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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatttttgtatcaacttattacttgacaattattgcctatagttttttttgtggaactgctatgatctcactatgcaacatccattggtaatttgtcagGAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTAAAGAAAAGTGGTAAAACAGATAATGTTGCTTGGGCTTTTGGGCTTGGAT

Basic information

species Vitis vinifera
transcript Vv11s0103g00120.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0103g00120.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA18G52890.1 (Glycine max), 3'ss of exon 7
atatttttgtatcaacttattacttgacaattattgcctatagttttttttgtggaactgctatgatctcactatgcaacatccattg-gtaatttgt--cagGAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTAAAGAAAAGTGGTAAAACAGATAATGTTGCTTGGGCTTTTGGGCTTGGAT
   ||| |   |   ||| ||   |  |  ||  | ||| |  |||          | |  | | ||   |  | | ||  || |||   |  ||| |  ||||| || |||||||||||||| || ||||| |||||||||||||| ||  | |||| || ||| ||| |  |||||||||||||||||||||| || || |
---tttattcctatgcttgttttatttctcttcatccctgttttttcccactcaatagttttctaataaaatcaagtaatgtctattatatcttttattgcagGAAAAGTGGTTGGAAGTTTTGGGGTGTGGAGTGACAGAGCAAGAGATTCTGAAGAGAAATGGGAAACCTAATAATGTTGCTTGGGCTTTTGGTCTAGGGT

upper sequence: Vv11s0103g00120.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA02G10060.1 (Glycine max), 3'ss of exon 5
atatttttgtatcaacttattacttgacaattattgcctatagttttttttgtggaactgctatgatctcactatgcaacatccattg-gtaatttgt--cagGAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTAAAGAAAAGTGGTAAAACAGATAATGTTGCTTGGGCTTTTGGGCTTGGAT
   ||| |   |   ||| ||   |  |  ||  | ||| |  |||          | |  | | ||   | || | ||  |  | |   |  ||| |  ||||| || |||||||||||||| || ||||| |||||||||||||| ||  | |||| || ||| ||| |  |||| ||||||||||||||||| || || |
---tttattcctatgcttgttttatttctcttcatccctgttttttcccactcaatagttttgtaataaaattaagtaatgtttaatatatcttttattgcagGAAAAGTGGTTGGAAGTTTTGGGGTGTGGAGTGACAGAGCAAGAGATTCTGAAGAGAAATGGGAAACCTAATAAGGTTGCTTGGGCTTTTGGCCTAGGGT
















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|352798745|gb|FQ478380.1|FQ478380
EST:     CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAG                         GAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
genomic: CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAGgtatgcttct ... aatttgtcagGAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
EST: gi|352790555|gb|FQ478194.1|FQ478194
EST:     CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAG                         GAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
genomic: CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAGgtatgcttct ... aatttgtcagGAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
EST: gi|349825743|gb|FQ421842.1|FQ421842
EST:     CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAG                         GAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
genomic: CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAGgtatgcttct ... aatttgtcagGAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
EST: gi|351054533|gb|FQ452009.1|FQ452009
EST:     CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAG                         GAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
genomic: CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAGgtatgcttct ... aatttgtcagGAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
EST: gi|351044982|gb|FQ449236.1|FQ449236
EST:     CATATTTCCCTTTCACCAACCCATCANTTGAACTTGAGATATATTTTCAG                         GAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
genomic: CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAGgtatgcttct ... aatttgtcagGAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
EST: gi|352790299|gb|FQ481498.1|FQ481498
EST:     CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAG                         GAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
genomic: CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAGgtatgcttct ... aatttgtcagGAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
EST: gi|349813045|gb|FQ411285.1|FQ411285
EST:     CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAA                         GAGAAATGGTTGGAAATTTTAG
genomic: CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAGgtatgcttct ... aatttgtcagGAGAAATGGTTGGAAGTTTTAG
EST: gi|349819738|gb|FQ402675.1|FQ402675
EST:     CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAG                         GAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
genomic: CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAGgtatgcttct ... aatttgtcagGAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
EST: gi|351045887|gb|FQ441270.1|FQ441270
EST:     CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAG                         GAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
genomic: CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAGgtatgcttct ... aatttgtcagGAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
EST: gi|351027076|gb|FQ439937.1|FQ439937
EST:     CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAG                         GAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
genomic: CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAGgtatgcttct ... aatttgtcagGAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
EST: gi|349808821|gb|FQ406671.1|FQ406671
EST:     CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAG                         GAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
genomic: CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAGgtatgcttct ... aatttgtcagGAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
EST: gi|351045846|gb|FQ441031.1|FQ441031
EST:     CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAG                         GAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
genomic: CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAGgtatgcttct ... aatttgtcagGAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
EST: gi|351032114|gb|FQ460371.1|FQ460371
EST:     CATATTTCCCTCTCACCAACCCATCATTTGAACTTGAGATATATTTTCAG                         GAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
genomic: CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAGgtatgcttct ... aatttgtcagGAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
EST: gi|352786352|gb|FQ478961.1|FQ478961
EST:     CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAG                         GAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
genomic: CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAGgtatgcttct ... aatttgtcagGAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
EST: gi|351053292|gb|FQ459160.1|FQ459160
EST:     CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAG                         GAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
genomic: CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAGgtatgcttct ... aatttgtcagGAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
EST: gi|351049456|gb|FQ450057.1|FQ450057
EST:     CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAG                         GAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
genomic: CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAGgtatgcttct ... aatttgtcagGAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
EST: gi|351048459|gb|FQ448733.1|FQ448733
EST:     CATATTTCCCTCTCACCAACCCATCATTTGAACTTGAGATATATTTTCAG                         GAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
genomic: CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAGgtatgcttct ... aatttgtcagGAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
EST: gi|351032730|gb|FQ462444.1|FQ462444
EST:     CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAG                         GAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
genomic: CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAGgtatgcttct ... aatttgtcagGAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
EST: gi|352789829|gb|FQ478644.1|FQ478644
EST:     CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAG                         GAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
genomic: CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAGgtatgcttct ... aatttgtcagGAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
EST: gi|351052538|gb|FQ456386.1|FQ456386
EST:     CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAG                         GAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
genomic: CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAGgtatgcttct ... aatttgtcagGAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
EST: gi|349807616|gb|FQ402007.1|FQ402007
EST:     CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAG                         GAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
genomic: CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAGgtatgcttct ... aatttgtcagGAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
EST: gi|351048130|gb|FQ442100.1|FQ442100
EST:     CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGGTATATTTTCAG                         GAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
genomic: CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAGgtatgcttct ... aatttgtcagGAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
EST: gi|351052564|gb|FQ456412.1|FQ456412
EST:     CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAG                         GAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
genomic: CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAGgtatgcttct ... aatttgtcagGAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
EST: gi|351043334|gb|FQ451386.1|FQ451386
EST:     CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAG                         GAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
genomic: CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAGgtatgcttct ... aatttgtcagGAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
EST: gi|33406238|gb|CF211865.1|CF211865
EST:     CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAG                         GAGAAATGGTTG
genomic: CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAGgtatgcttct ... aatttgtcagGAGAAATGGTTG
EST: gi|351019220|gb|FQ429380.1|FQ429380
EST:     CATATTTCCCTTTCACCAACCCATCACTTGAACTTGAGATATATTTTCAG                         GAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
genomic: CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAGgtatgcttct ... aatttgtcagGAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
EST: gi|349815992|gb|FQ403595.1|FQ403595
EST:     CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAG                         GAGAAATGGTTGGAAGTTTTACGTTGTGGGGTGACAGAGCAAGAAATATTA
genomic: CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAGgtatgcttct ... aatttgtcagGAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
EST: gi|349808786|gb|FQ406636.1|FQ406636
EST:     CATATTTCCCTCTCACCAACCCATCATTTGAACTTGAGATATATTTTCAG                         GAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
genomic: CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAGgtatgcttct ... aatttgtcagGAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
EST: gi|33406146|gb|CF211773.1|CF211773
EST:     CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAG                         GAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
genomic: CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAGgtatgcttct ... aatttgtcagGAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
EST: gi|349814979|gb|FQ410202.1|FQ410202
EST:     CATATTTCCCTCTCACCAACCCATCATTTGAACTTGAGATATATTTTCAG                         GAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACGGAGCAAGAAATATTA
genomic: CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAGgtatgcttct ... aatttgtcagGAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
EST: gi|349830653|gb|FQ416951.1|FQ416951
EST:     CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAG                         GAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
genomic: CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAGgtatgcttct ... aatttgtcagGAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
EST: gi|351038109|gb|FQ465226.1|FQ465226
EST:     CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAG                         GAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA
genomic: CATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAGgtatgcttct ... aatttgtcagGAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttgtggaactgctatgatctcactatgcaacatccattggtaatttgtcagGAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTAAAGAAAAGTGGTAAAACAGATAATGTTGCTTGGGCTTTTGGGCTTGGAT
                    atctcac  putative branch site (score: 3)
                                            taatttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatttttgtatcaacttattacttgacaattattgcctatagttttttttgtggaactgctatgatctcactatgcaacatccattggtaatttgtcagGAGAAATGGTTGGAAGTTTTAGGTTGTGGGGTGACAGAGCAAGAAATATTAAAGAAAAGTGGTAAAACAGATAATGTTGCTTGGGCTTTTGGGCTTGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - tgcctat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgctat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acatcca