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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaatgatttagaaaaaaaatgttcatctgctagtttttacttcgttctgtcaaatttcatgcattgtatcaagatggtgtttttccatcttaatttgcagGCTATGCTTGAAATAAATGAACATATGCATAAAGTATGGAAGAATCAAGTGGAGGAAAAGTCTTTGCAGTCGAATATTTCTAGCTGGATTATGAATCTTC

Basic information

species Vitis vinifera
transcript Vv04s0008g05270.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g05270.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os03g63500.1 (Oryza sativa), 3'ss of exon 5
aaatgatttagaaaaaaaatgttcatctgctagtt-tttacttcgttc-tgtcaaatttcatgcattgtatcaagatggtgtt--tttccatcttaatttgcagGCTATGCTTGAAATAAATGAACATATGCATAAAGTATGGAAGAATCAAGTGGAGGAAAAGTCTTTGCAGTCGAATATTTCTAGCTGGATTATGAATCTTC
 |||  | | |||  ||  |||| |   | ||      || |  |||  |||    ||   |    | | ||   || |||||   |||| | |||   |||||||||||||||||||| |||| ||||||||| | ||||||||||  |  |  ||||| |||||| |  |||||| |  ||  || |||||    |  || |
gaattctgt-gaactaacttgttgaatggttaccaacatattcagttggtgttctgttgtttagcatttttctgaatagtgttgagttccttttta---tgcagGCTATGCTTGAAATACATGATCATATGCATGATGTATGGAAGAGACGTGATGAGGACAAGTCTATTGAGTCGAGTGCTTTCAGTTGGATATCAAGCCTCC

upper sequence: Vv04s0008g05270.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G115372_T01 (Zea mays), 3'ss of exon 6
-aaatgatttagaaaaaaaatgttcatctgctagtttttacttcgttctgtcaaatttcatgcattgtatcaagatggtgtttttccatcttaatttgcagGCTATGCTTGAAATAAATGAACATATGCATAAAGTATGGAAGAATCAAGTGGAGGAAAAGTCTTTGCAGTCGAATATTTCTAGCTGGATTATGAATCTTC
  | | |  || ||  | ||  || |  |  ||||| ||   |  |  |    |  ||  |||   | ||    ||     |     | | |    ||||||| |||||||||||| |||| ||||||||| | ||||||||||  |  |  || || || ||| | || || | |  ||  || |||||    |  ||||
gcattaacataaaactataa-attaactttttagttattttattttaattgttaccttgttgccaaggatttgcataagactggagtaccctttgatgcagGCCATGCTTGAAATACATGATCATATGCATGATGTATGGAAGAGACGTGATGATGACAAATCTATTCACTCAAGTGCTTTCAGTTGGATATCAAGCCTTC
















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|294966883|gb|GW839758.1|GW839758
EST:     GTGCCACTGAAGGAATTGTTAAACATCGAAGAAGGTTTCACTTTCATGAG                         GCTATGCTTGAAATAAATGAACATATGCATAAAGTATGGAAGAATCAAGTG
genomic: GTGCTACTGAAGGAATTGTTAAACATCGAAGAAGGTTTCACTTTCATGAGgtgaaaatta ... taatttgcagGCTATGCTTGAAATAAATGAACATATGCATAAAGTATGGAAGAATCAAGTG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgtcaaatttcatgcattgtatcaagatggtgtttttccatcttaatttgcagGCTATGCTTGAAATAAATGAACATATGCATAAAGTATGGAAGAATCAAGTGGAGGAAAAGTCTTTGCAGTCGAATATTTCTAGCTGGATTATGAATCTTC
                                          tcttaat  putative branch site (score: 3)
                                tgtttttccatctt  CT-rich tract
                                         atcttaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaatgatttagaaaaaaaatgttcatctgctagtttttacttcgttctgtcaaatttcatgcattgtatcaagatggtgtttttccatcttaatttgcagGCTATGCTTGAAATAAATGAACATATGCATAAAGTATGGAAGAATCAAGTGGAGGAAAAGTCTTTGCAGTCGAATATTTCTAGCTGGATTATGAATCTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - -aaaaaaa
- - - - - - - - - - - -catctgc
- - - - - - - - - - - - - - - - - - - - - - - ctgtcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatggtg