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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcacttgttactcagcatgatgttgaactgcggttttagttctccagtcttgtggttgacattttatttaacgtaagaactgagtgcctgacactttccctttgcagATCCAGATGAAAAGTATAGGTATGAGATCAAGGACATACTTGAAATGGAAATGAAGATCTTAGAAGCTCTCAACTATTATTTAGTTGTATTCCATCCTTA

Basic information

species Vitis vinifera
transcript Vv00s0360g00050.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0360g00050.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os09g32680.4 (Oryza sativa), 3'ss of exon 4
gtaatcacttgttactcagcatgatgttgaactgcggttttagttctccagtcttgtggttgacattttatttaacgtaagaactgagtgcctgacactttccctt----tgcagATCCAGATGAAAAGTATAGGTATGAGATCAAGGACATACTTGAAATGGAAATGAAGATCTTAGAAGCTCTCAACTATTATTTAGTTGTATTCCATCCTTA
                  | | |      ||       |  |      ||   || | |   | |  |    |||| ||| |||| |     ||       |||      || || | | ||||| |||||  ||| ||| |||||||| || |||||||||||||||||| || | || || ||  |||||||||||||||| | ||| || ||
------------------gtaaggctcataatcataaatgga----cacatatttatcgggaagaactgcactaacctaa-aactaaacatgtgctctccccccgcaaaatgtagCTTCTGATGAGAAGTACCGGTTTGAAATCAAGGATATCCTTGAAATGGAAATGAAGCTCCTGGAGGCACTTGACTATTATTTAGTTGTTTACCACCCATA

upper sequence: Vv00s0360g00050.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G408242_T01 (Zea mays), 3'ss of exon 2
-----------------------gtaatcacttgttactcagcatgatgttgaactgcggttttagttctccagtcttgtggttgacattttattta-acgtaagaactg-agtgcctgacactttcccttt-------------------gcagATCCAGATGAAAAGTATAGGTATGAGATCAAGGACATACTTGAAATGGAAATGAAGATCTTAGAAGCTCTCAACTATTATTTAGTTGTATTCCATCCTTA
                          |   ||||| | |    || |    ||  || ||| |  ||  |  |  | | |  ||  |    |||||| | |||| ||||| |||   ||||  | || || |                   |||| | | ||||| |||||| ||| ||| || ||||| || |||||||||||||||||| || | ||||||||| |||||||||| ||||| |||||||| ||
gtggaggagagtacagtgcaagcccgacttcttgt-attttatataaaaaagatgtgtggtgt--gtcttataaccatat--ttatcgccatatttacatgtaaaaactgcagtagatgaccttctctctctctctccctctcttcaaagtgcagGTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAATGAAGCTCCTGGAAGCTCTCGACTATTATTTGGTTGTTTTCCATCCATA

upper sequence: Vv00s0360g00050.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G408242_T03 (Zea mays), 3'ss of exon 5
gtaatcacttgttactcagcatgatgttgaactgcggttttagttctccagtct--tgtggttgacattttatttaacgtaagaactgagtgcctgacactttccctttgcagATCCAGATGAAAAGTATAGGTATGAGATCAAGGACATACTTGAAATGGAAATGAAGATCTTAGAAGCTCTCAACTATTATTTAGTTGTATTCCATCCTTA
         |||  || |  |  || || | |  |   ||||  | |  |  ||   || | |||| || | | |          ||   | |||  |   |||    ||||| | | ||||| |||||| ||| ||| || ||||| || |||||||||||||||||| || | ||||||||| |||||||||| ||||| |||||||| ||
--------gtgtgtcttataaccatatttatcgccatatttacatgtaaaaactgcagtagatgaccttctctct----------ctctctccctctc---ttcaaagtgcagGTTCCGATGATAAGTATCGGTTTGAAATTAAGGATATTCTTGAAATGGAAATGAAGCTCCTGGAAGCTCTCGACTATTATTTGGTTGTTTTCCATCCATA

upper sequence: Vv00s0360g00050.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA08G46170.2 (Glycine max), 3'ss of exon 6
---------------gtaatcacttgttactcagcatgatgttgaactgcggttttagt-------------tctcca-----gtcttgtggt-tgacattt---tatttaacgtaagaactgagtgcctgacactttccctttgcagATCCAGATGAAAAGTATAGGTATGAGATCAAGGACATACTTGAAATGGAAATGAAGATCTTAGAAGCTCTCAACTATTATTTAGTTGTATTCCATCCTTA
                ||||   || ||| |  || |  ||||||  |  | | |||               | ||||     ||||  || | | | ||||   |||||    |     ||||  ||       |||    | |||||    ||||| |||||||| ||||| |||||||||||||||||||||||||||||||| ||||||||||| || |||||  | ||||||| |||||| ||
gtaagctgttagcttataattttttcttaatttgcttcgtgttgacttttgatcttaaaagtgaataatttgtttccaaatttgtctcatgctattatatttcattatttcctttctatgctgaaagcacagtgattttgaat-gcagACAGTGATGACAAGTATAGATATGAAATCAAGGACATACTTGAAATGGAAATGAAGATTTTAGAAGCTCTTAATTATTACCTGGTTGTATACCATCCATA

upper sequence: Vv00s0360g00050.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA18G33140.1 (Glycine max), 3'ss of exon 5
-----------------gtaatcacttgttactcagcatgatgttgaactgcggttttag-------ttctccagtcttgtggttgac-------attttatttaacgtaagaactgagtgcctgacactttccctttgcagATCCAGATGAAAAGTATAGGTATGAGATCAAGGACATACTTGAAATGGAAATGAAGATCTTAGAAGCTCTCAACTATTATTTAGTTGTATTCCATCCTTA
                  |||     | ||| |  || | ||||| |  |  | |  ||        |  |    |  ||  |||| |       ||| |||||    |     ||||  ||       |||   | ||||||  | ||||| |||||||| ||||| |||||||||||||||||||||||||||||||| |||||||| || || |||||  | ||||||| |||||| ||
gtaagctgtgttagcttataaatttgtcttattttgcttcatgttaacttctgatcgtaaaagtgaataatttgtttctgaagttgtctcatgctattatatttcctttctatgctgaaagcacagtgattttg-tatgcagACACTGATGACAAGTATAGATATGAAATCAAGGACATACTTGAAATGGAAATGAAGATTTTAGAAGCGCTTAATTATTACCTGGTTGTATACCATCCATA

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|110421670|gb|EC987970.1|EC987970
EST:     TCAGAAAATTAA                         ATCCAGATGAAAAGTATAGGTATGAGATCAAGGACATACTTGAAATGGAAA
genomic: TCAGAAAATTAAgtaatcactt ... ccctttgcagATCCAGATGAAAAGTATAGGTATGAGATCAAGGACATACTTGAAATGGAAA
EST: gi|110695053|gb|EE072630.1|EE072630
EST:     AGAAAGCACTGTGCAGGCTAGACTTCTTGTATTTTACGTCAGAAAATTAA                         ATCCAGATGAAAAGTATAGGTATGAGATCAAGGACATACTTGAAATGGAAA
genomic: AGAAAGCACTGTGCAGGCTAGACTTCTTGTATTTTACGTCAGAAAATTAAgtaatcactt ... ccctttgcagATCCAGATGAAAAGTATAGGTATGAGATCAAGGACATACTTGAAATGGAAA
EST: gi|110709326|gb|EE084688.1|EE084688
EST:     AGAAAGCACTGTGCAGGCTAGACTTCTTGTATTTTACGTCAGAAAATTAA                         ATCCAGATGAAAAGTATAGGTATGAGATCAAGGACATACTTGAAATGGAAA
genomic: AGAAAGCACTGTGCAGGCTAGACTTCTTGTATTTTACGTCAGAAAATTAAgtaatcactt ... ccctttgcagATCCAGATGAAAAGTATAGGTATGAGATCAAGGACATACTTGAAATGGAAA
EST: gi|110364321|gb|EC923868.1|EC923868
EST:     AGAAAGCACTGTGCAGGCTAGACTTCTTGTATTTTACGTCAGAAAATTAA                         ATCCAGATGAAAAGTATAGGTATGAGATCAAGGACATACTTGAAATGGAAA
genomic: AGAAAGCACTGTGCAGGCTAGACTTCTTGTATTTTACGTCAGAAAATTAAgtaatcactt ... ccctttgcagATCCAGATGAAAAGTATAGGTATGAGATCAAGGACATACTTGAAATGGAAA
EST: gi|161719540|gb|FC067026.1|FC067026
EST:     AGAAAGCACTGTGCAGGCTAGACTTCTTGTATTTTACGTCAGAAAATTAA                         ATCCAGATGAAAAGTATAGGTATGAGATCAAGGACATACTTGAAATGGAAA
genomic: AGAAAGCACTGTGCAGGCTAGACTTCTTGTATTTTACGTCAGAAAATTAAgtaatcactt ... ccctttgcagATCCAGATGAAAAGTATAGGTATGAGATCAAGGACATACTTGAAATGGAAA
EST: gi|110730965|gb|EE108649.1|EE108649
EST:     AGAAAGCACTGTGCAGGCTAGACTTCTTGTATTTTACGTCAGAAAATTAA                         ATCCAGATGAAAAGTATAGGTATGAGATCAAGGACATACTTGAAATGGAAA
genomic: AGAAAGCACTGTGCAGGCTAGACTTCTTGTATTTTACGTCAGAAAATTAAgtaatcactt ... ccctttgcagATCCAGATGAAAAGTATAGGTATGAGATCAAGGACATACTTGAAATGGAAA
EST: gi|77582414|gb|DV220179.1|DV220179
EST:     AGAAAGCACTGTGCAGGCTAGACTTCTTGTATTTTACGTCAGAAAATTAA                         ATCCAGATGAAAAGTATAGGTATGAGATCAAGGACATACTTGAAATGGAAA
genomic: AGAAAGCACTGTGCAGGCTAGACTTCTTGTATTTTACGTCAGAAAATTAAgtaatcactt ... ccctttgcagATCCAGATGAAAAGTATAGGTATGAGATCAAGGACATACTTGAAATGGAAA
EST: gi|110713415|gb|EE089326.1|EE089326
EST:     AGAAAGCACTGTGCAGGCTAGACTTCTTGTATTTTACGTCAGAAAATTAA                         ATCCAGATGAAAAGTATAGGTATGAGATCAAGGACATACTTGAAATGGAAA
genomic: AGAAAGCACTGTGCAGGCTAGACTTCTTGTATTTTACGTCAGAAAATTAAgtaatcactt ... ccctttgcagATCCAGATGAAAAGTATAGGTATGAGATCAAGGACATACTTGAAATGGAAA
EST: gi|32247896|gb|CD713715.1|CD713715
EST:     AGAAAGCACTGTGCAGGCTAGACTTCTTGTATTTTACGTCAGAAAATTAA                         ATCCAGATGAAAAGTATAGGTATGAGATCAAGGACATACTTGAAATGGAAA
genomic: AGAAAGCACTGTGCAGGCTAGACTTCTTGTATTTTACGTCAGAAAATTAAgtaatcactt ... ccctttgcagATCCAGATGAAAAGTATAGGTATGAGATCAAGGACATACTTGAAATGGAAA
EST: gi|349814319|gb|FQ398759.1|FQ398759
EST:     AGAAAGCACTGTGCAGGCTAGACTTCTTGTATTTTACGTCAGAAAATTAA                         ATCCAGATGAAAAGTATAGGTATGAGATCAAGGACGTACTTGAAATGGAAA
genomic: AGAAAGCACTGTGCAGGCTAGACTTCTTGTATTTTACGTCAGAAAATTAAgtaatcactt ... ccctttgcagATCCAGATGAAAAGTATAGGTATGAGATCAAGGACATACTTGAAATGGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggttgacattttatttaacgtaagaactgagtgcctgacactttccctttgcagATCCAGATGAAAAGTATAGGTATGAGATCAAGGACATACTTGAAATGGAAATGAAGATCTTAGAAGCTCTCAACTATTATTTAGTTGTATTCCATCCTTA
                                 gcctgac  putative branch site (score: 3)
                                       cactttccctttgc  CT-rich tract
        attttatttaacgtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatcacttgttactcagcatgatgttgaactgcggttttagttctccagtcttgtggttgacattttatttaacgtaagaactgagtgcctgacactttccctttgcagATCCAGATGAAAAGTATAGGTATGAGATCAAGGACATACTTGAAATGGAAATGAAGATCTTAGAAGCTCTCAACTATTATTTAGTTGTATTCCATCCTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC