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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgacaacatttacatttttttcattaacctttgattggtgctatcactactgcttctatgaatgttgtgatatttattgtcatttgtcatcgtcaaggaggaacagacagcactttctggtactgttcattgatttttgaatttggaaacagGGCCAGGATGATTTATGTGAGGATTTCTTTGCTTATAATCGGGCAAAAGGAACCCTTTATGATGGTGAAACAAGGCTATTCCTACGCAACAATG

Basic information

species Vitis vinifera
transcript Vv07s0031g03150.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0031g03150.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA05G33140.1 (Glycine max), 3'ss of exon 3
gtgtgacaacatttacatttttttcattaacctttgattggtgctatcactactgcttctatgaatgttgtgatatttattgtcatttgtcatcgtcaaggaggaacagacagcactttctggtactgttcattgatttttgaatttggaaacagGGCCAGGATGATTTATGTGAGGATTTCTTTGCTTATAATCGGGCAAAAGGAACCCTTTATGATGGTGAAACAAGGCTATTCCTACGCAACAATG
                                                               |||  |||| ||   | | ||| |    || || ||           | | | | |     | |||| ||    | |  || | | | ||||||||| |||||| ||||||| | ||||||||| ||||| ||||||||||||||||| ||||||||||||||  | || ||  | || |||| ||
-------------------------------------------------------------gtaatactgtgttaaacact-tcactctgtat-gttaa-----------ctggattcttgttcattgttgatgttgtctccaaatggtatacagGGCCATGATGATCTATGTGAAGCTTTCTTTGCCTATAACCGGGCAAAAGGAACCCTCTATGATGGTGAAACTCGACTTTTTTTTCGAAACAGTG

upper sequence: Vv07s0031g03150.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA08G00740.2 (Glycine max), 3'ss of exon 4
gtgtgacaacatttacatttttttcattaacctttgattggtgctatcactactgcttctatgaatgttgtgatatttattgtcatttgtcatcgtcaaggaggaacagacagcactttctggtactgttcattgatttttgaatttggaaacagGGCCAGGATGATTTATGTGAGGATTTCTTTGCTTATAATCGGGCAAAAGGAACCCTTTATGATGGTGAAACAAGGCTATTCCTACGCAACAATG
                                                                     || | || |  ||| |          ||    | |    ||| | | |       | |||| ||    | |  || |   | ||||||||| |||||| ||||||| | ||||||||| ||||| ||||||||||||||||| ||||||||||||||  | || ||  | || |||| ||
---------------------------------------------------------------------gtaaaatattgtgttagacacttcactcttatatg--ttgactggattcatgttcattgttgatgttgtctccaaatgttatacagGGCCATGATGATCTATGTGAAGCTTTCTTTGCCTATAACCGGGCAAAAGGAACCCTCTATGATGGTGAAACTCGACTCTTTTTTCGAAACAGTG

upper sequence: Vv07s0031g03150.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT5G63620.2 (Arabidopsis thaliana), 3'ss of exon 3
gtgtgacaacatttacatttttttcattaacctttgattggtgctatcactactgcttctatgaatgttgtgatatttattgtcatttgtcatcgtcaaggaggaacagacagcactttctggtactgttcattgatttttgaatttggaaacagGGCCAGGATGATTTATGTGAGGATTTCTTTGCTTATAATCGGGCAAAAGGAACCCTTTATGATGGTGAAACAAGGCTATTCCTACGCAACAATG
                                                           |  ||| |   |  ||||  || ||||  |      | |     |||| |  |||  ||| | |          |||| ||| |||||||| ||||||||| |||||| ||||||| || ||||||||||| ||  | || || ||||| ||||| ||||| |||||  | || ||  | ||  |  |||
----------------------------------------------------------gtgagaacgaaattgtattgctt-tcatcggattctctaatctgagaactg-tagc--tttttagc---------tgatattttaatttggatacagGGCCATGATGATCTATGTGAAGACTTCTTTGCTTACAACAGAGCCAAGGGAACTCTTTACGATGGCGAAACTCGTCTCTTTTTGCGACATGATG

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|161718078|gb|FC068581.1|FC068581
EST:     TTGTTGGAGCTTTCATCATGCCCTGTGGTAGCTGTTTCTTCTGTAACAGG                         GGCCAGGATGATTTATGTGAGGATTTCTTTGCTTATAATCGGGCAAAAGGA
genomic: TTGTTGGAGCTTTCATCATGCCCTGTGGTAGCTGTTTCTTCTGTAACAGGgtgtgacaac ... ttggaaacagGGCCAGGATGATTTATGTGAGGATTTCTTTGCTTATAATCGGGCAAAAGGA
EST: gi|161715089|gb|FC063332.1|FC063332
EST:     TTGTTGGAGCTTTCATCATGCCCTGTGGTAGCTGTTTCTTCTGTAACAGG                         GGCCAGGATGATTTATGTGAGGATTTCTTTGCTTATAATCGGGCAAAAGGA
genomic: TTGTTGGAGCTTTCATCATGCCCTGTGGTAGCTGTTTCTTCTGTAACAGGgtgtgacaac ... ttggaaacagGGCCAGGATGATTTATGTGAGGATTTCTTTGCTTATAATCGGGCAAAAGGA
EST: gi|161718151|gb|FC065657.1|FC065657
EST:     TTGTTGGAGCTTTCATCATGCCCTGTGGTAGCTGTTTCTTCTGTAACAGG                         GGCCAGGATGATTTATGTGAGGATTTCTTTGCTTATAATCGGGCAAAAGGA
genomic: TTGTTGGAGCTTTCATCATGCCCTGTGGTAGCTGTTTCTTCTGTAACAGGgtgtgacaac ... ttggaaacagGGCCAGGATGATTTATGTGAGGATTTCTTTGCTTATAATCGGGCAAAAGGA
EST: gi|161713964|gb|FC063149.1|FC063149
EST:     TTGTTGGAGCTTTCATCATGCCCTGTGGTAGCTGTTTCTTCTGTAACAGG                         GGCCAGGATGATTTATGTGAGGATTTCTTTGCTTATAATCGGGCAAAAGGA
genomic: TTGTTGGAGCTTTCATCATGCCCTGTGGTAGCTGTTTCTTCTGTAACAGGgtgtgacaac ... ttggaaacagGGCCAGGATGATTTATGTGAGGATTTCTTTGCTTATAATCGGGCAAAAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaggaacagacagcactttctggtactgttcattgatttttgaatttggaaacagGGCCAGGATGATTTATGTGAGGATTTCTTTGCTTATAATCGGGCAAAAGGAACCCTTTATGATGGTGAAACAAGGCTATTCCTACGCAACAATG
                              cattgat  putative branch site (score: 4)
                               attgatttttgaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgacaacatttacatttttttcattaacctttgattggtgctatcactactgcttctatgaatgttgtgatatttattgtcatttgtcatcgtcaaggaggaacagacagcactttctggtactgttcattgatttttgaatttggaaacagGGCCAGGATGATTTATGTGAGGATTTCTTTGCTTATAATCGGGCAAAAGGAACCCTTTATGATGGTGAAACAAGGCTATTCCTACGCAACAATG

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