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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttctggcctagacatagaaatttatgaacaattggtggaagtactccttctgccatgatttctgatcaattagtactaagaacgatcctgttttcttcctgggtttttgcagCTTCTGAAGGACGGATACCAATGGAGAAAGTATGGGCAGAAGGTCACCAGAGATAACCCTTCTCCCAGAGCCTACTTCAAGTGCTCCTTTGCCCCAACCT

Basic information

species Vitis vinifera
transcript Vv04s0008g05760.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g05760.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os02g08440.4 (Oryza sativa), 3'ss of exon 2
---------gtaagttctggcctagacatagaaatttatgaacaattggtggaagta--ctccttctgccatgatttctgatcaattagtactaagaacgatcctgttttcttcctgggtttttgcagCTTCTGAAGGACGGATACCAATGGAGAAAGTATGGGCAGAAGGTCACCAGAGATAACCCTTCTCCCAGAGCCTACTTCAAGTGCTCCTTTGCCCCAACCT
            |   |      | |       || |     ||  ||    |  ||   || || ||   ||| ||||   |  ||  |      |   |||||||| |     ||  |   ||||| |  |||| || || ||||||||||| |||||||| |||||||||||||  || ||||| |  || |||||||||||||  ||||| ||||| ||  |||
gtacgaatccccaaccccaattaacatccgatcatctcatttcatgtgcctaacttaacttctttttgttctgaattctagcc--ttgattaattaattaatcctgttcttgcaatgaatccatgcagGTGGTGAAAGATGGGTACCAATGGAGGAAGTATGGTCAGAAGGTCACCAAGGACAACCCCTGCCCAAGAGCCTACTTCAGATGCTCATTTGCTCCCGCCT

upper sequence: Vv04s0008g05760.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G111711_T01 (Zea mays), 3'ss of exon 2
-----------------------gtaagttctggcctagacatagaaatttatgaacaattggtggaagtactccttctgccatgatttctgatcaattagtactaagaacgatcctgttttcttcctgggtttttgcagCTTCTGAAGGACGGATACCAATGGAGAAAGTATGGGCAGAAGGTCACCAGAGATAACCCTTCTCCCAGAGCCTACTTCAAGTGCTCCTTTGCCCCAACCT
                       ||      | || |   | |     ||| |        ||   |     | | |  |  | | |   | || | | | ||    |  |   |  |||       |         |||    |||||||||| ||||||||| | ||||| ||||||||||| ||||  || ||||| |  ||  | |||||||||  ||||||||| || ||  | |
gtaagtaacggaggatgccgcccgtgcaccatcgcttcttcttctttttttctctcgcgccggatcagcgtgtgcgtacggtacggtcaataattattaactagctcgtgcc-ccacgttgaacaaataaaacaaaacagGCGGTGAAGGACGGGTACCAATGGCGGAAGTACGGGCAGAAGGTGACCAAGGACAACCCCTGCCCGCGCGCCTACTTCCGGTGCTCCTTCGCGCCGTCGT

upper sequence: Vv04s0008g05760.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA17G33890.1 (Glycine max), 3'ss of exon 2
gtaagttctggcctagacatagaaatttatgaacaattggtggaagtactccttc----tgccatgatttctgatcaatt---agtacta----agaac---gatcctgttttcttc---ctgggtttttgcagCTTCTGAAGGACGGATACCAATGGAGAAAGTATGGGCAGAAGGTCACCAGAGATAACCCTTCTCCCAGAGCCTACTTCAAGTGCTCCTTTGCCCCAACCT
||||||||      |   || |   |||    | || | ||   |    |   |     |    |||  | | ||||| |   |||||||     |||    ||   |||||| ||     || ||   |  ||  | ||| ||||||||| |||||||| || ||||| ||||| ||||| || |||||||||||||| ||||| ||||||| ||||||||||||||||| ||
gtaagttcctaaa-atttattgttgtttcctgataacttgtattatagttttgtgtatatattgtgaggtttaatcaactccaagtactatctgggaatcctgaatttgttttttttattttgtgtaactaaagTATGTGATGGACGGATATCAATGGAGGAAATATGGTCAGAAAGTCACTAGGGATAACCCTTCTCCTAGAGCTTACTTCAGGTGCTCCTTTGCCCCAAGCT

upper sequence: Vv04s0008g05760.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA14G11960.1 (Glycine max), 3'ss of exon 3
gtaagttctggcctagacatagaaatttatgaacaattg--gtggaagtactccttctgccatgatttctgatcaatt---agtactaa----gaac---gatcctgttttcttcctgggttt--ttgcagCTTCTGAAGGACGGATACCAATGGAGAAAGTATGGGCAGAAGGTCACCAGAGATAACCCTTCTCCCAGAGCCTACTTCAAGTGCTCCTTTGCCCCAACCT
||||||||      | |  | |   |||   |  || |    |   |||  |   | |     ||    | || || |   ||||||||    |||    ||   |||||| ||  | ||| |  ||  ||  | ||| ||||||||| |||||||| || ||||| ||||||||||| || |||||||||||||| || || ||||||| |||||||| ||||||||  |
gtaagttcctaaa-atatgttgttgtttcctagtaacttctattatagttgtgtctatattgggaagcttaattaactccaagtactaactgggaatcctgaatttgtttttttttttggtataattaaagTATGTGATGGACGGATATCAATGGAGGAAATATGGTCAGAAGGTCACTAGGGATAACCCTTCTCCTAGGGCTTACTTCAGGTGCTCCTCTGCCCCAAGTT

upper sequence: Vv04s0008g05760.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA04G06480.1 (Glycine max), 3'ss of exon 1
gtaagttctggcctagacatagaaatttatgaacaattggtggaagtactccttctgccatgatttctgatcaattagtactaag-aacgatcctgttttcttcctgggtttttgcagCTTCTGAAGGACGGATACCAATGGAGAAAGTATGGGCAGAAGGTCACCAGAGATAACCCTTCTCCCAGAGCCTACTTCAAGTGCTCCTTTGCCCCAACCT
                 |||     |   |  | |  |  |   | |  |  ||  |  |  ||||        | ||||||||   | | ||||   || ||   ||| | ||| ||  | ||| ||||||||| || |||||||| ||||| || || ||||||||||||||||||||||| || || ||||||||||| || | |||||||| ||
----------------gcatgtgcttaattatatagctttttagactgtt--ttgagtaagtatttgcagatgctaagtactaactgaggttccttaattttttggggggtgttgaagTATGTGAGGGACGGATATCAGTGGAGAAAATATGGTCAAAAAGTCACCAGAGATAACCCTTCTCCTAGGGCTTACTTCAAGTGTTCATATGCCCCAAGCT

upper sequence: Vv04s0008g05760.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA06G06530.1 (Glycine max), 3'ss of exon 2
gtaagttctggcctagacatagaaatttatgaac-aattggtggaagtactccttctgccatgatttctgatcaattagtactaagaacgatcctgttttcttcctgggtttttgcagCTTCTGAAGGACGGATACCAATGGAGAAAGTATGGGCAGAAGGTCACCAGAGATAACCCTTCTCCCAGAGCCTACTTCAAGTGCTCCTTTGCCCCAACCT
             ||   ||| |  ||| |  || |  |  |   ||||    || ||       |||| |  | | |   |  ||||      |  |||  |  | |  | ||| ||  | ||| ||||||||| || |||||||| || || ||||| ||||| ||||||||||||||||| || || ||||||||||| || | |||||| | ||
---------tcattaattatatagctttttagactagctactttgagtaagtattttg----aggttctaagtactaa---ccgagaat--ctttaatttgatttttgtgtgttgaagTATGTGAGGGACGGATATCAGTGGAGAAAATACGGTCAGAAAGTCACTAGAGATAACCCTTCTCCTAGGGCTTACTTCAAGTGTTCATATGCCCCTAGCT

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|71863063|gb|DT012118.1|DT012118
EST:     GAAAGGTCTCTAGAGTTGTTGTAAAGACCGAGAAGTCTGACAATAGCCTG                         CTTCTGAAGGACGGATACCAATGGAGAAAGTATGGGCAGAAGGTCACCAGA
genomic: GAAAGGTCTCTAGAGTTGTTGTAAAGACAGAGAAGTCTGACAATAGCCTGgtaagttctg ... gtttttgcagCTTCTGAAGGACGGATACCAATGGAGAAAGTATGGGCAGAAGGTCACCAGA
EST: gi|29785116|gb|CB341851.2|CB341851
EST:     GAAAGGTCTCTAGAGTTGTTGTAAAGACCGAGAAGTCTGACAATAGCCTG                         CTTCTGAAGGACGGATACCAATGGAGAAAGTATGGGCAGAAGGTCAGCAGA
genomic: GAAAGGTCTCTAGAGTTGTTGTAAAGACAGAGAAGTCTGACAATAGCCTGgtaagttctg ... gtttttgcagCTTCTGAAGGACGGATACCAATGGAGAAAGTATGGGCAGAAGGTCACCAGA
EST: gi|29785607|gb|CB342780.2|CB342780
EST:     GAAAGGTCTCTAGAGTTGTTGTAAAGACCGAGAAGTCTGACAATAGCCTG                         CTTCTGAAGGACGGATACCAATGGAGAAAGTATGGGCAGAAGGTCACCAGA
genomic: GAAAGGTCTCTAGAGTTGTTGTAAAGACAGAGAAGTCTGACAATAGCCTGgtaagttctg ... gtttttgcagCTTCTGAAGGACGGATACCAATGGAGAAAGTATGGGCAGAAGGTCACCAGA
EST: gi|28963677|gb|CB342710.1|CB342710
EST:     GAAAGGTCTCTAGAGTTGTTGTAAAGACCGAGAAGTCTGACAATAGCCTG                         CTTCTGAAGGACGGATACCAATGGAGAAAGTATGGGCAGAAGGTCACCAGA
genomic: GAAAGGTCTCTAGAGTTGTTGTAAAGACAGAGAAGTCTGACAATAGCCTGgtaagttctg ... gtttttgcagCTTCTGAAGGACGGATACCAATGGAGAAAGTATGGGCAGAAGGTCACCAGA
EST: gi|71859000|gb|DT008055.1|DT008055
EST:     GAAAGGTCTCTAGAGTTGTTGTAAAGACCGAGAAGTCTGACAATAGCCTG                         CTTCTGAAGGACGGATACCAATGGAGAAAGTATGGGCAGAAGGTCACCAG
genomic: GAAAGGTCTCTAGAGTTGTTGTAAAGACAGAGAAGTCTGACAATAGCCTGgtaagttctg ... gtttttgcagCTTCTGAAGGACGGATACCAATGGAGAAAGTATGGGCAGAAGGTCACCAG
EST: gi|161716070|gb|FC069125.1|FC069125
EST:     GAAAGGTCTCTAGAGTTGTTGTAAAGACCGAGAAGTCTGACAATAGCCTG                         CTTCTGAAGGACGGATACCAATGGAGAAAGTATGGGCAGAAGGTCACCAGA
genomic: GAAAGGTCTCTAGAGTTGTTGTAAAGACAGAGAAGTCTGACAATAGCCTGgtaagttctg ... gtttttgcagCTTCTGAAGGACGGATACCAATGGAGAAAGTATGGGCAGAAGGTCACCAGA
EST: gi|71862553|gb|DT011608.1|DT011608
EST:     GAAAGGTCTCTAGAGTTGTTGTAAAGACCGAGAAGTCTGACAATAGCCTG                         CTTCTGAAGGACGGATACCAATGGAGAAAGTATGGGCAGAAGG
genomic: GAAAGGTCTCTAGAGTTGTTGTAAAGACAGAGAAGTCTGACAATAGCCTGgtaagttctg ... gtttttgcagCTTCTGAAGGACGGATACCAATGGAGAAAGTATGGGCAGAAGG
EST: gi|71861352|gb|DT010407.1|DT010407
EST:     GAAAGGTCTCTAGAGTTGTTGTAAAGACCGAGAAGTCTGACAATAGCCTG                         CTTCTGAAGGAC
genomic: GAAAGGTCTCTAGAGTTGTTGTAAAGACAGAGAAGTCTGACAATAGCCTGgtaagttctg ... gtttttgcagCTTCTGAAGGAC
EST: gi|83274425|gb|DV938522.1|DV938522
EST:     GAAAGGTCTCTAGAGTTGTTGTAAAGACCGAGAAGTCTGACAATAGCCTG                         CTTCTGAAGGACGGATACCAATGGAGAAAGTATGGGCAGAAGGTCACCAGA
genomic: GAAAGGTCTCTAGAGTTGTTGTAAAGACAGAGAAGTCTGACAATAGCCTGgtaagttctg ... gtttttgcagCTTCTGAAGGACGGATACCAATGGAGAAAGTATGGGCAGAAGGTCACCAGA
EST: gi|110703174|gb|EE079787.1|EE079787
EST:     GAAAGGTCTCTAGAGTTGTTGTAAAGACCGAGAAGTCTGACAATAGCCTG                         CTTCTGAAGGACGGATACCAATGGAGAAAGTATGGGCAGAAGGTCACCAGA
genomic: GAAAGGTCTCTAGAGTTGTTGTAAAGACAGAGAAGTCTGACAATAGCCTGgtaagttctg ... gtttttgcagCTTCTGAAGGACGGATACCAATGGAGAAAGTATGGGCAGAAGGTCACCAGA
EST: gi|71862955|gb|DT012010.1|DT012010
EST:     GAAAGGTCTCTAGAGTTGTTGTAAAGACCGAGAAGTCTGACAATAGCCTG                         CTTCTGAAGGACGGATACCAATGGAGAAAGTATGGGCAGAAGGTCACCAGA
genomic: GAAAGGTCTCTAGAGTTGTTGTAAAGACAGAGAAGTCTGACAATAGCCTGgtaagttctg ... gtttttgcagCTTCTGAAGGACGGATACCAATGGAGAAAGTATGGGCAGAAGGTCACCAGA
EST: gi|110387873|gb|EC952573.1|EC952573
EST:     GAAAGGTCTCTAGAGTTGTTGTAAAGACCGAGAAGTCTGACAATAGCCTG                         CTTCTGAAGGACGGATACCAATGGAGAAAGTATGGGCAGAAGGTCACCAGA
genomic: GAAAGGTCTCTAGAGTTGTTGTAAAGACAGAGAAGTCTGACAATAGCCTGgtaagttctg ... gtttttgcagCTTCTGAAGGACGGATACCAATGGAGAAAGTATGGGCAGAAGGTCACCAGA
EST: gi|71860157|gb|DT009212.1|DT009212
EST:     GAAAGGTCTCTAGAGTTGTTGTAAAGACCGAGAAGTCTGACAATAGCCTG                         CTTCTGAAGGACGGATACCAATGGAGAAA
genomic: GAAAGGTCTCTAGAGTTGTTGTAAAGACAGAGAAGTCTGACAATAGCCTGgtaagttctg ... gtttttgcagCTTCTGAAGGACGGATACCAATGGAGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttctgatcaattagtactaagaacgatcctgttttcttcctgggtttttgcagCTTCTGAAGGACGGATACCAATGGAGAAAGTATGGGCAGAAGGTCACCAGAGATAACCCTTCTCCCAGAGCCTACTTCAAGTGCTCCTTTGCCCCAACCT
  ttctgat  putative branch site (score: 3)
                                              tttttgc  putative PPT
       atcaatta  TA-rich tract