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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactatctctccttgcttatttgcaaatattatacttgatactaagaatgccaaccagcattagtgtgcatatagttcaaatttttcttacattttggtaaatgttgtgtcgttcttcagAAAACCAGTGAAAAAGGTGGGAGCGTTTTGTTGGCTTTCCCTTGCTATTTGCATTATTGAACTACTCATTTGCATCAAGTTTGGACATG

Basic information

species Vitis vinifera
transcript Vv01s0011g04370.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g04370.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os01g02890.1 (Oryza sativa), 3'ss of exon 10
gtactatctctccttgcttatttgcaaatattatacttg-atactaagaatgccaaccagcattagtgtgcatatagttcaaatttttcttacattttggtaa---atgttgtgtcgtt--cttcagAAAACCAGTGAAAAAGGTGGGAGCGTTTTGTTGGCTTTCCCTTGCTATTTGCATTATTGAACTACTCATTTGCATCAAGTTTGGACATG
                          |  ||| ||  || || || | |||   | | | ||    ||   ||| |||||| |   ||| |||   ||  |||   |  |||| |   |   | ||| ||||| || |||||||||||  | || |||||||||||||| |||||||||||| | || || ||  | |||||||||||||||||||
-------------------------cagcattctaactgcatgcttacaataggatcaaacagct-tggctata-agttcacagaattcatacccattaataatataacttgtctgaatgattgcagGAAACCTGTTAAAAAGGTGGGGTCTTTCTGTTGGCTTTCCCTAGCTATTTGCATTTTGGAGCTTCTACTATGCATCAAGTTTGGACATG

upper sequence: Vv01s0011g04370.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G110834_T02 (Zea mays), 3'ss of exon 10
gtactatctctccttgcttatttgcaaatattatacttgatactaagaatgccaa---ccagcattagtgtgcat-atagttcaaatttttcttac-attttggtaaatgttgtgtcgtt--cttcagAAAACCAGTGAAAAAGGTGGGAGCGTTTTGTTGGCTTTCCCTTGCTATTTGCATTATTGAACTACTCATTTGCATCAAGTTTGGACATG
                        ||| |    || || ||||||      ||||       |||||||    || || |      |||||||| |     |  ||| ||||      ||   ||||| |||||| | |||||||||||| | || || ||||||||||| ||||| |||||| | || || || || ||||||||||||||||| |
------------------------caagt----tagtttatactagtgcaaccaagtgttgccattagtaattattatggcatttttttttctttctggaataataattgtttgacgattggtttcagCAAACCATTTAAAAAGGTGGGATCCTTCTGCTGGCTTTCCCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACG

upper sequence: Vv01s0011g04370.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G095757_T01 (Zea mays), 3'ss of exon 11
gtactatctctccttgcttatttgcaaatattatacttgatactaagaatgccaaccagcattagtgtgcatatagttcaaatttttcttacattttggtaaatgttgtgtcgttcttcagAAAACCAGTGAAAAAGGTGGGAGCGTTTTGTTGGCTTTCCCTTGCTATTTGCATTATTGAACTACTCATTTGCATCAAGTTTGGACATG
                   ||   | | |    || || ||||||      ||||        | |  | |  ||   ||||| |||  |  | |    |   | |  |       ||||| |||||| | |||||||||||| | || || ||||||||||| ||||| |||||| | || || || || |||||||||||||| ||||
----------------ggaatcaacgagt----taatttatactagtgcaaccaagtgttgccatta-gtaattatgacaaatcttttctgaaataatttttgtttgataattgctttcagCAAACCATTTAAAAAGGTGGGATCCTTCTGCTGGCTTTCCCTGGCTATATGCATTGTAGAGCTCCTGATCTGCATCAAGTTTGGGCATG

upper sequence: Vv01s0011g04370.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA20G25830.2 (Glycine max), 3'ss of exon 12
--------------------------------------------gtactatctctccttgcttatttgcaaatattatacttgatactaa-gaatgccaaccagcattagtgtgcatatagttcaaatttttcttacattttggtaaatgttgtgtcgttcttcagAAAACCAGTGAAAAAGGTGGGAGCGTTTTGTTGGCTTTCCCTTGCTATTTGCATTATTGAACTACTCATTTGCATCAAGTTTGGACATG-----------
                                              |  |  ||   ||  |   ||    ||| | |  || ||  | | ||||| ||    | | ||   | |  | | ||  |  |||| |    |  |  ||   ||||||   || |||||||| |||||||||||||| ||||| | ||||||||| || ||||| ||||||||| | ||||| || |||||||| ||||||||||| |           
gtacagtcttctgcatctctcttgtttccctcccacccctacccaaaagaagtcatatttttctgttttgcatagtgtgtttaatgttgatgaatgaca-ttggaaatatcctactaagattttgacattttttcctgtcata-tattcgttgtga-atttttcagAAAGCCAGTGAAAAAGGTCGGAGCATATTGTTGGCTCTCTCTTGCCATTTGCATTGTGGAACTTCTGATTTGCATTAAGTTTGGACACGGTAGTTCTCTT

upper sequence: Vv01s0011g04370.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA20G25830.1 (Glycine max), 3'ss of exon 12
--------------------------------------------gtactatctctccttgcttatttgcaaatattatacttgatactaa-gaatgccaaccagcattagtgtgcatatagttcaaatttttcttacattttggtaaatgttgtgtcgttcttcagAAAACCAGTGAAAAAGGTGGGAGCGTTTTGTTGGCTTTCCCTTGCTATTTGCATTATTGAACTACTCATTTGCATCAAGTTTGGACATG
                                              |  |  ||   ||  |   ||    ||| | |  || ||  | | ||||| ||    | | ||   | |  | | ||  |  |||| |    |  |  ||   ||||||   || |||||||| |||||||||||||| ||||| | ||||||||| || ||||| ||||||||| | ||||| || |||||||| ||||||||||| |
gtacagtcttctgcatctctcttgtttccctcccacccctacccaaaagaagtcatatttttctgttttgcatagtgtgtttaatgttgatgaatgaca-ttggaaatatcctactaagattttgacattttttcctgtcata-tattcgttgtga-atttttcagAAAGCCAGTGAAAAAGGTCGGAGCATATTGTTGGCTCTCTCTTGCCATTTGCATTGTGGAACTTCTGATTTGCATTAAGTTTGGACACG

upper sequence: Vv01s0011g04370.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA10G41430.1 (Glycine max), 3'ss of exon 11
gtactatctctccttgcttatttgcaaatattatacttgatactaagaatgccaaccagcattagtgtgcatatagttcaaatttt--tcttacattttggtaaatgttgtgtcgttctt-cagAAAACCAGTGAAAAAGGTGGGAGCGTTTTGTTGGCTTTCCCTTGCTATTTGCATTATTGAACTACTCATTTGCATCAAGTTTGGACATG
    ||  | |   ||| | | | |   | |    |      |||   |    ||    |||| | |   ||       |||||||    ||   |  |  || ||    |||  || || |||||| |||||||||||||| || || | ||||||||| || ||||| ||||||||| | ||||| || |||||||| ||||||||||| |
---gtacatttttctgcatctct-ctcgtttccctcccacccctacccaaaagaagtcacattggag-atatcctaccaaaattttgacattttttcctcatatattccttgtgattttttcagAAAGCCAGTGAAAAAGGTTGGGGCATATTGTTGGCTCTCTCTTGCCATTTGCATTGTGGAACTTCTGATTTGCATTAAGTTTGGACACG

upper sequence: Vv01s0011g04370.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT1G15110.1 (Arabidopsis thaliana), 3'ss of exon 11
gtactatctctccttgcttatttgcaaatattatacttgatactaagaatgccaaccagcattagtgtgcatatagttcaaatttttcttacattttggtaaatgttgtgtcgttcttcagAAAACCAGTGAAAAAGGTGGGAGCGTTTTGTTGGCTTTCCCTTGCTATTTGCATTATTGAACTACTCATTTGCATCAAGTTTGGACATG
                       | |||   ||||     | |     ||        |  ||||| || | | ||||      ||   || |  |||   | | ||| || ||||  ||||||||| ||||||||||||||||| || |||||||| || || |  || |||||  | ||||| ||||| |||||||||||||||  ||
-----------------------gtaaa-gctatagccactgc----gatattggttggagttagtttggaaagagtt------ttgtatataacttgtgtagttttg-gttgttca-cagAAAACCTGTGAAAAAGGTGGGAGCATTCTGTTGGCTGTCACTGGGGATATGCATAGTAGAACTTCTCATCTGCATCAAGTTTGGAAGTG

upper sequence: Vv01s0011g04370.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT1G15110.2 (Arabidopsis thaliana), 3'ss of exon 11
gtactatctctccttgcttatttgcaaatattatacttgatactaagaatgccaaccagcattagtgtgcatatagttcaaatttttcttacattttggtaaatgttgtgtcgttcttcagAAAACCAGTGAAAAAGGTGGGAGCGTTTTGTTGGCTTTCCCTTGCTATTTGCATTATTGAACTACTCATTTGCATCAAGTTTGGACATG----
                       | |||   ||||     | |     ||        |  ||||| || | | ||||      ||   || |  |||   | | ||| || ||||  ||||||||| ||||||||||||||||| || |||||||| || || |  || |||||  | ||||| ||||| |||||||||||||||  ||    
-----------------------gtaaa-gctatagccactgc----gatattggttggagttagtttggaaagagtt------ttgtatataacttgtgtagttttg-gttgttca-cagAAAACCTGTGAAAAAGGTGGGAGCATTCTGTTGGCTGTCACTGGGGATATGCATAGTAGAACTTCTCATCTGCATCAAGTTTGGAAGTGGTAG

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|110360098|gb|EC922718.1|EC922718
EST:     CTAATTGCAATACCAACAATTCGTGAGTACAATTCATACTTACAGGACAG                         AAAACCAGTGAAAAAGGTGGGAGCGTTTTGTTGGCTTTCCCTTGCTATTTG
genomic: CTAATTGCAATACCAACAATTCGTGAGTACAATTCATACTTACAGGACAGgtactatctc ... cgttcttcagAAAACCAGTGAAAAAGGTGGGAGCGTTTTGTTGGCTTTCCCTTGCTATTTG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgcatatagttcaaatttttcttacattttggtaaatgttgtgtcgttcttcagAAAACCAGTGAAAAAGGTGGGAGCGTTTTGTTGGCTTTCCCTTGCTATTTGCATTATTGAACTACTCATTTGCATCAAGTTTGGACATG
                   ttcttac  putative branch site (score: 2)
                                            tcgttcttc  putative PPT
          ttcaaatttttcttac  TA-rich tract