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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtagtaccttaaaatatttcatcttctgtcaggttctgtcagttgatggtgactgttctttggttttctgatatgaattttgatgtgtttccattttttctttgaaacaaagGTATGCATATGCTGTAGCATCTGCATTGCATGGTGTGCAGCATATCCTTCGTAAAGACTTCATGCTACAG

Basic information

species Vitis vinifera
transcript Vv06s0009g03360.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0009g03360.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os05g32060.1 (Oryza sativa), 3'ss of exon 4
gtgagtagtaccttaaaatatttcatcttctgtcaggttctgtcagttgatggtgactgttctttggttttctgatatgaattttgatgtgtttccattttttctttgaaa---caaagGTATGCATATGCTGTAGCATCTGCATTGCATGGTGTGCAGCATATCCTTCGTAAAGACTTCATGCTACAG
                               ||| ||| || | |  ||      | |  |  |||  ||    ||    |        |  ||  || |||  | |  |     | ||||||||||||||||| ||   ||||||||||||||||||  | | ||||||||| || || ||| | |||
-------------------------------gtc-ggtactattatgtgtacagtatttcttcttgacttaaacatgcacaccccttattaatttgatctttcatattcatgtttatagGTATGCATATGCTGTCGCTAGTGCATTGCATGGTGTGCACTACAGCCTTCGTAAGGATTTTATGATTCAG

upper sequence: Vv06s0009g03360.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G035595_T02 (Zea mays), 3'ss of exon 4
gtgagtagtaccttaaaatatttcatcttctgtcaggttctgtcagttgatggtgactgttctttggttttctgatatgaattttgatgtgtttccattttttctttgaaacaaagGTATGCATATGCTGTAGCATCTGCATTGCATGGTGTGCAGCATATCCTTCGTAAAGACTTCATGCTACAG
                        |     |      | ||||  |   |  |||   ||||||  |||  || ||    |  ||  |    |||||   || ||||||     ||||||||||| ||||| ||    ||||||||||| || || ||||||||||||||||| |||||| | |||
----------------------gtaagaattactttatcctgtatgcaaaccgtgcaagttcttatgttcacttatt---acattattacaattccagCCTT-CTTTGACCTTTAGGTATGCATACGCTGTTGCTAGCGCATTGCATGGAGTTCATCATATCCTTCGTAAAGATTTCATGATCCAG

upper sequence: Vv06s0009g03360.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA02G44810.1 (Glycine max), 3'ss of exon 6
---------------------------------------gtgagtagtaccttaaaatatttcatcttctgtcaggttctgtcagttgatggtgactgttctttggttttctgatatgaat---tttgatgtgtttccatttt--ttctttg--aaacaaagGTATGCATATGCTGTAGCATCTGCATTGCATGGTGTGCAGCATATCCTTCGTAAAGACTTCATGCTACAG
                                         |  |  |   |||  || | |||| | |||   | |  | ||| || ||  |   |  |     ||  |||| ||| |||   | | |  |  | |   |||  |||| ||   |  |||||||||| |||||||| ||||||||||||||||||||  ||||||  ||||| |||||||| ||||| |||
gtgagtattaccatagaaattcacgaattcacgattcggaggcttcattttttattatttatcatttactgat-gttcttttcattttataatttttcctggaccgtggtctg-tattaataggtctaaccttctgctgctttgattctctgttgagtaaagGTATGCTTATGCTGTGGCATCTGCATTGCATGGTGTAAAGCATAATCTTCGCAAAGACTTTATGCTTCAG

upper sequence: Vv06s0009g03360.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA14G03930.1 (Glycine max), 3'ss of exon 4
gtgagtagtaccttaaaatat-----ttcatcttctgtcaggttctgtcagttgatggtgact--gttctttggtttt---------ctgatatgaatt-------ttgatgtgtttccatttt--ttctttg--aaacaaagGTATGCATATGCTGTAGCATCTGCATTGCATGGTGTGCAGCATATCCTTCGTAAAGACTTCATGCTACAG
||||||| |||  || ||  |     ||||| || | | |  |  | |    ||||  |   |   || | |   |||         ||| | || | |        | |  |  | |   |||  |||| ||   |  |||||||||| ||||||||  |||||||||||||||||||  ||||||  ||||| |||||||| ||||| |||
gtgagtattactgtagaaattcaagattcattttttattatttattatttactgatattcttttcattttataacttttactggaccctggtctgtactaataggtctaaccttctgctgctttgattctctgttgagtaaagGTATGCTTATGCTGTGACATCTGCATTGCATGGTGTAGAGCATAATCTTCGAAAAGACTTTATGCTTCAG

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|110364715|gb|EC928173.1|EC928173
EST:     GAAAGGATGATCCAGAAGACAGATAAAGCTTTTGGATGGGTGCTAGAAAT                         GTATGCATATGCTGTAGCATCTGCATTGCATGGTGTGCAGCATATCCTTCG
genomic: GAAA-GATGATCCAG-AGACAGATAAAGCTTTTGGATGGGTGCTAGAAATgtgagtagta ... tgaaacaaagGTATGCATATGCTGTAGCATCTGCATTGCATGGTGTGCAGCATATCCTTCG
EST: gi|110422611|gb|EC988938.1|EC988938
EST:     ATGAAAGATGATCCAGAGACAGATAAAGCTTTTGGATGGGTGCTAGAAAT                         GTATGCATATGCTGTAGCATCTGCATTGCATGGTGTGCAGCATATCCTTCG
genomic: ATGAAAGATGATCCAGAGACAGATAAAGCTTTTGGATGGGTGCTAGAAATgtgagtagta ... tgaaacaaagGTATGCATATGCTGTAGCATCTGCATTGCATGGTGTGCAGCATATCCTTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttggttttctgatatgaattttgatgtgtttccattttttctttgaaacaaagGTATGCATATGCTGTAGCATCTGCATTGCATGGTGTGCAGCATATCCTTCGTAAAGACTTCATGCTACAG
                            tgtttccattttttct  CT-rich tract
                                   attttttctttgaaa  TA-rich tract