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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgctctagttcaccatctctacttttgttttttttttaacctatagtgacttactatacattgaatttgtttacttcagttttgcacaattttattttcctgaccattttcagatttctgcctctataagcatgtgctcttttgtggattcagGAAAAGGTCAATGTTCATGGTGGAGCTGTATCTTTGGGACATCCAATAGGTTGCAGTGGTGCTCGTATCTTGGTCACATTGTTAGGG

Basic information

species Vitis vinifera
transcript Vv00s0531g00050.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0531g00050.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os09g07830.3 (Oryza sativa), 3'ss of exon 11
gtgag-tgctctagttca-ccatctctacttttg------ttttttttttaacctatagtgacttactatacattgaatttgtttact---tcagttttgc--acaatttt--attttcctgaccattttcagatttctgcctctataagcatgtgctcttttgtggattcagGAAAAGGTCAATGTTCATGGTGGAGCTGTATCTTTGGGACATCCAATAGGTTGCAGTGGTGCTCGTATCTTGGTCACATTGTTAGGG
|| || |||  ||||||| | ||   || || ||       || ||||||||  | |  |     | |  |  |    |   || |||   | |  || ||   |||| ||   | |  |  |  ||||    |||  | |||  |||  |   || | ||| |    |  |||||||  | ||||| ||||| |||||||| ||||| ||||||||  | || |||||||||||||| || ||||||||  || | || 
gtaagctgccttagttcaactataattatttctggaactaattgttttttaaattgttcttggaaattgcatttaagttcccttcactatttgaaattcgctggcaatctttagtgtggcccaatatttatgtattagttccttaatactctgctggtattt-gctcctgtagGAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGATGCAGTGGTGCTCGAATTTTGGTCACCCTGCTTGGT

upper sequence: Vv00s0531g00050.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM5G830250_T01 (Zea mays), 3'ss of exon 10
gtgagtg----ctctagttcaccatctctacttttgttttttttttaacctatagtgacttac-tatacattgaatttgtttacttcagttttgca-caattttattttcctgaccattttcagatttctgcctctataagcatgtgctcttttgtggattcagGAAAAGGTCAATGTTCATGGTGGAGCTGTATCTTTGGGACATCCAATAGGTTGCAGTGGTGCTCGTATCTTGGTCACATTGTTAGGG
|| ||||    || || |  || | |  |  || ||  ||||      |  |   | |||| | ||| ||||   | | |||   |  | | |||| ||     || |    |  |||    | | |  |  |||||  | |  ||     | ||||  | |||||||||   |||||||||||||||||||||||||| ||||||||  | || |||||||||||||| || |||               
gtaagtgtcatctttactaaactaccattctttgtggattttaaaagtcaaaacatcactttcatatgcattcgctatttttttatttgctatgcagcagcaacatgtaatcg--catgacaatagtattctctctactaacg-gta----tatgtgcgtgcagGAAAAGACTAATGTTCATGGTGGAGCTGTATCTTTAGGACATCCTCTTGGGTGCAGTGGTGCTCGCATTTTG---------------

upper sequence: Vv00s0531g00050.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM5G866758_T02 (Zea mays), 3'ss of exon 12
gtgagtg----ctctagttcaccatctctacttttgttttttttttaacctatagtgacttac------tatacattgaatttgtttacttcagttttgcacaattttattttcctgac-cattttcagatttctgcctctataagcatgtgctcttttgtggattcagGAAAAGGTCAATGTTCATGGTGGAGCTGTATCTTTGGGACATCCAATAGGTTGCAGTGGTGCTCGTATCTTGGTCACATTGTTAGGG
|| ||||    || || |  ||   |  |  || ||  ||||         | | | |||| |      || | ||||  | | |||  ||   |  |   ||     |   |       |||| | | | |  |  || ||  | ||      | | ||||  | ||||||||| | ||||||||||| ||||||||||| || ||||||||  | || |||||||||||||| || ||||| ||  |  | || 
gtaagtgtcacctgtattaaactgccattctttgtggattttagaagttaaacaatcactttcagaaagtacatattgtctcttttttgttatttgctatgcagcagcaacgtgtaattgcattataacagtattatctgtactaacag-----catatgtgtttgcagGAAAAGATTAATGTTCATGGAGGAGCTGTATCCTTAGGACATCCTCTCGGGTGCAGTGGTGCTCGCATTTTGGTTACCCTTATTGGT

upper sequence: Vv00s0531g00050.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA07G39870.1 (Glycine max), 3'ss of exon 12
gtgagtgctctagttcaccatctctacttttgttttttttttaacctatagtgacttactatacattgaatttgtttacttcagttttgcacaattttattttcctgaccattttcagatttctgcctctataagcatgtgctcttttgtggattcagGAAAAGGTCAATGTTCATGGTGGAGCTGTATCTTTGGGACATCCAATAGGTTGCAGTGGTGCTCGTATCTTGGTCACATTGTTAGGG
||||||| |  |||  |           | || |  ||||||   || |  |  ||   |   ||||    ||| || || || | |  ||   | |  |      | ||| |   ||||   |           ||||| ||   |     || |||||||| || || ||  ||||||||||||| || ||||| |||||  | ||||||||||| ||||| ||||| |||||||| ||||||
gtgagtgtttaagtgaa-----------tatgctcatttttttggctgttctagctgcttcagcatt----ttggttcctccattctgccatggtatagtg-----gcccaataatagataatt-----------catgtacttcctatcaaatgcagGAAAAAGTTAACGTGTATGGTGGAGCTGTGTCATTGGGGCATCCCTTGGGTTGCAGTGGAGCTCGCATCTTAGTCACATTATTAGGG

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|30301836|gb|CB978630.1|CB978630
EST:     GTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCT                         GAAAAGGTCAATGTTCATGGTGGAGCTGTATCTTTGGGACATCCAATAGGT
genomic: GTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCTgtgagtgctc ... gtggattcagGAAAAGGTCAATGTTCATGGTGGAGCTGTATCTTTGGGACATCCAATAGGT
EST: gi|30301768|gb|CB978562.1|CB978562
EST:     GTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCT                         GAAAAGGTCAATGTTCATGGTGGAGCTGTATCTTTGGGACATCCAATAGGT
genomic: GTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCTgtgagtgctc ... gtggattcagGAAAAGGTCAATGTTCATGGTGGAGCTGTATCTTTGGGACATCCAATAGGT
EST: gi|30329769|gb|CD013031.1|CD013031
EST:     GTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCT                         GAAAAGGTCAATGTTCATGGTGGAGCTGTATCTTTGGGACATCCAATAGGT
genomic: GTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCTgtgagtgctc ... gtggattcagGAAAAGGTCAATGTTCATGGTGGAGCTGTATCTTTGGGACATCCAATAGGT
EST: gi|110414965|gb|EC980831.1|EC980831
EST:     CAAAAGTTGCTTGGTCTTGATCCT                         GAAAAGGTCAATGTTCATGGTGGAGCTGTATCTTTGGGACATCCAATAGGT
genomic: CAAAAGTTGCTTGGTCTTGATCCTgtgagtgctc ... gtggattcagGAAAAGGTCAATGTTCATGGTGGAGCTGTATCTTTGGGACATCCAATAGGT
EST: gi|34362568|gb|CF404153.1|CF404153
EST:     GTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCT                         GAAAAGGTCAATGTTCATGGTGGAGCTGTATCTTTGGGACATCCAATAGGT
genomic: GTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCTgtgagtgctc ... gtggattcagGAAAAGGTCAATGTTCATGGTGGAGCTGTATCTTTGGGACATCCAATAGGT
EST: gi|110358833|gb|EC923335.1|EC923335
EST:     GTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCT                         GAAAAGGTCAATGTTCATGGTGGAGCTGTATCTTTGGGACATCCAATAGGT
genomic: GTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCTgtgagtgctc ... gtggattcagGAAAAGGTCAATGTTCATGGTGGAGCTGTATCTTTGGGACATCCAATAGGT
EST: gi|34545214|gb|CF513446.1|CF513446
EST:     GTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCT                         GAAAAGGTCAATGTTCATGGTGGAGCTGTATCTTTGGGACATCCAATAGGT
genomic: GTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCTgtgagtgctc ... gtggattcagGAAAAGGTCAATGTTCATGGTGGAGCTGTATCTTTGGGACATCCAATAGGT
EST: gi|110381509|gb|EC934651.1|EC934651
EST:     GTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCT                         GAAAAGGTCAATGTTCATGGTGGAGCTGTATCTTTGGGACATCCAATAGGT
genomic: GTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCTgtgagtgctc ... gtggattcagGAAAAGGTCAATGTTCATGGTGGAGCTGTATCTTTGGGACATCCAATAGGT
EST: gi|30298600|gb|CB975394.1|CB975394
EST:     GTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCT                         GAAAAGGTCAATGTTCATGGTGGAGCTGTATCTTTGGGACATCCAATAGGT
genomic: GTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCTgtgagtgctc ... gtggattcagGAAAAGGTCAATGTTCATGGTGGAGCTGTATCTTTGGGACATCCAATAGGT
EST: gi|110376548|gb|EC941608.1|EC941608
EST:     GTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCT                         GAAAAGGTCAATGTTCATGGTGGAGCTGTATCTTTGGGACATCCAATAGGT
genomic: GTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCTgtgagtgctc ... gtggattcagGAAAAGGTCAATGTTCATGGTGGAGCTGTATCTTTGGGACATCCAATAGGT
EST: gi|34546208|gb|CF514440.1|CF514440
EST:     GCTCTTGCC-NTCAAAAGTTGCTTGGTCTTGATCCT                         GAAAAGGTCAATGTTCACGGTGGAGCTGTATCTTTGGGACATCCAATAGGT
genomic: GCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCTgtgagtgctc ... gtggattcagGAAAAGGTCAATGTTCATGGTGGAGCTGTATCTTTGGGACATCCAATAGGT
EST: gi|27585769|gb|CB008464.1|CB008464
EST:     GTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCT                         GAAAAGGTCAATGTTCATGGTGGAGCTGTATCTTTGGGACATCCAATAGGT
genomic: GTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCTgtgagtgctc ... gtggattcagGAAAAGGTCAATGTTCATGGTGGAGCTGTATCTTTGGGACATCCAATAGGT
EST: gi|110378421|gb|EC943552.1|EC943552
EST:     GTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCT                         GAAAAGGTCAATGTTCATGGTGGAGCTGTATCTTTGGGACATCCAATAGGT
genomic: GTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCTgtgagtgctc ... gtggattcagGAAAAGGTCAATGTTCATGGTGGAGCTGTATCTTTGGGACATCCAATAGGT
EST: gi|110395476|gb|EC961142.1|EC961142
EST:     GTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCT                         GAAAAGGTCAATGTTCATGGTGGAGCTGTATCTTTGGGACATCCAATAGGT
genomic: GTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCTgtgagtgctc ... gtggattcagGAAAAGGTCAATGTTCATGGTGGAGCTGTATCTTTGGGACATCCAATAGGT
EST: gi|110361851|gb|EC925352.1|EC925352
EST:     GTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCT                         GAAAAGGTCAATGTTCATGGTGGAGCTGTATCTTTGGGACATCCAATAGGT
genomic: GTTGTAGCTCTTGCCAATCAAAAGTTGCTTGGTCTTGATCCTgtgagtgctc ... gtggattcagGAAAAGGTCAATGTTCATGGTGGAGCTGTATCTTTGGGACATCCAATAGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctgaccattttcagatttctgcctctataagcatgtgctcttttgtggattcagGAAAAGGTCAATGTTCATGGTGGAGCTGTATCTTTGGGACATCCAATAGGTTGCAGTGGTGCTCGTATCTTGGTCACATTGTTAGGG
 tcctgac  putative branch site (score: 2)
                                      ctcttttgt  putative PPT
       attttca  TA-rich tract