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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttgtatcccaccttctactttgaaatgtgtatacgacacagttttttgccctgtgtctgacattacttgcttttccctctctgatatatagTCCAGGCATTCAATTCTGTGGGTGACCGATTTTCCAATGTTTGAGTGGAACAGTGCAGAGCAGAGGCTTGAG

Basic information

species Vitis vinifera
transcript Vv03s0088g00500.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0088g00500.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os01g06020.1 (Oryza sativa), 3'ss of exon 5
-----------------------------------------gtaagtttgtatc-ccaccttctactttgaaatgtgtatacgacacagttttttgccctgtgtctgacat---tacttgc-ttttccctctctgatata-tagTCCAGGCATTCAATTCTGTGGGTGACCGATTTTCCAATGTTTGAGTGGAACAGTGCAGAGCAGAGGCTTGAG
                                         |    || |  |  |    ||    | ||| |   ||      ||     ||| |   ||   |||| ||    |  | | |||||  | |    |||  |||||    ||||||||||| |||||||| ||||||||||||||||| ||||||||||  ||||||||    |||
gtaagtctgtgaatatgaatgctattttattgagattctgtgcctcttcgcctttctgtattaccttctgagagcagtcctgatcatctgctttagttatgctcctgatatcttcatctacattttctgttttctttatgctagTCAGCACATTCAATTCTTTGGGTGACGGATTTTCCAATGTTTGAATGGAACAGTGATGAGCAGAGATACGAG

upper sequence: Vv03s0088g00500.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G378717_T01 (Zea mays), 3'ss of exon 10
-----------------------------------------------------------------------gtaagtttgtatcccaccttctactttgaaatgtgtatacgacacagttttttgccctgtgt-ctgacattacttgcttttccctctctgatatat----agTCCAGGCATTCAATTCTGTGGGTGACCGATTTTCCAATGTTTGAGTGGAACAGTGCAGAGCAGAGGCTTGAG
                                                                        | |  |  | | |       |  ||||  || | | || ||      | ||||  ||   | ||   |  | |||| ||| | | |   |||| |    ||||    |||||| |||| |||||||| ||||||||||||||| | ||||||||||  ||||| ||    |||
gtgagtcacaaattgagtaatatgatgatccctattgctgttatgctttatacattactcatgacacatcgatgaaatgttgttctttgccatcatttgctatttctttatgatgattctgtttgtgcttcatactcctaacatttgcctttgcattttctatattttgccagTCTGCACATTCAGTTCTTTGGGTGACAGATTTTCCAATGTTTCAATGGAACAGTGATGAGCAAAGATACGAG

upper sequence: Vv03s0088g00500.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA05G34820.1 (Glycine max), 3'ss of exon 10
gtaagtttgtatcccaccttctactttgaaa-tgtgtatacgacacagttttttgccctgtgtctgacattacttgcttttccctctctgatatatagTCCAGGCATTCAATTCTGTGGGTGACCGATTTTCCAATGTTTGAGTGGAACAGTGCAGAGCAGAGGCTTGAG
||||||| ||        || ||     ||| |||   |    | ||  | |||   || | ||| | |||| ||| || |   ||| |||  | |||  ||||||||||||| ||||| | || |||||||| ||||||||||||||   | |||||||||||||||||
gtaagttggtgattggttttgtagagaaaaaatgttcctctttctcaactattt---ctttttctaatattatttggttattt-tctttgagttttagGGCAGGCATTCAATTTTGTGGATAACTGATTTTCCGATGTTTGAGTGGAATGATCCAGAGCAGAGGCTTGAG

upper sequence: Vv03s0088g00500.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT4G33760.1 (Arabidopsis thaliana), 3'ss of exon 10
gtaagtttgtatcccaccttctactttgaaatgtgtatacgacacagttttttgccctgtgtctgacattacttgcttttccctctctgatatatagTCCAGGCATTCAATTCTGTGGGTGACCGATTTTCCAATGTTTGAGTGGAACAGTGCAGAGCAGAGGCTTGAG
||||||||   | |||    | |      ||    | |  |   || ||  |  |     | || | |||   |||  || | ||| |  |||| |||||| ||| ||||||||||||||||| ||||| |||||||| ||||||||     |||||||||||||||||
gtaagttt---ttccattggcca------aacacttttttgttccacttgatgaca----gactcagatt-tatgccatttcttctatattatacagTCCAAGCACTCAATTCTGTGGGTGACAGATTTCCCAATGTTCGAGTGGAATGAGCCAGAGCAGAGGCTTGAG

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|351048178|gb|FQ442148.1|FQ442148
EST:     TAGACAGACTTAGGGTATTTATAGCCCACGAACTGGGTTTGGTTGATCAT                         TCCAGGCATTCAATTCTGTGGGTGACCGATTTTCCGATGTTTGAGTGGAAC
genomic: TAGACAGACTTAGGGTATTTATAGCCCACGAACTGGGTTTGGTTGATCATgtaagtttgt ... tgatatatagTCCAGGCATTCAATTCTGTGGGTGACCGATTTTCCAATGTTTGAGTGGAAC
EST: gi|352786206|gb|FQ478817.1|FQ478817
EST:     TAGACAGACTTAGGGTATTTATAGCCCACGAACTGGGTTTGGTTGATCAT                         TCCAGGCATTCAATTCTGTGGGTGACCGATTTTCCGATGTTTGAGTGGAAC
genomic: TAGACAGACTTAGGGTATTTATAGCCCACGAACTGGGTTTGGTTGATCATgtaagtttgt ... tgatatatagTCCAGGCATTCAATTCTGTGGGTGACCGATTTTCCAATGTTTGAGTGGAAC
EST: gi|351046227|gb|FQ442605.1|FQ442605
EST:     TAGACAGACTTAGGGTATTTATAGCCCACGAACTGGGTTTGGTTGATCAT                         TCCAGGCATTCAATTCTGTGGGTGACCGATTTTCCGATGTTTGAGTGGAAC
genomic: TAGACAGACTTAGGGTATTTATAGCCCACGAACTGGGTTTGGTTGATCATgtaagtttgt ... tgatatatagTCCAGGCATTCAATTCTGTGGGTGACCGATTTTCCAATGTTTGAGTGGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacagttttttgccctgtgtctgacattacttgcttttccctctctgatatatagTCCAGGCATTCAATTCTGTGGGTGACCGATTTTCCAATGTTTGAGTGGAACAGTGCAGAGCAGAGGCTTGAG
                        cattacttgcttttcc  CT-rich tract
                                             tgatatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttgtatcccaccttctactttgaaatgtgtatacgacacagttttttgccctgtgtctgacattacttgcttttccctctctgatatatagTCCAGGCATTCAATTCTGTGGGTGACCGATTTTCCAATGTTTGAGTGGAACAGTGCAGAGCAGAGGCTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG