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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgatttcaatcaaaagggtttattgttgtgtgtgttatagagaagtggttgaccaattcaactttcttgaattctaatttccgaagtactattattgcagTGAGGAAGACATGCTAAAGAAGCTCGGTGACCTTATGAACAAGAGCCACGACAGCTGCAGTGTTTTATACGAGTGCAG

Basic information

species Vitis vinifera
transcript Vv05s0077g00690.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0077g00690.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G458549_T01 (Zea mays), 3'ss of exon 10
---------------------tgatttcaatcaaaagggtttattgttgt-gtgtgttatagagaagtggttgaccaattcaactttcttgaattctaatttccgaagtactattattgcagTGAGGAAGACATGCTAAAGAAGCTCGGTGACCTTATGAACAAGAGCCACGACAGCTGCAGTGTTTTATACGAGTGCAG
                     ||  ||   || |    || |||  |    ||   ||  |    ||| ||  |    |    |||| |   |   |||          | || |  ||||||||||||| || ||| ||||| || ||||| ||||||||| |||||||  |||||||||| ||  ||||||| |||||
gtgggcccactattcgtaatctgcattttctctaggttgtgtatcctcacagtacattggaagttagtcgtaaaaatgtgtg-ctttgtcataacataacgcatacgaca-tactgctgcagTGAGGAAGGCAAGCTTAAGAAACTTGGTGATCTTATGAACGAGAGCCATTACAGCTGCAGCGTGCTATACGAATGCAG

upper sequence: Vv05s0077g00690.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA17G03990.1 (Glycine max), 3'ss of exon 10
---tgatttcaatcaaaagggtttattgtt-gtgtgtgttatagagaagtggttgaccaatt-caactttcttgaattctaatttccgaagtactattattgcagTGAGGAAGACATGCTAAAGAAGCTCGGTGACCTTATGAACAAGAGCCACGACAGCTGCAGTGTTTTATACGAGTGCAG
     ||        |        || ||| |  | | || ||      | ||     |  |  |  ||||||  ||  ||| | |  || || | |     |||||| || ||||||||||||||||| ||||||||||||||| |||| ||  | |||||||| |||||||| || |||||
aaaaaatccttgaggactaatcccatagtttgcatatattgtaattcttttgtaagtaacctgtaggtttcttttatgttaactactcaattatttt-----cagTGACGAGGACATGCTAAAGAAGCTTGGTGACCTTATGAACGAGAGTCATCATAGCTGCAGCGTTTTATATGAATGCAG

upper sequence: Vv05s0077g00690.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA07G36610.1 (Glycine max), 3'ss of exon 10
---------------------------------------------------------------------------tgatttcaatcaaaagggtttattgttgtgtgtgttataga-gaagtggttgaccaattcaactttcttgaattctaatttccgaagtactattattg-cagTGAGGAAGACATGCTAAAGAAGCTCGGTGACCTTATGAACAAGAGCCACGACAGCTGCAGTGTTTTATACGAGTGCAG
                                                                           | || |   | |||||   ||| |  |   |   || |||| | | |  ||    || | | ||         | | || | |   |  | ||||||  ||| || || ||||||||||||||||| || |||||||||||| | || ||  | |||||||| |||||||| || |||||
gtgagtcttttggatctatcttatgtagctatgcatctgtgctgtttgttttcaatgtaattctcattaacattttcatattgcttaaaag---ttagtagttcatagcttctagaagtaattcttttgtaagtgatctaaaggtttcttttatattcactgctcaattattttcagCGACGAGGACATGCTAAAGAAGCTTGGCGACCTTATGAACGAAAGTCATCATAGCTGCAGCGTTTTATATGAATGCAG

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|37184342|gb|CF603696.1|CF603696
EST:     GAGGCCAGGCGTGTTCATGCTTTCAGGGACACTGTGTTGTCAGGGTTAAG                         TGAGGAAGACATGCTAAAGAAGCTCGGTGACCTTATGAACAAGAGCCACGA
genomic: GAGGCCAGGCGTGTTCATGCTTTCAGGGACACTGTGTTGTCAGGGTTAAGgtgagtcatc ... attattgcagTGAGGAAGACATGCTAAAGAAGCTCGGTGACCTTATGAACAAGAGCCACGA
EST: gi|110410868|gb|EC976562.1|EC976562
EST:     GAGGCCAGGCGTGTTCATGCTTTCAGGGACACTGTGTTGTCAGGGTTAAG                         TGAGGAAGACATGCTAAAGAAGCTCGGTGACCTTATGAACAAGAGCCACGA
genomic: GAGGCCAGGCGTGTTCATGCTTTCAGGGACACTGTGTTGTCAGGGTTAAGgtgagtcatc ... attattgcagTGAGGAAGACATGCTAAAGAAGCTCGGTGACCTTATGAACAAGAGCCACGA
EST: gi|30299412|gb|CB976206.1|CB976206
EST:     GAGGCCAGGCGTGTTCATGCTTTCAGGGACACTGTGTTGTCAGGGTTAAG                         TGAGGAAGACATGCTAAAGAAGCTCGGTGACCTTATGAACAAGAGCCCCGA
genomic: GAGGCCAGGCGTGTTCATGCTTTCAGGGACACTGTGTTGTCAGGGTTAAGgtgagtcatc ... attattgcagTGAGGAAGACATGCTAAAGAAGCTCGGTGACCTTATGAACAAGAGCCACGA
EST: gi|27583346|gb|CB006041.1|CB006041
EST:     GAGGCCAGGCGTGTTCATGCTTTCAGGGACACTGTGTTGTCAGGGTTAAG                         TGAGGAAGACATGCTAAAGAAGCTCGGTGACCTTATGAACAAGAGCCACGA
genomic: GAGGCCAGGCGTGTTCATGCTTTCAGGGACACTGTGTTGTCAGGGTTAAGgtgagtcatc ... attattgcagTGAGGAAGACATGCTAAAGAAGCTCGGTGACCTTATGAACAAGAGCCACGA
EST: gi|33406611|gb|CF212238.1|CF212238
EST:     GAGGCCAGGCGTGTTCATGCTTTCAGGGACACTGTGTTGTCAGGGTTAAG                         TGAGGAAGACATGCTAAAGAAGCTCGGTGACCTTATGAACAAGAGCCACGA
genomic: GAGGCCAGGCGTGTTCATGCTTTCAGGGACACTGTGTTGTCAGGGTTAAGgtgagtcatc ... attattgcagTGAGGAAGACATGCTAAAGAAGCTCGGTGACCTTATGAACAAGAGCCACGA
EST: gi|33407058|gb|CF212685.1|CF212685
EST:     GAGGCCAGGCGTGTTCATGCTTTCAGGGACACTGTGTTGTCAGGGTTAAG                         TGAGGAAGACATGCTAAAGAAGCTCGGTGACCTTATGAACAAGAGCCACGA
genomic: GAGGCCAGGCGTGTTCATGCTTTCAGGGACACTGTGTTGTCAGGGTTAAGgtgagtcatc ... attattgcagTGAGGAAGACATGCTAAAGAAGCTCGGTGACCTTATGAACAAGAGCCACGA
EST: gi|110392261|gb|EC957554.1|EC957554
EST:     GAGGCCAGGCGTGTTCATGCTTTCAGGGACACTGTGTTGTCAGGGTTAAG                         TGAGGAAGACATGCTAAAGAAGCTCGGTGACCTTATGAACAAGAGCCACGA
genomic: GAGGCCAGGCGTGTTCATGCTTTCAGGGACACTGTGTTGTCAGGGTTAAGgtgagtcatc ... attattgcagTGAGGAAGACATGCTAAAGAAGCTCGGTGACCTTATGAACAAGAGCCACGA
EST: gi|110430378|gb|EC996932.1|EC996932
EST:     GGCCAGGCGTGTTCATGCTTTCAGGGACACTGTGTTGTCAGGGTTAAG                         TGAGGAAGACATGCTAAAGAAGCTCGGTGACCTTATGAACAAGAGCCACGA
genomic: GGCCAGGCGTGTTCATGCTTTCAGGGACACTGTGTTGTCAGGGTTAAGgtgagtcatc ... attattgcagTGAGGAAGACATGCTAAAGAAGCTCGGTGACCTTATGAACAAGAGCCACGA
EST: gi|30137246|gb|CB922584.1|CB922584
EST:     GAGGCCAGGCGTGTTCATGCTTTCAGGGACACTGTGTTGTCAGGGTTAAG                         TGAGGAAGACATGCTAAAGAAGCTCGGTGACCTTATGAACAAGAGCCACGA
genomic: GAGGCCAGGCGTGTTCATGCTTTCAGGGACACTGTGTTGTCAGGGTTAAGgtgagtcatc ... attattgcagTGAGGAAGACATGCTAAAGAAGCTCGGTGACCTTATGAACAAGAGCCACGA
EST: gi|110392865|gb|EC957405.1|EC957405
EST:     GAGGCCAGGCGTGTTCATGCTTTCAGGGACACTGTGTTGTCAGGGTTAAG                         TGAGGAAGACATGCTAAAGAAGCTCGGTGACCTTATGAACAAGAGCCACGA
genomic: GAGGCCAGGCGTGTTCATGCTTTCAGGGACACTGTGTTGTCAGGGTTAAGgtgagtcatc ... attattgcagTGAGGAAGACATGCTAAAGAAGCTCGGTGACCTTATGAACAAGAGCCACGA
EST: gi|27585689|gb|CB008384.1|CB008384
EST:     GAGGCCAGGCGTGTTCATGCTTTCAGGGACACTGTGTTGTCAGGGTTAAG                         TGAGGAAGACATGCTAAAGAAGCTCGGTGACCTTATGAACAAGAGCCACGA
genomic: GAGGCCAGGCGTGTTCATGCTTTCAGGGACACTGTGTTGTCAGGGTTAAGgtgagtcatc ... attattgcagTGAGGAAGACATGCTAAAGAAGCTCGGTGACCTTATGAACAAGAGCCACGA
EST: gi|27585107|gb|CB007802.1|CB007802
EST:     GAGGCCAGGCGTGTTCATGCTTTCAGGGACACTGTGTTGTCAGGGTTAAG                         TGAGGAAGACATGCTAAAGAAGCTCGGTGACCTTATGAACAAGAGCCACGA
genomic: GAGGCCAGGCGTGTTCATGCTTTCAGGGACACTGTGTTGTCAGGGTTAAGgtgagtcatc ... attattgcagTGAGGAAGACATGCTAAAGAAGCTCGGTGACCTTATGAACAAGAGCCACGA
EST: gi|32246094|gb|CD711913.1|CD711913
EST:     GAGGCCAGGCGTGTTCATGCTTTCAGGGACACTGTGTTGTCAGGGTTAAG                         TGAGGAAGACATGCTAAAGAAGCTCGGTGACCTTATGAACAAGAGCCACGA
genomic: GAGGCCAGGCGTGTTCATGCTTTCAGGGACACTGTGTTGTCAGGGTTAAGgtgagtcatc ... attattgcagTGAGGAAGACATGCTAAAGAAGCTCGGTGACCTTATGAACAAGAGCCACGA
EST: gi|30299334|gb|CB976128.1|CB976128
EST:     GAGGCCAGGCGTGTTCATGCTTTCAGGGACACTGTGTTGTCAGGGTTAAG                         TGAGGAAGACATGCTAAAGAAGCTCGGTGACCTTATGAACAAGAGCCACGA
genomic: GAGGCCAGGCGTGTTCATGCTTTCAGGGACACTGTGTTGTCAGGGTTAAGgtgagtcatc ... attattgcagTGAGGAAGACATGCTAAAGAAGCTCGGTGACCTTATGAACAAGAGCCACGA
EST: gi|110406864|gb|EC972451.1|EC972451
EST:     GAGGCCAGGCGTGTTCATGCTTTCAGGGACACTGTGTTGTCAGGGTTAAG                         TGAGGAAGACATGCTAAAGAAGCTCGGTGACCTTATGAACAAGAGCCACGA
genomic: GAGGCCAGGCGTGTTCATGCTTTCAGGGACACTGTGTTGTCAGGGTTAAGgtgagtcatc ... attattgcagTGAGGAAGACATGCTAAAGAAGCTCGGTGACCTTATGAACAAGAGCCACGA
EST: gi|33406531|gb|CF212158.1|CF212158
EST:     GAGGCCAGGCGTGTTCATGCTTTCAGGGACACTGTGTTGTCAGGGTTAAG                         TGAGGAAGACATGCTAAAGAAGCTCGGTGACCTTATGAACAAGAGCCACGA
genomic: GAGGCCAGGCGTGTTCATGCTTTCAGGGACACTGTGTTGTCAGGGTTAAGgtgagtcatc ... attattgcagTGAGGAAGACATGCTAAAGAAGCTCGGTGACCTTATGAACAAGAGCCACGA
EST: gi|294964251|gb|GW838054.1|GW838054
EST:     GAGGCCAGGCGTGTTCATGCTTTCAGGGACACTGCGTTGTCAGGGTTAAG                         TGAGGAAGACATGCTAAAGAAGCTCGGTTGAC-TTATGAACAAAGAGCCA
genomic: GAGGCCAGGCGTGTTCATGCTTTCAGGGACACTGTGTTGTCAGGGTTAAGgtgagtcatc ... attattgcagTGAGGAAGACATGCTAAAGAAGCTCGGT-GACCTTATGAACAA-GAGCCA
EST: gi|110732746|gb|EE108300.1|EE108300
EST:     GAGGCCAGGCGTGTTCATGCTTTCAGGGACACTGTGTTGTCAGGGTTAAG                         TGAGGAAGACATGCTAAAGAAGCTCGGTGACCTTATGAACAAGAGCCACGA
genomic: GAGGCCAGGCGTGTTCATGCTTTCAGGGACACTGTGTTGTCAGGGTTAAGgtgagtcatc ... attattgcagTGAGGAAGACATGCTAAAGAAGCTCGGTGACCTTATGAACAAGAGCCACGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggttgaccaattcaactttcttgaattctaatttccgaagtactattattgcagTGAGGAAGACATGCTAAAGAAGCTCGGTGACCTTATGAACAAGAGCCACGACAGCTGCAGTGTTTTATACGAGTGCAG
                          ttctaat  putative branch site (score: 2)
                     ttgaattctaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgatttcaatcaaaagggtttattgttgtgtgtgttatagagaagtggttgaccaattcaactttcttgaattctaatttccgaagtactattattgcagTGAGGAAGACATGCTAAAGAAGCTCGGTGACCTTATGAACAAGAGCCACGACAGCTGCAGTGTTTTATACGAGTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - -aatcaaa
- - - - - - - - - - - - - -gtgtgtg
- - - - - - - - - - - - - - - - - - atagaga
- - - - - - - - - - - - - - - - - - - - - - gtggttg
- - - - - - - - - - - - - - - - - - - - - - - - - - ccaattc