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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAGAGCAGCTGAGATTCTTGGCCATCAGCGTGGTGAAAAATATGTGCATCCAAATGACCATGTTAACAGATCACAATCTTCTAATGATACATTCCCTACTgtaagccttttgaacaagaatagccatgatttttaagataactatctacttaaatggcttgacccatttcattgttgaaatgatgattttttactggtttttattgaattctatgtttgttgtttgtccag

Basic information

species Vitis vinifera
transcript Vv07s0005g00880.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g00880.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os03g21950.1 (Oryza sativa), 5'ss of exon 4
TAGAGCAGCTGAGATTCTTGGCCATCAGCGTGGTGAAAAATATGTGCATCCAAATGACCATGTTAACAGATCACAATCTTCTAATGATACATTCCCTACTgtaagccttttgaacaagaatagccatgatttttaag-ataactatctacttaaatggcttgacccatttcattgttgaaatgatgattttttactggtttttattgaattctatgtttgttgtttgtccag
||| || |||||||||||||| ||| ||||||| || || | ||| || || ||||| ||||| ||||||||||| || || ||||||||||| || ||||||||  ||    |      | ||| | ||||| | |   |  || ||      |||   |||   ||    ||| ||| ||  | |                                             
TAGGGCCGCTGAGATTCTTGGACATAAGCGTGGCGAGAAGTTTGTACACCCTAATGATCATGTGAACAGATCACAGTCCTCAAATGATACATTTCCCACTgtaagatttcactatttttttggccgtcattttaatgtgcatttacctttgctgatgttatgatttat---gttgctgacattttcag--------------------------------------------

upper sequence: Vv07s0005g00880.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G010823_T01 (Zea mays), 5'ss of exon 4
TAGAGCAGCTGAGATTCTTGGCCATCAGCGTGGTGAAAAATATGTGCATCCAAATGACCATGTTAACAGATCACAATCTTCTAATGATACATTCCCTACTgtaagccttttgaacaagaatagccatgatttttaagataactatctacttaaatggct-tgacccatttcattgttgaaatgatgattttttactggtttttattgaattctatgtttgttgtttgtccag
||| ||| ||||||| ||||| ||  |||| ||||| || | |||||| |||||||||||||| || || ||||||||||| ||||||||||| || ||||||||||||   ||| |   |     | | | |||  || |||  || |  | |||  | | |  |||  |||||  |     |                                                
TAGGGCATCTGAGATCCTTGGACACAAGCGCGGTGAGAAGTTTGTGCACCCAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACTgtaagcctt---aactatttttatt-tcagtattactattactg-ctgc--agatgtttattattcatggcattgacgtttccag-----------------------------------------------

upper sequence: Vv07s0005g00880.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G348729_T01 (Zea mays), 5'ss of exon 7
TAGAGCAGCTGAGATTCTTGGCCATCAGCGTGGTGAAAAATATGTGCATCCAAATGACCATGTTAACAGATCACAATCTTCTAATGATACATTCCCTACTgtaagccttttgaacaagaatagccatgatttttaagataactatctacttaaatggcttgacccatttcattgttgaaatgatgattttttactggtttttattgaattctatgtttgttgtttgtccag
||| ||| ||||||| ||||| ||  || | ||| | || | |||||| |||||||||||||| || || ||||||||||| ||||||||||| || ||||||||| ||    |     ||   ||  |||  ||  |  ||| |                                                                                      
TAGGGCATCTGAGATCCTTGGACACAAGGGCGGTCAGAAGTTTGTGCACCCAAATGACCATGTGAATAGGTCACAATCTTCAAATGATACATTTCCCACTgtaagctttaactatttttatt-tcactattactattactactgtag------------------------------------------------------------------------------------

upper sequence: Vv07s0005g00880.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA02G01930.2 (Glycine max), 5'ss of exon 4
TAGAGCAGCTGAGATTCTTGGCCATCAGCGTGGTGAAAAATATGTGCATCCAAATGACCATGTTAACAGATCACAATCTTCTAATGATACATTCCCTACTgtaagccttttgaacaagaatagccatgatttttaagataact--atctact-taaatggcttgacccatttcattg-ttgaaatgatgattttttac-tggttttta--ttgaattctatgtttgttg---tttgtccag
  ||||||| ||||||||||||||| |||||||||| || | |||||| |||||||||||||| || |||||||| |||||||||||||||||||| ||||||||||| ||| |     ||   |   | |||   | | | |   |  ||| | |||||  |        | ||   |||   |  |  | | |||| |||| |  |  ||  | ||||| ||||||    | | |||||
CCGAGCAGCAGAGATTCTTGGCCATAAGCGTGGTGAGAAGTTTGTGCACCCAAATGACCATGTCAATAGATCACAGTCTTCTAATGATACATTCCCAACTgtaagcctcttgtaatgatatgttcccaaatttattgttgaattggttcactgtcaatggtgtacaattcctgatgaattgttttcctactgtgttacctggtatacaatttttaatctatatttgtttacttctttccag

upper sequence: Vv07s0005g00880.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA10G02040.1 (Glycine max), 5'ss of exon 4
TAGAGCAGCTGAGATTCTTGGCCATCAGCGTGGTGAAAAATATGTGCATCCAAATGACCATGTTAACAGATCACAATCTTCTAATGATACATTCCCTACTgtaagccttttgaa--caagaatagccatgatttt--------taagataactatctacttaaatggcttgacccatttca-----ttgttgaaatgatgattttttactg-----gtttttattgaattctatgtttgttgtttgtccag--------------------
  ||||||| ||||||||||||||| |||| ||||  || |  ||||| |||||||||||||| || ||||| || |||||||||||||||||||| || |||||||| ||| |   |   |||      |||||        | |  |  ||  |||  |   |||    |  | |   |     ||  | | |   || ||    ||||     || ||  || || | |   ||| || ||  ||                       
CCGAGCAGCAGAGATTCTTGGCCATAAGCGCGGTGGGAAGTTCGTGCACCCAAATGACCATGTCAATAGATCGCAGTCTTCTAATGATACATTCCCAACCgtaagcctcttgtaattatatatatttccaattttttttttgttgaattgtcttgctatctgtgtggtgcaattcctgataaactgtttcttatactttgtttacccactgttctggtcttgtttaaagtattgatttctttttaatctgtaattgtttacttctttccag

upper sequence: Vv07s0005g00880.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA02G01920.1 (Glycine max), 5'ss of exon 4
TAGAGCAGCTGAGATTCTTGGCCATCAGCGTGGTGAAAAATATGTGCATCCAAATGACCATGTTAACAGATCACAATCTTCTAATGATACATTCCCTACTgtaagccttttgaa--caagaatagccatgattttt---------aagataactatctacttaaatggcttgacccatttca---ttgttgaaatgatgattttttactg----gtttttatt-gaattctatgtttgttgtttgtccag--------------------
  ||||||| ||||||||| | ||| |||| ||||  || |  ||||| |||||||||||||| || |||||||| ||||| |||||||||||||| ||||||||||| ||| |   |   |||  |  | |||||          | ||  ||  | |  |   | |    || | |   |   ||  | |||   || || |  ||||    | | || ||  || | |   ||| || ||  || |                     
CCGAGCAGCAGAGATTCTTTGGCATAAGCGGGGTGGGAAGTTAGTGCACCCAAATGACCATGTCAATAGATCACAGTCTTCAAATGATACATTCCCAACTgtaagcctcttgtaattatatatattcccgtttttttttgttgttgatatgtctcgccatctgtgtagtgcaactcttgatagactttcttaaactttgtttatccactgtacagctcttgtttaaagtattgatttctttttaatctatatttgtttacttctttccag

upper sequence: Vv07s0005g00880.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT5G50950.3 (Arabidopsis thaliana), 5'ss of exon 3
TAGAGCAGCTGAGATTCTTGGCCATCAGCGTGGTGAAAAATATGTGCATCCAAATGACCATGTTAACAGATCACAATCTTCTAATGATACATTCCCTACTgtaagccttt-tgaacaagaatagccatgatttttaagataactatctacttaa--atggcttgacccatttcattgttgaaatgatgattttttactggtttttattgaattctatgtttgttgtt-tgtccag-------------------------------------
||||||||||||||||||||| ||  | ||||||||||||  |||||| |||||||||||||| ||||||||||||||||||||||| || || || ||||||||| ||  |   ||     |    | |||   || |    |   | |||||   |   |  |    || |  ||||    | |    ||  |  |  ||  |||     | |||| |   || | |||| ||                                     
TAGAGCAGCTGAGATTCTTGGTCACAAACGTGGTGAAAAAATTGTGCACCCAAATGACCATGTGAACAGATCACAATCTTCTAATGACACTTTTCCAACTgtaagctttagtttgcattctcattagtcattaccaataattttgcatgcttaacgttcattcaattgcttacggtgttcgtgtaaccgattgcttttatttcctata----tgtatgctcactgctctgtcaagtactacttgacggtcgtataattttggttttgtatag

upper sequence: Vv07s0005g00880.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT2G47510.2 (Arabidopsis thaliana), 5'ss of exon 5
TAGAGCAGCTGAGATTCTTGGCCATCAGCGTGGTGAAAAATATGTGCATCCAAATGACCATGTTAACAGATCACAATCTTCTAATGATACATTCCCTACTgtaagcct---tttgaacaagaatagccatgatttttaagataactatctacttaaatggcttgacccatttcattgttgaaatgatgattttttactggtttttattgaa--------ttctatgtttgttgtttgtccag
||||||||||||||||||||| |   | |||||||| |||| |||||| |||||||||||||| |||||||||||||||||||| || || || ||||| |||||| |   |||| |    |    |||  | |||| | ||  || |    ||  |    ||  |    ||   |||||      |    ||| |    || | |||||         || | | ||||   |||||| ||
TAGAGCAGCTGAGATTCTTGGTCGCAAACGTGGTGAGAAATGTGTGCACCCAAATGACCATGTGAACAGATCACAATCTTCTAACGACACTTTTCCTACCgtaagctttcatttgcattccagctaccaatactttttacatg-ctttaagtttttaaaatttttctttcttatatgttggctcacttccctttcaac--ttctaattgacggtcttttttttttttttggcttttgtctag

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|352782338|gb|FQ470241.1|FQ470241
EST:     CAAATGACCATGTTAACAGATCACAATCTTCTAATGATACATTCCCTACT                         GTTATGCACATTGCAGCCGCAACAAAAATAAATTCAAGATTAATA
genomic: CAAATGACCATGTTAACAGATCACAATCTTCTAATGATACATTCCCTACTgtaagccttt ... gtttgtccagGTTATGCACATTGCAGCCGCAACAGAAATAAATTCAAGATTAATA
EST: gi|110713618|gb|EE089697.1|EE089697
EST:     CAAATGACCATGTTAACAGATCACAATCTTCTAATGATACATTCCCTACT                         GTTATGCACATTGCAGCCGCAACAGAAATAAATTCAAGATTAATACCAAGT
genomic: CAAATGACCATGTTAACAGATCACAATCTTCTAATGATACATTCCCTACTgtaagccttt ... gtttgtccagGTTATGCACATTGCAGCCGCAACAGAAATAAATTCAAGATTAATACCAAGT
EST: gi|161712595|gb|FC062197.1|FC062197
EST:     CAAATGACCATGTTAACAGATCACAATCTTCTAATGATACATTCCCTACT                         GTTATGCACATTGCAG
genomic: CAAATGACCATGTTAACAGATCACAATCTTCTAATGATACATTCCCTACTgtaagccttt ... gtttgtccagGTTATGCACATTGCAG
EST: gi|352773939|gb|FQ473071.1|FQ473071
EST:     CAAATGACCATGTTAACAGATCACAATCTTCTAATGATACATTCCCTACT                         GTTATGCACATTGCAGCCGCAACAGAAATAAATTCAAGATTAATACCAAGT
genomic: CAAATGACCATGTTAACAGATCACAATCTTCTAATGATACATTCCCTACTgtaagccttt ... gtttgtccagGTTATGCACATTGCAGCCGCAACAGAAATAAATTCAAGATTAATACCAAGT
EST: gi|33402485|gb|CF208112.1|CF208112
EST:     CAAATGACCATGTTAACAGATCACAATCTTCTAATGATACATTCCCTACT                         GTTATGCACATTGCAGCCGCAACAGAAATAAATTCAAGATTAATACCAAGT
genomic: CAAATGACCATGTTAACAGATCACAATCTTCTAATGATACATTCCCTACTgtaagccttt ... gtttgtccagGTTATGCACATTGCAGCCGCAACAGAAATAAATTCAAGATTAATACCAAGT
EST: gi|352773568|gb|FQ472350.1|FQ472350
EST:     CAAATGACCATGTTAACAGATCACAATCTTCTAATGATACATTCCCTACT                         GTTATGCACATTGCAGCCGCAACAGAAATAAATTCAAGATTAATACCAAGT
genomic: CAAATGACCATGTTAACAGATCACAATCTTCTAATGATACATTCCCTACTgtaagccttt ... gtttgtccagGTTATGCACATTGCAGCCGCAACAGAAATAAATTCAAGATTAATACCAAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAGAGCAGCTGAGATTCTTGGCCATCAGCGTGGTGAAAAATATGTGCATCCAAATGACCATGTTAACAGATCACAATCTTCTAATGATACATTCCCTACTgtaagccttttgaacaagaatagccatgatttttaagataactatctacttaaatggcttgacccatttcattgttgaaatgatgattttttactggtttttattgaattctatgtttgttgtttgtccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA