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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttctatatgcaatgtggctattgaaatttacacttcttacttgtcctcctacttgctctgtaataaaatgttctggatttgcagATGCAACATATTTCCTTGAAGTGGATCGGCTACTTCGACCAGGAGGGTACCTTGTAATCTCTGGTCCCCCTGTACTATGGCCTAAACAAGATAAGGAATG

Basic information

species Vitis vinifera
transcript Vv15s0048g01990.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0048g01990.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA09G40110.2 (Glycine max), 3'ss of exon 3
gtgagttctatat-gcaatgtggctattgaaatttacacttcttacttgtcctcctacttgctctgtaataaaatgttctggatttgcagATGCAACATATTTCCTTGAAGTGGATCGGCTACTTCGACCAGGAGGGTACCTTGTAATCTCTGGTCCCCCTGTACTATGGCCTAAACAAGATAAGGAATG
|| ||||||  || |||       | |  | || | |   ||||     | ||  | ||| | ||  |||  |        |  ||||||||||  | |||||| ||||||||||  |  ||||||| || || || ||  |||| ||||||||||||||||| |  ||||||||||||||||| |||||
gtaagttcttcattgcagctcacttgtgcatatattccaatcttctgcatgcttgtcctttccct--aatgcagcaaatgtgccttgcagATGCCTCTTATTTCATTGAAGTGGACAGATTACTTCGTCCTGGTGGATATTTTGTCATCTCTGGTCCCCCTGTTCAGTGGCCTAAACAAGATAAAGAATG

upper sequence: Vv15s0048g01990.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA07G08360.1 (Glycine max), 3'ss of exon 3
gtgagttctatatgcaatgtggctattg-aaattt---acacttcttacttgtcctcctacttgctctgtaataaaatgttctggatttgcagATGCAACATATTTCCTTGAAGTGGATCGGCTACTTCGACCAGGAGGGTACCTTGTAATCTCTGGTCCCCCTGTACTATGGCCTAAACAAGATAAGGAATG
|| ||||||  ||   |  || |  ||| | || |   | |||||| | | | | ||     ||| ||  |||  |     || |  ||||||||||| | |||||| ||||||||||  |  ||||||| || || || ||  | || || |||||||||||||| |  ||||||||||||||||| |||||
gtaagttcttaattgcagctgacctttgcatatcttgcaaacttctaaatagacatcac---tgccct--aatgcagaaaccttgccttgcagATGCATCTTATTTCATTGAAGTGGACAGATTACTTCGCCCTGGTGGATATTTAGTCATTTCTGGTCCCCCTGTTCAGTGGCCTAAACAAGATAAAGAATG

upper sequence: Vv15s0048g01990.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA03G01870.1 (Glycine max), 3'ss of exon 3
gtgagttctatatgcaatgtggctattgaaatttacacttcttacttgtcctcctacttg--ctctgtaataaaatgttctggatttgcagATGCAACATATTTCCTTGAAGTGGATCGGCTACTTCGACCAGGAGGGTACCTTGTAATCTCTGGTCCCCCTGTACTATGGCCTAAACAAGATAAGGAATG
|| ||||||  || || ||  |   ||   ||  |   | |  |||| |    | |  |    ||  ||||  |     || |  ||||||||| | | |||||| ||||||||||  |  ||||||| || || || ||  | || || |||||||||||||| |  ||||||||||||||||| |||||
gtaagttcttcat-cactgccgacctttgcat--atcttgcaaacttctaaatcgaaataacttccctaatgcagaaaccttgccttgcagATGTATCTTATTTCATTGAAGTGGACAGATTACTTCGCCCTGGTGGATATTTAGTCATTTCTGGTCCCCCTGTTCAGTGGCCTAAACAAGATAAAGAATG

upper sequence: Vv15s0048g01990.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT4G00740.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgagttctatatgcaatgtggctattgaaatttacacttcttac---ttgtcctcctacttgctct-gtaataaaatgttctggatttgcagATGCAACATATTTCCTTGAAGTGGATCGGCTACTTCGACCAGGAGGGTACCTTGTAATCTCTGGTCCCCCTGTACTATGGCCTAAACAAGATAAGGAATG
|||||| |  |  |  || |  || |    || |||   | || |   || |      | ||  |||  |  |     ||  |   | |||||||||||| || ||| | ||||| ||| || |||| || || ||||| || |||||||||||||| || ||||||| ||||||||||||||| || |||||
gtgagtcccttgggttatatacctctacttatgtacgtgtgttgcggtttttagcagcaattattcttattgtgtttggtgatttgtctgcagATGCAACTTACTTCATCGAAGTAGATAGGTTACTGCGCCCTGGAGGATATCTTGTAATCTCTGGCCCACCTGTACAATGGCCTAAACAAGACAAAGAATG

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|110701114|gb|EE078359.1|EE078359
EST:     ATTTGACTTGGTGCACTGCTCTCGATGTTTGATCCCTTTTACCGCTTATA                         ATGCAACATATTTCCTTGAAGTGGATCGGCTACTTCGACCAGGAGGGTACC
genomic: ATTTGACTTGGTGCACTGCTCTCGATGTTTGATCCCTTTTACCGCTTATAgtgagttcta ... ggatttgcagATGCAACATATTTCCTTGAAGTGGATCGGCTACTTCGACCAGGAGGGTACC
EST: gi|110710132|gb|EE086201.1|EE086201
EST:     ATTTGACTTGGTGCACTGCTCTCGATGTTTGATCCCTTTTACCGCTTATA                         ATGCAACATATTTCCTTGAAGTGGATCGGCTACTTCGACCAGGAGGGTACC
genomic: ATTTGACTTGGTGCACTGCTCTCGATGTTTGATCCCTTTTACCGCTTATAgtgagttcta ... ggatttgcagATGCAACATATTTCCTTGAAGTGGATCGGCTACTTCGACCAGGAGGGTACC
EST: gi|37187830|gb|CF607183.1|CF607183
EST:     ATTTGACTTGGTGCACTGCTCTCGATGTTTGATCCCTTTTACCGCTTATA                         ATGCAACATATTTCCTTGAAGTGGATCGGCTACTTCGACCAGGAGGGTACC
genomic: ATTTGACTTGGTGCACTGCTCTCGATGTTTGATCCCTTTTACCGCTTATAgtgagttcta ... ggatttgcagATGCAACATATTTCCTTGAAGTGGATCGGCTACTTCGACCAGGAGGGTACC
EST: gi|110687173|gb|EE064354.1|EE064354
EST:     ATTTGACTTGGTGCACTGCTCTCGATGTTTGATCCCTTTTACCGCTTATA                         ATGCAACATATTTCCTTGAAGTGGATCGGCTACTTCGACCAGGAGGGTACC
genomic: ATTTGACTTGGTGCACTGCTCTCGATGTTTGATCCCTTTTACCGCTTATAgtgagttcta ... ggatttgcagATGCAACATATTTCCTTGAAGTGGATCGGCTACTTCGACCAGGAGGGTACC
EST: gi|32249709|gb|CD715528.1|CD715528
EST:     ATTTGACTTGGTGCACTGCTCTCGATGTTTGATCCCTTTTACCGCTTATA                         ATGCAACATATTTCCTTGAAGTGGATCGGCTACTTCGACCAGGAGGGTACC
genomic: ATTTGACTTGGTGCACTGCTCTCGATGTTTGATCCCTTTTACCGCTTATAgtgagttcta ... ggatttgcagATGCAACATATTTCCTTGAAGTGGATCGGCTACTTCGACCAGGAGGGTACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acacttcttacttgtcctcctacttgctctgtaataaaatgttctggatttgcagATGCAACATATTTCCTTGAAGTGGATCGGCTACTTCGACCAGGAGGGTACCTTGTAATCTCTGGTCCCCCTGTACTATGGCCTAAACAAGATAAGGAATG
    ttcttac  putative branch site (score: 2)
                             tgtaataaaatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttctatatgcaatgtggctattgaaatttacacttcttacttgtcctcctacttgctctgtaataaaatgttctggatttgcagATGCAACATATTTCCTTGAAGTGGATCGGCTACTTCGACCAGGAGGGTACCTTGTAATCTCTGGTCCCCCTGTACTATGGCCTAAACAAGATAAGGAATG

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