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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATCTTTAAGCAAAGGGTGACAAATGTGGTGTTTATGGGAATGGGCGAACCAATGTTGAACCTGAAATCAGTTATTGAAGCTCACCGTTGCTTGAATAAGgtcacttattaactctttcatgcacaattgttaatcatctatatgctggttctaattttttcatttagctaaagttcataacaagtcaaccgatttttct...

Basic information

species Vitis vinifera
transcript Vv13s0019g01070.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g01070.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: LOC_Os01g74190.1 (Oryza sativa), 5'ss of exon 6
GATCTTTAAGCAAAGGGTGACAAATGTGGTGTTTATGGGAATGGGCGAACCAATGTTGAACCTGAAATCAGTTATTGAAGCTCACCGTTGCTTGAATAAGgtcactta---ttaactctttcatgcacaattgttaatcatcta---tatgctggttctaattttttcatttagctaaagttcata-acaagtcaac--cgatttttct--------
||  ||  | || |||||||||||||| ||||| ||||| ||||| || || ||||||||||||||||||||| | || || || || |||||||| |||||     |   | || | |||  |       | ||  |||  ||   | ||    |  |  |  ||  ||    | | | ||  ||  |   |||||   ||||||| |        
GACGTTCCAACACAGGGTGACAAATGTAGTGTTCATGGGGATGGGTGAGCCTATGTTGAACCTGAAATCAGTTTTAGAGGCACATCGATGCTTGAACAAGgtttgccaaactgaatttttttcttagttccttttgctcaagtagtttttgtgaatcattgtcattgtatcatacaataatttgtatgcctttcaactttgattttttttttggcag

upper sequence: Vv13s0019g01070.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G168412_T01 (Zea mays), 5'ss of exon 5
GATCTTTAAGCAAAGGGTGACAAATGTGGTGTTTATGGGAATGGGCGAACCAATGTTGAACCTGAAATCAGTTATTGAAGCTCACCGTTGCTTGAATAAGgtcacttattaactctttcatgcacaattgt-------taatcatct-atatgctggtt--cta-----attttttcat-ttagctaaagttcataacaagtcaaccgatttttct-------
||  || || || |||||||||||||| ||||| ||||| ||||| || || ||| ||||||| || |||||| | ||||| ||||  ||||| |||||||||  ||   || |   |     ||| |  |       |  | || | ||  |    ||  | |     || ||| ||| | ||||| |  |  ||||||||     |||||           
GACGTTCAAACACAGGGTGACAAATGTTGTGTTCATGGGGATGGGTGAGCCCATGATGAACCTCAAGTCAGTTCTAGAAGCACACCAATGCTTCAATAAGgtctgttgacaagtaactaggctacattcctctcatcctgttaatttgatgcgacaatttaccatgaatatctttccatataagctataactt-taacaagtgcgtggatttcatgctgtcag

upper sequence: Vv13s0019g01070.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G395039_T01 (Zea mays), 5'ss of exon 4
GATCTTTAAGCAAAGGGTGACAAATGTGGTGTTTATGGGAATGGGCGAACCAATGTTGAACCTGAAATCAGTTATTGAAGCTCACCGTTGCTTGAATAAGgtcacttattaactctttcatgcacaattgt-------taatcatct-atatgctggtt--cta-----attttttcatttagctaaagttcataacaagtcaaccgatttttct-------
||  || ||  | |||||||||||||| ||||| || || ||||| || || ||| ||||||| || |||||| | ||||| ||||  ||||| |||||||||  ||   || |   |     ||| |  |       |  | || | ||  |    ||  | |     || | | ||| ||    | |    ||||||||     |||||           
GACGTTCAAATACAGGGTGACAAATGTTGTGTTCATTGGGATGGGTGAGCCCATGATGAACCTCAAGTCAGTTCTAGAAGCACACCAATGCTTCAATAAGgtctgttgacaagtaactaggctacattcctctcatcctgttaatttgatgcgacaatttaccatgagtatctctccatataagctatgactttaacaagtgcgtggatttcatgctgtcag

upper sequence: Vv13s0019g01070.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA14G07450.1 (Glycine max), 5'ss of exon 6
GATCTTTAAGCAAAGGGTGACAAATGTGGTGTTTATGGGAATGGGCGAACCAATGTTGAACCTGAAATCAGTTATTGAAGCTCACCGTTGCTTGAATAAGgtcacttattaactctttcatgcacaattgttaatcatctatatgctggttctaattttttcatttagct-aaagttcataacaagtcaaccgatttttct----
| |||| ||| | |||||||||||||| ||||||||||||||||| ||||||||||| ||||||||  ||||  ||||||| |||||||||||||||||||| | | | | | | |   |||    ||| ||     || | ||||    ||||  |    |||     | | | | ||||   | |  | |     |       
GGTCTTCAAGAATAGGGTGACAAATGTAGTGTTTATGGGAATGGGTGAACCAATGTTAAACCTGAAGGCAGTACTTGAAGCACACCGTTGCTTGAATAAGgtgaataaatgaatgtgatatgtgacattatttgct-tccaaatgc--actcta--tgccacatgggattgagaatgcatatgtaatttatcttcaatagaagtg

upper sequence: Vv13s0019g01070.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA02G41500.1 (Glycine max), 5'ss of exon 6
GATCTTTAAGCAAAGGGTGACAAATGTGGTGTTTATGGGAATGGGCGAACCAATGTTGAACCTGAAATCAGTTATTGAAGCTCACCGTTGCTTGAATAAGgtcacttattaactctttcatgcacaattgttaatcatctatatgctggttctaattttttcatttagctaaagttcataacaagtcaaccgatttttct---
| |||| ||| | |||||||||||||| ||||||||||||||||| ||||||||||| ||||||||  ||||  ||||||| |||| ||||||||||||||| |   | | ||| |   |||    ||| ||   | || | |||||   | |    ||   |      |  |  | | |   ||  | |  | |||  |   
GGTCTTCAAGAATAGGGTGACAAATGTAGTGTTTATGGGAATGGGTGAACCAATGTTAAACCTGAAGGCAGTACTTGAAGCACACCATTGCTTGAATAAGgtgaacaaatgactgtgatatgtgacattattt-ccttccaaatgcttacttttgagttgcaacggtattcta--tgagattgagatatcaaactttcatgta

upper sequence: Vv13s0019g01070.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT2G39670.1 (Arabidopsis thaliana), 5'ss of exon 6
GATCTTTAAGCAAAGGGTGACAAATGTGGTGTTTATGGGAATGGGCGAACCAATGTTGAACCTGAAATCAGTTATTGAAGCTCACCGTTGCTTGAATAAGgtcactt-----attaactctttcatgcacaattgttaatcatctatatgctggttctaattttttcatttagctaaagttcataacaagtcaaccgatttttct
  | || ||||| ||||||||||||||||| || ||||||||||| || || ||||||||||| || |||||  |||| ||||| ||||| ||||| ||||| || |     | || |  |||| ||    |   |   |           || ||  | || || |       | | |  ||    || | ||  |        
CGTGTTCAAGCATAGGGTGACAAATGTGGTTTTCATGGGAATGGGTGAGCCGATGTTGAACCTAAAGTCAGTACTTGATGCTCATCGTTGTTTGAACAAGgtaacatttgccaatagccatttcctgtttcaacatggttttgtgcagaaatgattgaagttcttgctaagtatttagg--cactgtaaattaattggaaag---

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|351046512|gb|FQ453128.1|FQ453128
EST:     CGATGTTAAACCTGAAATCAGTTATTGAAGCTCACCGTTGCTTGAATAAG                         GACGTGCAAATTGGGCAAAGAATGATCACAATTTCCTCCGTAGGGGTTCCC
genomic: CAATGTTGAACCTGAAATCAGTTATTGAAGCTCACCGTTGCTTGAATAAGgtcacttatt ... ctgttttaagGATGTGCAAATTGGGCAAAGAATGATCACAATTTCCTCCGTAGGGGTTCCC
EST: gi|352794375|gb|FQ481606.1|FQ481606
EST:     CGATGTTAAACCTGAAATCAGTTATTGAAGCTCACCGTTGCTTGAATAAG                         GACGTGCAAATTGGGCAAAGAATGATCACAATTTCCTCCGTAGGGGTTCCC
genomic: CAATGTTGAACCTGAAATCAGTTATTGAAGCTCACCGTTGCTTGAATAAGgtcacttatt ... ctgttttaagGATGTGCAAATTGGGCAAAGAATGATCACAATTTCCTCCGTAGGGGTTCCC
EST: gi|351048097|gb|FQ442067.1|FQ442067
EST:     CGATGTTAAACCTGAAATCAGTTATTGAAGCTCACCGTTGCTTGAATAAG                         GACGTGCAAATTGGGCAAAGAATGATCACAATTTCCTCCGTAGGGGTTCCC
genomic: CAATGTTGAACCTGAAATCAGTTATTGAAGCTCACCGTTGCTTGAATAAGgtcacttatt ... ctgttttaagGATGTGCAAATTGGGCAAAGAATGATCACAATTTCCTCCGTAGGGGTTCCC
EST: gi|352786528|gb|FQ479735.1|FQ479735
EST:     CGATGTTAAACCTGAAATCAGTTATTGAAGCTCACCGTTGCTTGAATAAG                         GACGTGCAAATTGGGCAAAGAATGATCACAATTTCCTCCGTAGGGGTTCCC
genomic: CAATGTTGAACCTGAAATCAGTTATTGAAGCTCACCGTTGCTTGAATAAGgtcacttatt ... ctgttttaagGATGTGCAAATTGGGCAAAGAATGATCACAATTTCCTCCGTAGGGGTTCCC
EST: gi|351038424|gb|FQ461116.1|FQ461116
EST:     CGATGTTAAACCTGAAATCAGTTATTGAAGCTCACCGTTGCTTGAATAAG                         GATGTGCAAATTGGGCAAAGAATGATCACAATTTCCTCCGTAGGGGTTCCC
genomic: CAATGTTGAACCTGAAATCAGTTATTGAAGCTCACCGTTGCTTGAATAAGgtcacttatt ... ctgttttaagGATGTGCAAATTGGGCAAAGAATGATCACAATTTCCTCCGTAGGGGTTCCC
EST: gi|351054685|gb|FQ462715.1|FQ462715
EST:     CGATGTTAAACCTGAAATCAGTTATTGAAGCTCGCCGTTGCTTGAATAAG                         GACGTGCAAATTGGGCAAAGAATGATCACAATTTCCTCCGTAGGGGTTCCC
genomic: CAATGTTGAACCTGAAATCAGTTATTGAAGCTCACCGTTGCTTGAATAAGgtcacttatt ... ctgttttaagGATGTGCAAATTGGGCAAAGAATGATCACAATTTCCTCCGTAGGGGTTCCC
EST: gi|351035218|gb|FQ458575.1|FQ458575
EST:     CGATGTTAAACCTGAAATCAGTTATTGAAGCTCACCGTTGCTTGAATAAG                         GATGTGCAAATTGGGCAAAGAATGATCACAATTTCCTCCGTAGGGGTTCCC
genomic: CAATGTTGAACCTGAAATCAGTTATTGAAGCTCACCGTTGCTTGAATAAGgtcacttatt ... ctgttttaagGATGTGCAAATTGGGCAAAGAATGATCACAATTTCCTCCGTAGGGGTTCCC
EST: gi|71874359|gb|DT023414.1|DT023414
EST:     CGATGTTAAACCTGAAATCAGTTATTGAAGCTCACCGTTGCTTGAATAAG                         GATGTGCAAATTGGGCAAAGAATGATCACAATTTCCTCCGTAGGGGTTCCC
genomic: CAATGTTGAACCTGAAATCAGTTATTGAAGCTCACCGTTGCTTGAATAAGgtcacttatt ... ctgttttaagGATGTGCAAATTGGGCAAAGAATGATCACAATTTCCTCCGTAGGGGTTCCC
EST: gi|351032693|gb|FQ462407.1|FQ462407
EST:     CGATGTTAAACCTGAAATCAGTTATTGAAGCTCACCGTTGCTTGAATAAG                         GACGTGCAAATTGGGCAAAGAATGATCACAATTTCCTCCGTAGGGGTTCCC
genomic: CAATGTTGAACCTGAAATCAGTTATTGAAGCTCACCGTTGCTTGAATAAGgtcacttatt ... ctgttttaagGATGTGCAAATTGGGCAAAGAATGATCACAATTTCCTCCGTAGGGGTTCCC
EST: gi|351044866|gb|FQ449120.1|FQ449120
EST:     CGATGTTAAACCTGAAATCAGTTATTGAAGCTCACCGTTGCTTGAATAAG                         GACGTGCAAATTGGGCAAAGAATGATCACAATTTCCTCCGTAGGGGTTCCC
genomic: CAATGTTGAACCTGAAATCAGTTATTGAAGCTCACCGTTGCTTGAATAAGgtcacttatt ... ctgttttaagGATGTGCAAATTGGGCAAAGAATGATCACAATTTCCTCCGTAGGGGTTCCC
EST: gi|352795590|gb|FQ480178.1|FQ480178
EST:     CGATGTTAAACCTGAAATCAGTTATTGAAGCTCACCGTTGCTTGAATAAG                         GATGTGCAAATTGGGCAAAGAATGATCACAATTTCCTCCGTAGGGGTTCCC
genomic: CAATGTTGAACCTGAAATCAGTTATTGAAGCTCACCGTTGCTTGAATAAGgtcacttatt ... ctgttttaagGATGTGCAAATTGGGCAAAGAATGATCACAATTTCCTCCGTAGGGGTTCCC
EST: gi|352793767|gb|FQ481122.1|FQ481122
EST:     CGATGTTAAACCTGAAATCAGTTATTGAAGCTCACCGTTGCTTGAATAAG                         GACGTGCAAATTGGGCAAAGAATGATCACAATTTCCTCCGTAGGGGTTCCC
genomic: CAATGTTGAACCTGAAATCAGTTATTGAAGCTCACCGTTGCTTGAATAAGgtcacttatt ... ctgttttaagGATGTGCAAATTGGGCAAAGAATGATCACAATTTCCTCCGTAGGGGTTCCC
EST: gi|77585559|gb|DV221873.1|DV221873
EST:     CGATGTTAAACCTGAAATCAGTTATTGAAGCTCACCGTTGCTTGAATAAG                         GATGTGCAAATTGGGCAAAGAATGATCACAATTTCCTCCGTAGGGGTTCCC
genomic: CAATGTTGAACCTGAAATCAGTTATTGAAGCTCACCGTTGCTTGAATAAGgtcacttatt ... ctgttttaagGATGTGCAAATTGGGCAAAGAATGATCACAATTTCCTCCGTAGGGGTTCCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATCTTTAAGCAAAGGGTGACAAATGTGGTGTTTATGGGAATGGGCGAACCAATGTTGAACCTGAAATCAGTTATTGAAGCTCACCGTTGCTTGAATAAGgtcacttattaactctttcatgcacaattgttaatcatctatatgctggttctaattttttcatttagctaaagttcataacaagtcaaccgatttttct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ataacaag