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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacctagtcccagctttcttactgactaataaaattgtgtatccgaattaggattagtgttattaaaagtaatcatattatgacttcattcttcttattgtgtttttatcagGTAGCTTTGAAATTCGAGCACAGAAACAGCAAAGGCTGCAACTATGGCCCTCCATATGAGTGGCAGGTGTACAA

Basic information

species Vitis vinifera
transcript Vv06s0004g01090.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g01090.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA08G47680.2 (Glycine max), 3'ss of exon 2
gtaacctagtcccagctttcttactgactaataaaattgtgtatccgaattaggattagtgttattaaaagtaatcatattatgacttcattcttcttattgtgtttttatcagGTAGCTTTGAAATTCGAGCACAGAAACAGCAAAGGCTGCAACTATGGCCCTCCATATGAGTGGCAGGTGTACAA
                               |||||   | | |    |      | | ||||   | || |    |    ||    | ||||||    | ||||||    ||||| ||||||||||| |||||||| |||||||||||||| |||||||||||||| || |||||||| ||||||||
------------------------------gtaaaagcttctcttgttacc----tcactgtttgaacaattttctacggcattgactgattctt----tcgtgttt----cagGTGGCTTTGAAATTTGAGCACAGGAACAGCAAAGGCTGTAACTATGGCCCTCCTTACGAGTGGCAAGTGTACAA

upper sequence: Vv06s0004g01090.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA18G53810.1 (Glycine max), 3'ss of exon 2
gtaacctagtcccagctttcttactgactaataaaattgtgtatccgaattaggattagtgttattaaaagtaatcatattatgacttcattcttcttattgtgtttttatcagGTAGCTTTGAAATTCGAGCACAGAAACAGCAAAGGCTGCAACTATGGCCCTCCATATGAGTGGCAGGTGTACAA-
                            ||| ||  || |       | | |   || |    |||     |     ||   ||| |  ||  |||||||  | | | | |||||| || |||||||| ||||| || |||||||||||||| || ||||||||||| || |||||||| || ||||| 
----------------------------taa-aagcttctcctgttaactcactgtttgaacaattttctatggatttaagttgattgaatgtttcttatcttttgtgtttcaggTGGCATTGAAATTTGAGCATAGGAACAGCAAAGGCTGTAATTATGGCCCTCCTTACGAGTGGCAAGTATACAAG

upper sequence: Vv06s0004g01090.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G44050.1 (Glycine max), 3'ss of exon 2
gtaacctagtcccagctttcttactgactaataaaattgtgtatccgaattaggattagtgttattaaaagtaatcatattatgacttcattcttcttattgtgtttttatcagGTAGCTTTGAAATTCGAGCACAGAAACAGCAAAGGCTGCAACTATGGCCCTCCATATGAGTGGCAGGTGTACAA
|||   |  || |   |||| |   | ||       |||||| |   ||||  | ||| |  | ||   | | ||     | | | || |||  |   ||   |  ||| |||||| ||| ||||||| || || |||||||| || ||||| |||||||||||||| || |||||||| || |||||
gtaggtt--tctctaatttcatctgggct-------ttgtgtgtt-aaatt--gtttaatacttttgtcattgatttggctttaagtttatttct---atctcgcatttctcagGTGGCTCTGAAATTTGAACATAGAAACAGTAAGGGCTGTAACTATGGCCCTCCTTACGAGTGGCAAGTATACAA

upper sequence: Vv06s0004g01090.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA20G38770.1 (Glycine max), 3'ss of exon 2
gtaacctagtcccagctttcttactgactaataaaattgtgtatccgaattaggattagtgttattaaaagtaatcatattatgacttcattcttcttattgtgtttttatcagGTAGCTTTGAAATTCGAGCACAGAAACAGCAAAGGCTGCAACTATGGCCCTCCATATGAGTGGCAGGTGTACAA
             || || ||        |   |   | ||| | | || | |  ||  |  | || | | | ||     | | | || |||  |   ||   |  ||| |||||| ||| ||||||| || || || ||||| || ||||| |||||||||||||| || |||||||| || |||||
-----------gtaggttcctctaatttcatccaggctttgtgtgctaaattgt-ttgatacttttgacattgatttggctttaagttgatttct---atctggcatttctcagGTGGCTCTGAAATTTGAACATAGGAACAGTAAGGGCTGTAACTATGGCCCTCCTTACGAGTGGCAAGTATACAA

upper sequence: Vv06s0004g01090.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT3G13670.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaacctagtcccagcttt-cttactgactaataaaattgtgtatccgaattaggattagtgttattaaaagtaatcatattatgacttcattcttcttattgtgtttttatcagGTAGCTTTGAAATTCGAGCACAGAAACAGCAAAGGCTGCAACTATGGCCCTCCATATGAGTGGCAGGTGTACAA
||||  ||   |   ||    ||||||      |  |||||  | |  || ||  |||  | |||    |  ||  | ||   || ||    |||||   ||    || ||| |||| ||| | || || ||||| || | |||||| || ||||||||||| |||||| ||||||||||||| |||||
gtaatataactcagtctgcgtttactgctgtggaggattgt-caccataaatatcattc-tattagcttagttatgcttacagtgtctcacatcttcacttt---cttatat-agGTTGCTCTAAAGTTTGAGCATAGGAGCAGCAAGGGTTGCAACTATGGTCCTCCACATGAGTGGCAGGTTTACAA

upper sequence: Vv06s0004g01090.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ38433 (Selaginella moellendorffii), 3'ss of exon 2
gtaacctagtcccagctttcttactgactaataaaattgtgtatccgaattaggattagtgttattaaaagtaatcatattatgacttcattcttcttattgtgtttttatcagGTAGCTTTGAAATTCGAGCACAGAAACAGCAAAGGCTGCAACTATGGCCCTCCATATGAGTGGCAGGTGTACAA
                                    | |  | | ||||    |||| |  | | |   | |     | ||      |||             | | || |||||| |||||||| || || ||||||| ||| ||||| ||||||||||| ||||| ||||||||||| || |||| 
-----------------------------------gtagactgttcgaa----gatttgc-tcagttggattggctctttt-----ctcagcggctgatcaaagatgttgtcagGTTGCTTTGAAGTTTGAACACAGAAGCAGTAAAGGATGCAACTATGGGCCTCCGTATGAGTGGCAAGTTTACAC

upper sequence: Vv06s0004g01090.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 2
gtaacctagtcccagctttcttactgactaataaaattgtgtatccgaattaggattagtgttattaaaagtaatcatattatgacttcattcttcttattgtgtttttatcagGTAGCTTTGAAATTCGAGCACAGAAACAGCAAAGGCTGCAACTATGGCCCTCCATATGAGTGGCAGGTGTACAA
                                        |||  |   |      |  | | | |   | |  || | |     |  |    |  | |    | | || |||||| |||||||| || || ||||||| ||| ||||| ||||||||||| ||||| ||||||||||| || |||| 
----------------------------------------gtagactgttcgaagattttctcagttggattgctcttttctcagcggc----tgatca--aagatgttgtcagGTTGCTTTGAAGTTTGAACACAGAAGCAGTAAAGGATGCAACTATGGGCCTCCGTATGAGTGGCAAGTTTACAC

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|161715152|gb|FC063639.1|FC063639
EST:     GCCGTGTTACAGGTGGAAATGAACGCACAGGTGGTCCTGGTGCTACGGAG                         GTAGCTTTGAAATTCGAGCACAGAAACAGCAAAGGCTGCAACTATGGCCCT
genomic: GCCGTGTTACAGGTGGAAATGAACGCACAAGTGGTCCTAGTGCTACGGAGgtaacctagt ... tttttatcagGTAGCTTTGAAATTCGAGCACAGAAACAGCAAAGGCTGCAACTATGGCCCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttattaaaagtaatcatattatgacttcattcttcttattgtgtttttatcagGTAGCTTTGAAATTCGAGCACAGAAACAGCAAAGGCTGCAACTATGGCCCTCCATATGAGTGGCAGGTGTACAA
                                             tttttatc  CT-rich tract
     ttaaaagtaatcatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacctagtcccagctttcttactgactaataaaattgtgtatccgaattaggattagtgttattaaaagtaatcatattatgacttcattcttcttattgtgtttttatcagGTAGCTTTGAAATTCGAGCACAGAAACAGCAAAGGCTGCAACTATGGCCCTCCATATGAGTGGCAGGTGTACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG