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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcagttaaactcccatgggtagagaactcagatttcagtagcagcctctttctattccttaaggagcattaactgtttaaccaatcccaatttgaacagACCGCCAGAGTTGCTGCTTGGGACCACAAGGTATGGTCCAGCTGTTGATATGTGGTCAGTTGGCTGTATCTTTGCAGAACTTCTGCATGGAAAACCTATC

Basic information

species Vitis vinifera
transcript Vv06s0009g01800.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0009g01800.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os05g32360.1 (Oryza sativa), 3'ss of exon 7
---gtaagcagttaaactcccatgggtagagaactcagatttcagtagcagcctctttctattccttaaggagcattaactgtttaaccaatcccaatttgaacagACCGCCAGAGTTGCTGCTTGGGACCACAAGGTATGGTCCAGCTGTTGATATGTGGTCAGTTGGCTGTATCTTTGCAGAACTTCTGCATGGAAAACCTATC
    |    | |||    |       |  |     || |||    ||   |  | |   | || |||         | ||  |||  |||||    ||||   |||||| |||||||||||||| || | ||| | |||||| ||||| ||||| |||||||| || || ||||| |||||||| |||||  ||||||| || || 
gtattgcagaattatgaacttgccattgaattttgcatattgtgtta-tggtatttagtttttgcttggatcatgctgaccatttg-ccaat---gatttt--cagACCTCCAGAGTTGCTGCTCGGAAGCACCAAGTATGGACCAGCAGTTGACATGTGGTCTGTCGGTTGTATTTTTGCAGAGCTTCTCAATGGAAAGCCAATT

upper sequence: Vv06s0009g01800.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os01g72790.1 (Oryza sativa), 3'ss of exon 7
gtaagcagttaaactcccatgggtagagaactcagatttcagtagcagcctctttctattccttaaggagcattaactgtttaaccaatcccaatttgaacagACCGCCAGAGTTGCTGCTTGGGACCACAAGGTATGGTCCAGCTGTTGATATGTGGTCAGTTGGCTGTATCTTTGCAGAACTTCTGCATGGAAAACCTATC
||| | |   ||  ||||||| | ||     ||   |   | |      ||||| || |   ||      ||||   | | |  |   |     | |   |||||| || |||||| | || |||| ||| |||||||||||||| ||||| ||||||||||| || ||||| ||||| || |||||  ||||||| || || 
gtatgga---aacttcccatgaggaggttcttccattcatatt-----tctcttactttctttt------cattg-ttctctctctcttatttgtgtatgcagACCTCCTGAGTTGTTACTCGGGAGCACGAGGTATGGTCCAGCCGTTGACATGTGGTCAGTGGGTTGTATTTTTGCTGAGCTTCTCAATGGAAAGCCAATA

upper sequence: Vv06s0009g01800.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G019267_T01 (Zea mays), 3'ss of exon 7
gtaagcagttaaactcccatgggtagagaactcagatttcagtagcagcctctttctattccttaaggagcattaactgtttaaccaatcccaatttga--acagACCGCCAGAGTTGCTGCTTGGGACCACAAGGTATGGTCCAGCTGTTGATATGTGGTCAGTTGGCTGTATCTTTGCAGAACTTCTGCATGGAAAACCTATC
|||     ||  |   |||||| |     |  ||   ||    | ||| | ||| |  ||  |   |  |||  | ||  ||||    |||    |||    |||||| ||||||||||| ||||| | ||||| |||||| ||||| ||||| ||||||||||| |||||||| ||||||||||||||  |||| || || || 
gtatagtattgtaaaaccatggttttgagaaacattgttgccaaacaggcccttacagttgtt---gttgca--agcttcttaagtcttcctggattggctgcagACCTCCAGAGTTGCTACTTGGAAGCACAAAGTATGGCCCAGCCGTTGACATGTGGTCAGTGGGCTGTATTTTTGCAGAACTTCTCAATGGGAAGCCAATA

upper sequence: Vv06s0009g01800.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA20G10960.1 (Glycine max), 3'ss of exon 6
gtaagcagttaaactccc--atgggtagaga-----actcagatttcagtagcagcctctttctattccttaaggagcattaac-tgtttaaccaatccca--atttgaacagACCGCCAGAGTTGCTGCTTGGGACCACAAGGTATGGTCCAGCTGTTGATATGTGGTCAGTTGGCTGTATCTTTGCAGAACTTCTGCATGGAAAACCTATC
    | | || |  |||   || |||    |     ||  |  ||    | | ||  |      ||    | | |  |||  || |  || |   ||  ||  || | |  ||||| || ||| ||||||||||||| ||||||||||| |||||||| ||||||||||| || || || || |||||||| ||||| ||||| || ||||||
----gtaatttatgtccataataggttttaattttgacctaagttcttttgggagggttgcatcatgaacttatgcccatacacattattgatttatttcattatattattagACCCCCTGAGCTGCTGCTTGGGACAACAAGGTATGGGCCAGCTGTAGATATGTGGTCTGTAGGGTGCATTTTTGCAGAGCTTCTTCATGGGAAGCCTATC

upper sequence: Vv06s0009g01800.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA02G44400.1 (Glycine max), 3'ss of exon 8
gtaagcagttaaactcccatgggtagagaactcagatttcagtagcagcctctttc-tattccttaag---gagcattaactgt-ttaaccaatcccaatttgaacagACCGCCAGAGTTGCTGCTTGGGACCACAAGGTATGGTCCAGCTGTTGATATGTGGTCAGTTGGCTGTATCTTTGCAGAACTTCTGCATGGAAAACCTATC
                                  |   |  ||  ||   | | || |  ||  | ||   |  || |   ||| || |    |    || |    ||||| || ||||||||||| ||||| |||| |||||| |||||||| ||||||||||| ||||| || || ||||| || ||||| || || || ||||||
----------------------------------gtaattggtgtcattttttatcatgatctatgagattggccaatgcatgtattgatttctttatatatatttagACCACCTGAGTTGCTGCTAGGGACAACAAAGTATGGACCAGCTGTGGATATGTGGTCTGTTGGGTGCATTTTTGCTGAGCTTCTTCAAGGGAAGCCTATC

upper sequence: Vv06s0009g01800.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA14G04410.1 (Glycine max), 3'ss of exon 7
gtaagcagttaaactcccatgggtagagaactcagatttcagtagcagcctctttctat---tccttaaggagcattaactgtttaaccaatcccaatt-tgaacagACCGCCAGAGTTGCTGCTTGGGACCACAAGGTATGGTCCAGCTGTTGATATGTGGTCAGTTGGCTGTATCTTTGCAGAACTTCTGCATGGAAAACCTATC
                                  |   |  ||  ||   | ||   ||   |  | ||   |    |    | ||   | |      | |    ||||| || ||||||||||| || || |||| |||||| |||||||| ||||||||||| ||||| || || ||||| || ||||| || || || ||||| 
----------------------------------gtaattggtgtcatttttttatcatgagttatcaaattggccaatgcatgtattgatttttggctatatctagACCACCTGAGTTGCTGCTAGGAACAACAAAGTATGGGCCAGCTGTGGATATGTGGTCTGTTGGGTGCATTTTTGCTGAGCTTCTTCAAGGGAAGCCTATA

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|110724472|gb|EE100331.1|EE100331
EST:     AATGATCACAATGGGAATCTTACAAATCGTGTTATTACCTTATGGTACAG                         ACCGCCAGAGTTGCTGCTTGGGACCACAAAGTATGGTCCAGCTGT-GATAT
genomic: AATGATCACAATGGGAATCTTACAAATCGTGTTATTACCTTATGGTACAGgtaagcagtt ... atttgaacagACCGCCAGAGTTGCTGCTTGGGACCACAAGGTATGGTCCAGCTGTTGATAT
EST: gi|110707937|gb|EE084906.1|EE084906
EST:     AATGATCACAATGGGAATCTTACAAATCGTGTTATTACCTTATGGTACAG                         ACCGCCAGAGTTGCTGCTTGGGACCACAAGGTATGGTCCAGCTGTTGATAT
genomic: AATGATCACAATGGGAATCTTACAAATCGTGTTATTACCTTATGGTACAGgtaagcagtt ... atttgaacagACCGCCAGAGTTGCTGCTTGGGACCACAAGGTATGGTCCAGCTGTTGATAT
EST: gi|161712182|gb|FC061554.1|FC061554
EST:     AATGATCACAATGGGAATCTTACAAATCGTGTTATTACCTTATGGTACAG                         ACCGCCAGAGTTGCTGCTTGGGACCACAAGGTATGGTCCAGCTGTTGATAT
genomic: AATGATCACAATGGGAATCTTACAAATCGTGTTATTACCTTATGGTACAGgtaagcagtt ... atttgaacagACCGCCAGAGTTGCTGCTTGGGACCACAAGGTATGGTCCAGCTGTTGATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctctttctattccttaaggagcattaactgtttaaccaatcccaatttgaacagACCGCCAGAGTTGCTGCTTGGGACCACAAGGTATGGTCCAGCTGTTGATATGTGGTCAGTTGGCTGTATCTTTGCAGAACTTCTGCATGGAAAACCTATC
                                            aatttgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcagttaaactcccatgggtagagaactcagatttcagtagcagcctctttctattccttaaggagcattaactgtttaaccaatcccaatttgaacagACCGCCAGAGTTGCTGCTTGGGACCACAAGGTATGGTCCAGCTGTTGATATGTGGTCAGTTGGCTGTATCTTTGCAGAACTTCTGCATGGAAAACCTATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA