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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGATTTGGAGGAGTAAAGAGGACTTGCCCGATGAGCTCATCTTTCATATCAACTATCTTGGAGCCGACCAACCTACCTTCACCCTCAACTTCTCCAAAGgtccccttccaaactactgctacatctttgagatcttttttgatgatcataatataatgcatgctaagtattaattttcctcccaatgcag

Basic information

species Vitis vinifera
transcript Vv04s0079g00600.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0079g00600.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA11G33280.1 (Glycine max), 5'ss of exon 3
GTGATTTGGAGGAGTAAAGAGGACTTGCCCGATGAGCTCATCTTTCATATCAACTATCTTGGAGCCGACCAACCTACCTTCACCCTCAACTTCTCCAAAGgtccccttccaaactactgctacatctttgagatcttttttgatgatcataatataatgcatgctaagt--attaattttcctcccaatgcag----------------------------------------------------------
|| || ||||| || || ||||||||||| || || ||||||||||| |||||||||||||| || || ||||| ||||||||||| |||||||||||||||        |    | ||||   | ||  || | | | |   |  |  ||||  |   ||    || |  |||| || | ||  |  ||||                                                           
GTTATCTGGAGAAGCAAGGAGGACTTGCCTGAGGAACTCATCTTTCACATCAACTATCTTGGTGCTGATCAACCCACCTTCACCCTTAACTTCTCCAAAGgtaaaacataattgaattgctcagtttt--agttgtatctaagtactactaattaacaacaaagcaaatttattacttgtgctttc--tgcaaccattctttggtttatgcacgagtatgtactcattgtttcacaaaatatgcaatgcag

upper sequence: Vv04s0079g00600.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA18G04940.1 (Glycine max), 5'ss of exon 5
GTGATTTGGAGGAGTAAAGAGGACTTGCCCGATGAGCTCATCTTTCATATCAACTATCTTGGAGCCGACCAACCTACCTTCACCCTCAACTTCTCCAAAGgtccccttccaaactactgctacatctttgag-atcttttttgatgatcataatataatgcatgctaagtattaattttcctc-----ccaatgcag------------------------------------------
|| || ||||| || ||  |||||||||| || || ||||||||||| |||||||||||||| || || ||||| ||||||||||| |||||||||||||||| |          | | ||   | ||||   |    |    |  | |   || || |  |  ||   ||| ||    | ||        |||||                                           
GTTATCTGGAGAAGCAAGCAGGACTTGCCTGAGGAACTCATCTTTCACATCAACTATCTTGGGGCTGATCAACCCACCTTCACCCTTAACTTCTCCAAAGgtcacacatattttaattcctcagtttttgtctactactaaaaacaacccctatttact-tacactttctatcaaacaccttcattggtttatgcacgagtatgtactcattgtttcacaaaatatcaaatgcatgcag

upper sequence: Vv04s0079g00600.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA02G40840.1 (Glycine max), 5'ss of exon 5
GTGATTTGGAGGAGTAAAGAGGACTTGCCCGATGAGCTCATCTTTCATATCAACTATCTTGGAGCCGACCAACCTACCTTCACCCTCAACTTCTCCAAAGgtcc----ccttccaaactactgctacatctttgagatct-tttttgatgatcataatataatgcatgcta-agtattaattttcctcccaatgcag---------------------------------------------------
|| |||||||| || || || ||| | || || || ||||| || || || |||||||| ||||| || ||||| |||||||||||||||||||||||||||      |   |  || |  | | | | |    |  |   |  ||||     || ||    | |    |  |  |||||||    |    ||   |                                                   
GTCATTTGGAGAAGCAAGGAAGACCTTCCTGAGGAACTCATTTTCCACATTAACTATCTAGGAGCTGATCAACCCACCTTCACCCTCAACTTCTCCAAAGgtaattgacacactcaattggttcaataacaactaactagatacttgacctgaattatgcttttccctttgtaccattaattagtttatgcatattgatcactactaggtagtaggtactaatttctttcatgaaatatgcaatgcag

upper sequence: Vv04s0079g00600.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA14G39170.1 (Glycine max), 5'ss of exon 6
GTGATTTGGAGGAGTAAAGAGGACTTGCCCGATGAGCTCATCTTTCATATCAACTATCTTGGAGCCGACCAACCTACCTTCACCCTCAACTTCTCCAAAGgtcccc----ttccaaactactgctacatctttgagatcttttttgatgatcataat-ataatgcatgctaagta---ttaattttcctcccaatgcag--------------------------------------------------
|| |||||||| || || || ||| | || || || ||||| || || || |||||||| ||||| || ||||| |||||||||||||||||||||||||||          |  || |  ||| | | ||   |  |   |     ||| | |||| ||  |     ||  |||    |||||    |    ||   |                                                  
GTCATTTGGAGAAGCAAGGAAGACCTTCCTGAGGAACTCATTTTCCACATTAACTATCTAGGAGCTGATCAACCCACCTTCACCCTCAACTTCTCCAAAGgtaattgaagcactcaattggtgcaataactactaactagataaaattgaccttaattattcttttccctttgtaccactaattagtatatgcatattgatcactactagtactaggtactaatttcttccatgaaatatgcaatgcag

upper sequence: Vv04s0079g00600.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: PP1S8_163V6.1 (Physcomitrella patens), 5'ss of exon 4
GTGATTTGGAGGAGTAAAGAGGACTTGCCCGATGAGCTCATCTTTCATATCAACTATCTTGGAGCCGACCAACCTACCTTCACCCTCAACTTCTCCAAAGgt--------ccccttccaaactactgctacatctttga--gatcttttttgatgatcataatataatgcatgctaagtattaattttcctcccaatgcag----------------------------------------------------------------------------------------------------
||  | ||| | || || |||||| | ||||| ||| | || |||||  |||||||  | |||||||| || || |||||||||||||||||||| ||||||        | | |   |||| ||| |  ||   |  |  ||||| || | |     |   | || |   | |        |   |      ||  |||                                                                                                     
GTTGTGTGGCGCAGCAAGGAGGACCTTCCCGAGGAGTTGATTTTTCACGTCAACTACTTGGGAGCCGATCAGCCCACCTTCACCCTCAACTTCTCTAAAGgtttgcactgctcttgttaaacgacttcaccagagtaaactgatctcttctaac--ctacggt-tactcttttcctgcagccatcgtctagaacagagcattcagcagcctcgagaacctcctgcgtgagggaaatgttgacagattggcgaggtcatcactacatctcactgtactaacgaccgttgtcttgtgagtcag

upper sequence: Vv04s0079g00600.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: EFJ18071 (Selaginella moellendorffii), 5'ss of exon 5
GTGATTTGGAGGAGTAAAGAGGACTTGCCCGATGAGCTCATCTTTCATATCAACTATCTTGGAGCCGACCAACCTACCTTCACCCTCAACTTCTCCAAAGgtccccttccaaactactgctacatctttgagatcttttttgatgatcataatataatgcatgctaagtattaattttcctcccaatgcag
|| || |||||  | || || ||  | || || |||||| |||| || ||||| ||||||||||||||||| || || ||||| ||||| || ||||||||| |  |     | |  |  |   |  |     ||| || | ||     |  | ||   ||                              
GTTATCTGGAGAGGCAAGGAAGATCTTCCGGAAGAGCTCGTCTTCCACATCAATTATCTTGGAGCCGACCAGCCAACTTTCACTCTCAATTTTTCCAAAGgttcttt----gagtgttcttttgttctatcactctcttatcatt-ctgtcttttaccacag-----------------------------

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|34545888|gb|CF514120.1|CF514120
EST:     CAACTATCTTGGAGCCGACCAACCTACCTTCACCCTCAACTTCTCCAAAG                         GTTCTAGTCAAGTTATTGCTCAGTATTATCAACTCATTCGCTTGGGCCATG
genomic: CAACTATCTTGGAGCCGACCAACCTACCTTCACCCTCAACTTCTCCAAAGgtccccttcc ... cccaatgcagGTTCTAGTCAAGTTATTGCTCAGTATTATCAACTCATTCGCTTGGGCCATG
EST: gi|352782596|gb|FQ476676.1|FQ476676
EST:     CAACTATCTTGGAGCCGACCAACCTACCTTCACCCTCAACTTCTCCAAAG                         GTTCTAGTCAAGTTATTGCTCAGTATTATCAACTCATTCGCTTGGGCCATG
genomic: CAACTATCTTGGAGCCGACCAACCTACCTTCACCCTCAACTTCTCCAAAGgtccccttcc ... cccaatgcagGTTCTAGTCAAGTTATTGCTCAGTATTATCAACTCATTCGCTTGGGCCATG
EST: gi|351022502|gb|FQ447024.1|FQ447024
EST:     CAACTATCTTGGAGCCGACCAACCTACCTTCACCCTCAACTTCTCCAAAG                         GTTCTAGTCAAGTTATTGCTCAGTATTATCAACTCATTCGCTTGGGCCATG
genomic: CAACTATCTTGGAGCCGACCAACCTACCTTCACCCTCAACTTCTCCAAAGgtccccttcc ... cccaatgcagGTTCTAGTCAAGTTATTGCTCAGTATTATCAACTCATTCGCTTGGGCCATG
EST: gi|28962726|gb|CB341759.1|CB341759
EST:     CCTCAACTTCTCCAAAG                         GTTCTAGTCAAGTTATTGCTCAGTATTATCAACTCATTCGCTTGGGCCATG
genomic: CCTCAACTTCTCCAAAGgtccccttcc ... cccaatgcagGTTCTAGTCAAGTTATTGCTCAGTATTATCAACTCATTCGCTTGGGCCATG
EST: gi|26264279|gb|CA815342.1|CA815342
EST:     AACTAGTCTTGGAGCCGACCAACCTACCTTCACCCTCAACTTCTCCAAAG                         GTTCTAGTCAAGTTATTGCTCAGTATTATCAACTCATTCGCTTGGGCCATG
genomic: AACTA-TCTTGGAGCCGACCAACCTACCTTCACCCTCAACTTCTCCAAAGgtccccttcc ... cccaatgcagGTTCTAGTCAAGTTATTGCTCAGTATTATCAACTCATTCGCTTGGGCCATG
EST: gi|26262418|gb|CA813481.1|CA813481
EST:     CAACTATCTTGGAGCCGACCAACCTACCTTCACCCTCAACTTCTCCAAAG                         GTTCTAGTCAAGTTATTGCTCAGTATTATCAACTCATTCGCTTGGGCCATG
genomic: CAACTATCTTGGAGCCGACCAACCTACCTTCACCCTCAACTTCTCCAAAGgtccccttcc ... cccaatgcagGTTCTAGTCAAGTTATTGCTCAGTATTATCAACTCATTCGCTTGGGCCATG
EST: gi|352794613|gb|FQ475111.1|FQ475111
EST:     GCCGACCAACCTACCTTCACCCTCAACTTCTCCAAAG                         GTTCTAGTCAAGTTATTGCTCAGTATTATCAACTCATTCGCTTGGGCCATG
genomic: GCCGACCAACCTACCTTCACCCTCAACTTCTCCAAAGgtccccttcc ... cccaatgcagGTTCTAGTCAAGTTATTGCTCAGTATTATCAACTCATTCGCTTGGGCCATG
EST: gi|110716839|gb|EE092172.1|EE092172
EST:     CAACTATCTTGGAGCCGACCAACCTACCTTCACCCTCAACTTCTCCAAAG                         GTTCTAGTCAAGTTATTGCTCAGTATTATCAACTCATTCGCTTGGGCCATG
genomic: CAACTATCTTGGAGCCGACCAACCTACCTTCACCCTCAACTTCTCCAAAGgtccccttcc ... cccaatgcagGTTCTAGTCAAGTTATTGCTCAGTATTATCAACTCATTCGCTTGGGCCATG
EST: gi|29785100|gb|CB341828.2|CB341828
EST:     CAACTATCTTGGAGCCGACCAACCTACCTTCACCCTCAACTTCTCCAAAG                         GTTCTAGTCAAGTTATTGCTCAGTATTATCAACTCATTCGCTTGGGCCATG
genomic: CAACTATCTTGGAGCCGACCAACCTACCTTCACCCTCAACTTCTCCAAAGgtccccttcc ... cccaatgcagGTTCTAGTCAAGTTATTGCTCAGTATTATCAACTCATTCGCTTGGGCCATG
EST: gi|30324791|gb|CD008053.1|CD008053
EST:     CAACTATCTTGGAGCCGACCAACCTACCTTCACCCTCAACTTCTCCAAAG                         GTTCTAGTCAAGTTATTGCTCAGTATTATCAACTCATTCGCTTGGGCCATG
genomic: CAACTATCTTGGAGCCGACCAACCTACCTTCACCCTCAACTTCTCCAAAGgtccccttcc ... cccaatgcagGTTCTAGTCAAGTTATTGCTCAGTATTATCAACTCATTCGCTTGGGCCATG
EST: gi|110720857|gb|EE097156.1|EE097156
EST:     CAACTATCTTGGAGCCGACCAACCTACCTTCACCCTCAACTTCTCCAAAG                         GTTCTAGTCAAGTTATTGCTCAGTATTATCAACTCATTCGCTTGGGCCATG
genomic: CAACTATCTTGGAGCCGACCAACCTACCTTCACCCTCAACTTCTCCAAAGgtccccttcc ... cccaatgcagGTTCTAGTCAAGTTATTGCTCAGTATTATCAACTCATTCGCTTGGGCCATG
EST: gi|352764778|gb|FQ471838.1|FQ471838
EST:     AACCTACCTTCACCCTCAACTTCTCCAAAG                         GTTCTAGTCAAGTTATTGCTCAGTATTATCAACTCATTCGCTTGGGCCATG
genomic: AACCTACCTTCACCCTCAACTTCTCCAAAGgtccccttcc ... cccaatgcagGTTCTAGTCAAGTTATTGCTCAGTATTATCAACTCATTCGCTTGGGCCATG
EST: gi|26266190|gb|CA817253.1|CA817253
EST:     ATCTTGGAGCCGACCAACCTACCTTCACCCTCAATTTCTCCAAAG                         GTTCTAGTCAAGTTATTGCTCAGTATTATCAACTCATTCGCTTGGGCCATG
genomic: ATCTTGGAGCCGACCAACCTACCTTCACCCTCAACTTCTCCAAAGgtccccttcc ... cccaatgcagGTTCTAGTCAAGTTATTGCTCAGTATTATCAACTCATTCGCTTGGGCCATG
EST: gi|110697963|gb|EE075429.1|EE075429
EST:     CAACTATCTTGGAGCCGACCAACCTACCTTCACCCTCAACTTCTCCAAAG                         GTTCTAGTCAAGTTATTGCTCAGTATTATCAACTCATTCGCTTGGGCCATG
genomic: CAACTATCTTGGAGCCGACCAACCTACCTTCACCCTCAACTTCTCCAAAGgtccccttcc ... cccaatgcagGTTCTAGTCAAGTTATTGCTCAGTATTATCAACTCATTCGCTTGGGCCATG
EST: gi|32270055|gb|CD719214.1|CD719214
EST:     CAACTATCTTGGAGCCGACCAACCTACCTTCACCCTCAACTTCTCCAAAG                         GTTCTAGTCAAGTTATTGCTCAGTATTATCAACTCATTCGCTTGGGCCATG
genomic: CAACTATCTTGGAGCCGACCAACCTACCTTCACCCTCAACTTCTCCAAAGgtccccttcc ... cccaatgcagGTTCTAGTCAAGTTATTGCTCAGTATTATCAACTCATTCGCTTGGGCCATG
EST: gi|110712431|gb|EE090048.1|EE090048
EST:     CAACTATCTTGGAGCCGACCAACCTACCTTCACCCTCAACTTCTCCAAAG                         GTTCTAGTCAAGTTATTGCTCAAGTATTATCAACTCATTCGCTTGGGCCAT
genomic: CAACTATCTTGGAGCCGACCAACCTACCTTCACCCTCAACTTCTCCAAAGgtccccttcc ... cccaatgcagGTTCTAGTCAAGTTATTGCTCA-GTATTATCAACTCATTCGCTTGGGCCAT
EST: gi|34548934|gb|CF517166.1|CF517166
EST:     GATC-ATCTTGGAGCCGACCAACCTACCTTCACCCTCAACTTCTCCAAAG                         GTTCTAGTCAAGTTATTGCTCAGTATTATCAACTCATTCGCTTGGGCCATG
genomic: -AACTATCTTGGAGCCGACCAACCTACCTTCACCCTCAACTTCTCCAAAGgtccccttcc ... cccaatgcagGTTCTAGTCAAGTTATTGCTCAGTATTATCAACTCATTCGCTTGGGCCATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGATTTGGAGGAGTAAAGAGGACTTGCCCGATGAGCTCATCTTTCATATCAACTATCTTGGAGCCGACCAACCTACCTTCACCCTCAACTTCTCCAAAGgtccccttccaaactactgctacatctttgagatcttttttgatgatcataatataatgcatgctaagtattaattttcctcccaatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG