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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaaatgagggattctatagtaattggaatcgggctgttgtgtgagttcgattgagtttcaatttctttgaacttcttttggcagATGGGATGGGTACGGCTGAGTGGAGAGCAGCCAAGAGTCCAGCATATTACAAGCGCGGGGACTATGTTCCTGGTTTGAAG

Basic information

species Vitis vinifera
transcript Vv01s0026g00990.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0026g00990.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os02g50620.1 (Oryza sativa), 3'ss of exon 1
gtaagaaatgagggattctatagtaattggaatcgggctgt----tgtgtgagttcgattga---gtttcaatttc--tttgaacttcttttggcagATGGGATGGGTACGGCTGAGTGGAGAGCAGCCAAGAGTCCAGCATATTACAAGCGCGGGGACTATGTTCCTGGTTTGAAG
|| ||       |     | | | |||    || |    ||    | ||   ||||  ||||   | |   || |   || ||  | | ||  |||||||||||||| || ||||||||||| ||||| ||||| || || || |||||||| || || ||||| ||||| ||||||
gtgagttcctgtgccgcttttgggaatcatgattgcatcgtgatatctgcttgttcatttgatgtgatatgatcttgattcgatttcccttgtgcagATGGGATGGGAACCGCTGAGTGGAGGGCAGCAAAGAGCCCTGCCTACTACAAGCGTGGTGATTATGTGCCTGGATTGAAG

upper sequence: Vv01s0026g00990.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G027627_T01 (Zea mays), 3'ss of exon 1
---------------------------gtaagaaatgagggattctatagtaattggaatcgg-gctgttgtgtgagttcgattgagtttc---aatttctttgaacttctt----ttggcagATGGGATGGGTACGGCTGAGTGGAGAGCAGCCAAGAGTCCAGCATATTACAAGCGCGGGGACTATGTTCCTGGTTTGAAG
                           || ||     || | |   |||||| |    ||||| |   ||  |  |    || || | |     | |  ||||| | | | |    |  |||||||||||||| ||||| |||||||| ||  ||||||| || || || |||||||||||||||||||| ||||| || |||
gtgagttcttctgttaccatgtgcttggtcagctggtagtgctgtgatagtactgttcatcggtgggattccgaaatcgagagtgggctagtggagtgactttggagtacctggtgtatgcagATGGGATGGGGACGGCAGAGTGGAGGGCCTCCAAGAGCCCGGCTTACTACAAGCGCGGGGACTATGTGCCTGGCTTAAAG

upper sequence: Vv01s0026g00990.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G361693_T01 (Zea mays), 3'ss of exon 1
----------gtaagaaatgagggattctatagta-attggaatcgggctg-ttgtgtgagttcgattgagtttcaatttctttgaacttcttttg-gcagATGGGATGGGTACGGCTGAGTGGAGAGCAGCCAAGAGTCCAGCATATTACAAGCGCGGGGACTATGTTCCTGGTTTGAAG
          | |  || |  |||| ||     |  ||||  ||    ||| ||   | |   | | |         | |   |    ||||||||   |||||||||||| || || |||||||| ||||| ||||| || || || |||||||| || |||||||| ||||| ||||||
gtgagttcgtgcatcaattccgggaatcggggttggattgagataaatctgattacattatgacaaatataacgtggtctgggtttgattcttttgtatagATGGGATGGGAACAGCGGAGTGGAGGGCAGCAAAGAGCCCTGCCTACTACAAGCGTGGCGACTATGTGCCTGGATTGAAG

upper sequence: Vv01s0026g00990.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA08G40380.1 (Glycine max), 3'ss of exon 1
-----------------gtaagaaatgagggattctatagtaattggaatcgggctgttgtgtgagttcgattgagtttcaatttctttgaacttcttttggcagATGGGATGGGTACGGCTGAGTGGAGAGCAGCCAAGAGTCCAGCATATTACAAGCGCGGGGACTATGTTCCTGGTTTGAAG
                 ||||    | |  ||    ||| ||||| |||  |||   |||| ||| || | ||  | || | ||  ||||   ||  |  | ||||||| ||||| || |||||||||||||| || |||||||| || ||||||||||| ||||| ||||||||||| ||||||
ttattttttattcttttgtaactgcttattgaaa--ataataatttgaaaagggactttgt-tgatttgggtttggattaatttggtttgg--tttgtgggacagATGGAATGGGGACAGCTGAGTGGAGAGCTGCTAAGAGTCCTGCTTATTACAAGCGTGGGGATTATGTTCCTGGATTGAAG

upper sequence: Vv01s0026g00990.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA18G17240.1 (Glycine max), 3'ss of exon 1
---------------gtaagaaatgagggattctatagtaattggaatcgggctgttgtgtgagttcgattgagtttcaatttctttgaacttcttttggcagATGGGATGGGTACGGCTGAGTGGAGAGCAGCCAAGAGTCCAGCATATTACAAGCGCGGGGACTATGTTCCTGGTTTGAAG
                |   || ||     |   | | | ||   ||   |||| |||| ||| || | ||  | || | ||  ||||   ||  |  | ||||||| ||||| || |||||||||||||| || ||||||||    ||||||||||| ||||| ||||||||||| ||||||
gttatttttttctctcttccaagtgcttattggaaaaatgatccaaacaaggcttttgt-tgatttgggtttcgattaatttggtttgg--tttgtgggacagATGGAATGGGGACAGCTGAGTGGAGAGCTGCTAAGAGTCCTAGTTATTACAAGCGTGGGGATTATGTTCCTGGATTGAAG

upper sequence: Vv01s0026g00990.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA02G03080.1 (Glycine max), 3'ss of exon 1
----------gtaagaaatgagggattctatagt--aattggaatcgggct--gttgtgtgagttcgattgagtttcaatttctttgaacttcttttggcagATGGGATGGGTACGGCTGAGTGGAGAGCAGCCAAGAGTCCAGCATATTACAAGCGCGGGGACTATGTTCCTGGTTTGAAG
                | ||| || || | | ||  | |||   | |   |  ||| | |   ||   ||||  ||  | |   ||| | |  ||   | |||||||||||| || || ||||||||||| ||||||||||| || ||||| ||||| ||||| || || ||||| ||||||
accttatatctcctagagtgaagggttgtgttgtttacttgtttttgaattttgttttttttttttttttgaagtttgagta--ttggattggttaatgtagATGGGATGGGGACTGCGGAGTGGAGAGCTGCCAAGAGTCCTGCTTATTATAAGCGTGGGGATTACGTGCCTGGCTTGAAG

upper sequence: Vv01s0026g00990.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT1G59900.1 (Arabidopsis thaliana), 3'ss of exon 1
gtaagaaatgagggattctatagtaattggaatcgggctgttgtgtgagttcgattgagtttcaatttct--ttgaacttcttttg-gcagATGGGATGGGTACGGCTGAGTGGAGAGCAGCCAAGAGTCCAGCATATTACAAGCGCGGGGACTATGTTCCTGGTTTGAAG
||||| | |   |  |||| |  |  ||    ||    |  | |||  ||| | ||  ||   | | |||  ||||| ||  | || |||||||| ||||| || ||||| |||||||| || ||||||||| | || |||||||| || || |||||||||||  | |||
gtaagcatttttgc-ttctttctttctttctttc---tttctttgtaggtttgtttt-gtcgtagtatctgattgaatttgatctgtgcagATGGAATGGGAACTGCTGAATGGAGAGCCGCTAAGAGTCCATCTTACTACAAGCGTGGTGATTATGTTCCTGGACTCAAG

upper sequence: Vv01s0026g00990.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S56_222V6.1 (Physcomitrella patens), 3'ss of exon 1
------------------------------------------------------------------------------gtaagaaatgagggattctatagtaattggaatcgg--gctgttgtgtgagttcgattgagtttcaatttc---tttgaacttcttttggcagATGGGATGGGTACGGCTGAGTGGAGAGCAGCCAAGAGTCCAGCATATTACAAGCGCGGGGACTATGTTCCTGGTTTGAAG
                                                                               |   | |||    ||| | |  || |   |||     | | |  |  | ||   |||  ||   ||||     || |  ||  |  || ||||||| ||||||||||| |||||| |  |||||||||| || | ||| ||||| ||||| || || |||||||| ||||||
gtgagtataattgctctaaaaccctaaatcgatgtgttgaacatttggagttatgcgggtagaaatgtagacttctggctcgaatatgttcaattgtcttctactaccaatgcatcgttctccttggcgtgaaattctgtcggaattaagaattggctctgttaatgacagATGGAATGGGTACGGCAGAGTGGCGGTCAGCCAAGAGCCCCGAATACTACAAACGCGGTGATTACGTTCCTGGATTGAAG

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|27585723|gb|CB008418.1|CB008418
EST:     AGCGGCGCTTTTGGATTTGCCAGCGATTTTGGTTTGCGAGAACAATCACT                         ATGGGATGGGTACGGCTGAGTGGAGAGCAGCCAAGAGTCCAGCATATTACA
genomic: AGCGGCGCTTTTGGATTTGCCAGCGATTTTGGTTTGCGAGAACAATCACTgtaagaaatg ... cttttggcagATGGGATGGGTACGGCTGAGTGGAGAGCAGCCAAGAGTCCAGCATATTACA
EST: gi|27583148|gb|CB005843.1|CB005843
EST:     AGCGGCGCTTTTGGATTTGCCAGCGATTTTGGTTTGCGAGAACAATCACT                         ATGGGATGGGTACGGCTGAGTGGAGAGCAGCCAAGAGTCCAGCATATTACA
genomic: AGCGGCGCTTTTGGATTTGCCAGCGATTTTGGTTTGCGAGAACAATCACTgtaagaaatg ... cttttggcagATGGGATGGGTACGGCTGAGTGGAGAGCAGCCAAGAGTCCAGCATATTACA
EST: gi|30298455|gb|CB975249.1|CB975249
EST:     AGAACAATCACT                         ATGGGATGGGTACGGCTGAGTGGAGAGCAGCCAAGAGTCCAGCATATTACA
genomic: AGAACAATCACTgtaagaaatg ... cttttggcagATGGGATGGGTACGGCTGAGTGGAGAGCAGCCAAGAGTCCAGCATATTACA
EST: gi|110384826|gb|EC949291.1|EC949291
EST:     TGCCAGCGATTTTGGTTTGCGAGAACAATCACT                         ATGGGATGGGTACGGCTGAGTGGAGAGCAGCCAAGAGTCCAGCATATTACA
genomic: TGCCAGCGATTTTGGTTTGCGAGAACAATCACTgtaagaaatg ... cttttggcagATGGGATGGGTACGGCTGAGTGGAGAGCAGCCAAGAGTCCAGCATATTACA
EST: gi|110415427|gb|EC981335.1|EC981335
EST:     AGCGGCGCTTTTGGATTTGCCAGCGATTTTGGTTTGCGAGAACAATCACT                         ATGGGATGGGTACGGCTGAGTGGAGAGCAGCCAAGAGTCCAGCATATTACA
genomic: AGCGGCGCTTTTGGATTTGCCAGCGATTTTGGTTTGCGAGAACAATCACTgtaagaaatg ... cttttggcagATGGGATGGGTACGGCTGAGTGGAGAGCAGCCAAGAGTCCAGCATATTACA
EST: gi|30133148|gb|CB918487.1|CB918487
EST:     GGCGGCGCTTTTGGATTTGCCAGCGATTTTGGTTTGCGAGAACAATCACT                         ATGGGATGGGTACGGCTGAGTGGAGAGCAGCCAAGAGTCCAGCATATTACA
genomic: AGCGGCGCTTTTGGATTTGCCAGCGATTTTGGTTTGCGAGAACAATCACTgtaagaaatg ... cttttggcagATGGGATGGGTACGGCTGAGTGGAGAGCAGCCAAGAGTCCAGCATATTACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgggctgttgtgtgagttcgattgagtttcaatttctttgaacttcttttggcagATGGGATGGGTACGGCTGAGTGGAGAGCAGCCAAGAGTCCAGCATATTACAAGCGCGGGGACTATGTTCCTGGTTTGAAG
                                          cttctttt  CT-rich tract
                          tttcaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaaatgagggattctatagtaattggaatcgggctgttgtgtgagttcgattgagtttcaatttctttgaacttcttttggcagATGGGATGGGTACGGCTGAGTGGAGAGCAGCCAAGAGTCCAGCATATTACAAGCGCGGGGACTATGTTCCTGGTTTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG