACATATTAGT
genomic: CTGGTGCTAGTGCTTATGCCCGTCTCTATGATTATGCACGTATTCGCAAGgtaactgcaa ... tatttgacagGTTTGTGACAAGCAGAAAGCTATCTTGTTGGCAGATATGGCACATATTAGT
EST: gi|30299931|gb|CB976725.1|CB976725
EST:     CTGGTGCTAGTGCTTATGCCCGTCTCTATGATTATGCACGTATTCGCAAG                         GTTTGTGACAAGCAGAAAGCTATCTTGTTGGCAGATATGGCACATATTAGT
genomic: CTGGTGCTAGTGCTTATGCCCGTCTCTATGATTATGCACGTATTCGCAAGgtaactgcaa ... tatttgacagGTTTGTGACAAGCAGAAAGCTATCTTGTTGGCAGATATGGCACATATTAGT
EST: gi|349823773|gb|FQ415184.1|FQ415184
EST:     CTGGTGCTAGTGCTTATGCCCGTCTCTATGATTATGCACGTATTCGCAAG                         GTTTGTGANCA-GCAGAAAGCTATCTTGTTGGCAGATATGGCACATATTAG
genomic: CTGGTGCTAGTGCTTATGCCCGTCTCTATGATTATGCACGTATTCGCAAGgtaactgcaa ... tatttgacagGTTTGTGA-CAAGCAGAAAGCTATCTTGTTGGCAGATATGGCACATATTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgacctcatttgatggtctggaaagtccaagttacatttttaaagtatttgacagGTTTGTGACAAGCAGAAAGCTATCTTGTTGGCAGATATGGCACATATTAGTGGGTTGGTTGCGGCTGGTGTTATCCCATCGCCATTTGAGTATGCAGATA
                            aagttacatttttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactgcaatcaaaacaatcatacatctgagtttcttttttttctctttttttggtttgacctcatttgatggtctggaaagtccaagttacatttttaaagtatttgacagGTTTGTGACAAGCAGAAAGCTATCTTGTTGGCAGATATGGCACATATTAGTGGGTTGGTTGCGGCTGGTGTTATCCCATCGCCATTTGAGTATGCAGATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT