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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttggatctcatgtatctcatcactcttctatttactgtttgtaggatactgaatgacattggattggtatcgtttgaaatgcagGGAATGGGATTTTTAGCTGGCTTACTGCTTCTTTATATGAGTGAAGAAGATGCATTCTGGTTGATGGTTGCATTACTTAAAGGAGCTGTTCATGCTCCAA

Basic information

species Vitis vinifera
transcript Vv14s0083g00540.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0083g00540.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os08g31840.2 (Oryza sativa), 3'ss of exon 4
gtttggatctcatgtatctcatcactcttctatttactgtttgtaggatactgaatgacattggattggtatcgtttga----aatgcagGGAATGGGATTTTTAGCTGGCTTACTGCTTCTTTATATGAGTGAAGAAGATGCATTCTGGTTGATGGTTGCATTACTTAAAGGAGCTGTTCATGCTCCAA
|||||  |   |  |  || |  | | ||    |      || |    |  ||| | | ||  | |   | | |  | |     ||||||||||||||||||||||||||||| || ||||||||||||||||||||||||||||| |||||  | ||||| || || || |||||||||||||| ||||
gtttgtgttaaaactg-ctgactagttttaggatataaacttattc--tgttgagtaatatgtgttctcttttgcataatcatgatgcagGGAATGGGATTTTTAGCTGGCTTGCTACTTCTTTATATGAGTGAAGAAGATGCATTTTGGTTATTAGTTGCTTTGCTGAAGGGAGCTGTTCATGCGCCAA

upper sequence: Vv14s0083g00540.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G047223_T02 (Zea mays), 3'ss of exon 4
gtttggatctcatgtatctcatcactcttctatttactgtttgtaggatact----gaatgacattggattg---gtatcgtttgaaatgcagGGAATGGGATTTTTAGCTGGCTTACTGCTTCTTTATATGAGTGAAGAAGATGCATTCTGGTTGATGGTTGCATTACTTAAAGGAGCTGTTCATGCTCCAA
|||||    |  ||  |    | ||   | | || |  | | | | |||       |||| | |||  ||||     |   ||     |||||||||||||||||||||||||  | |||||||||||||||||||| || ||||||||||||||  | || || || || || |||||||| ||||| ||||
gtttg----ttttgagttcggtgacctattttttca--gatagaaagatctctctggaataatattctattgtttacacaattcattttgcagGGAATGGGATTTTTAGCTGGGCTGCTGCTTCTTTATATGAGTGAGGAGGATGCATTCTGGTTATTAGTCGCGTTGCTAAAGGGAGCTGTCCATGCACCAA

upper sequence: Vv14s0083g00540.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA19G05360.1 (Glycine max), 3'ss of exon 4
gtttggatctcatgtatctcatcactcttctatttactgtttgtaggatactgaatgacattggattggtatcgtttgaaatgcagGGAATGGGATTTTTAGCTGGCTTACTGCTTCTTTATATGAGTGAAGAAGATGCATTCTGGTTGATGGTTGCATTACTTAAAGGAGCTGTTCATGCTCCAA
||||    |||| | | | ||||||  | || |   ||  ||  |   || |  || | ||||       ||  ||  || | ||||| |||||||||||||| ||  |  ||||||||||||||||||| || |||||||| |||||| |||| ||||| || |||||||| |||||||||||||
gtttta--ctcagg-accccatcaccttgctgt--gcttgttacaaagtatttcataatattgacc----att-ttaaaactccagGGCATGGGATTTTTAGCGGGGCTTTTGCTTCTTTATATGAGTGAGGAGGATGCATTTTGGTTGTTGGTGGCATTGCTAAAAGGAGCCGTTCATGCTCCAA

upper sequence: Vv14s0083g00540.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA13G07090.1 (Glycine max), 3'ss of exon 3
gtttggatctcatgtatctcatcactcttctatttactgtttgtaggatactgaatgacattggattggtatcgtttgaaatgcagGGAATGGGATTTTTAGCTGGCTTACTGCTTCTTTATATGAGTGAAGAAGATGCATTCTGGTTGATGGTTGCATTACTTAAAGGAGCTGTTCATGCTCCAA
||||    |||| | | | ||||||  |||| |   ||  ||  |   || |  || | |||| ||   |    ||  || | ||||| ||||| |||||||| ||  |  |||||||||||||||| || || |||||||| |||||| |||| ||||| || |||||||| |||||||||||||
gtttta--ctcaggaacc-catcacctttctgt--gcttgttacaaagtatttcataatattg-atcatt----ttaaaactacagGGGATGGGGTTTTTAGCGGGACTTTTGCTTCTTTATATGAGCGAGGAGGATGCATTTTGGTTGTTGGTGGCATTGCTAAAAGGAGCCGTTCATGCTCCAA

upper sequence: Vv14s0083g00540.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G02460.1 (Arabidopsis thaliana), 3'ss of exon 4
gtttggatctcatgtatctcatcactcttctatttactgtttgtaggatactgaatgacattggattggtatcgtttgaaatgcagGGAATGGGATTTTTAGCTGGCTTACTGCTTCTTTATATGAGTGAAGAAGATGCATTCTGGTTGATGGTTGCATTACTTAAAGGAGCTGTTCATGCTCCAA
|| |       |  ||| ||     | | | ||||    ||  |    ||  | |  |   |  ||   | |  | |    ||||||| ||||| ||| |||| || ||  ||||||| |||||||| ||||||||||| ||||||||  | ||||||||||||||||||||||||||||||||||
gtctatcctctagatatttcccttgtttcccatttttctttcttttagtatgggactaagattcatgattctaatatc---tgcagGGGATGGGGTTTATAGCCGGTTTGTTGCTTCTCTATATGAGCGAAGAAGATGCCTTCTGGTTATTAGTTGCATTACTTAAAGGAGCTGTTCATGCTCCAA

upper sequence: Vv14s0083g00540.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G15930.1 (Arabidopsis thaliana), 3'ss of exon 4
gtttggatctc-atgtatctcatcactcttctatttactgtttgtaggatactgaatgacattggat--tggtatcgtttgaaatgcagGGAATGGGATTTTTAGCTGGCTTACTGCTTCTTTATATGAGTGAAGAAGATGCATTCTGGTTGATGGTTGCATTACTTAAAGGAGCTGTTCATGCTCCAA
    | || || |   ||||  ||  |  |   | |         | | |||| | |   |  |  |  |||||        ||||||||||||||| ||  |||| || ||  |||||||||||||||| ||||||||||||||||||||  | ||||||||||| ||||||||||| ||  | ||||
----gtatttccagagatcttttcctttattcttatttgcccaagatggtactaattacgaaagactcatggtactaaaaataatgcagGGAATGGGTTTCATAGCCGGTTTGTTGCTTCTTTATATGAGCGAAGAAGATGCATTCTGGTTATTAGTTGCATTACTCAAAGGAGCTGTCCACTCCCCAA

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|161719620|gb|FC067048.1|FC067048
EST:     ATGTTTTGAAGGCATACTCTGTGTATGACAGAGATGTTGGATATGTTCAG                         GGAATGGGATTTTTAGCTGGCTTACTGCTTCTTTATATGAGTGAAGAAGAT
genomic: ATGTTTTGAAGGCATACTCTGTGTATGACAGAGATGTTGGATATGTTCAGgtttggatct ... tgaaatgcagGGAATGGGATTTTTAGCTGGCTTACTGCTTCTTTATATGAGTGAAGAAGAT
EST: gi|349829177|gb|FQ419687.1|FQ419687
EST:     ATGTTTTGAAGGCATACTCTGCGTATGACAGAGATGTTGGATATGTTCAG                         GGAATGGGATTTTTAGCTGGCTTACTGCTTCTTTATATGAGTGAAGAAGAT
genomic: ATGTTTTGAAGGCATACTCTGTGTATGACAGAGATGTTGGATATGTTCAGgtttggatct ... tgaaatgcagGGAATGGGATTTTTAGCTGGCTTACTGCTTCTTTATATGAGTGAAGAAGAT
EST: gi|351012823|gb|FQ430386.1|FQ430386
EST:     ATGTTTTGAAGGCATACTCTGTGTATGACAGAGATGTTGGATATGTTCAG                         GGAATGGGATTTTTAGCTGGCTTACTGCTTCTTTATATGAGTGAAGAAGAT
genomic: ATGTTTTGAAGGCATACTCTGTGTATGACAGAGATGTTGGATATGTTCAGgtttggatct ... tgaaatgcagGGAATGGGATTTTTAGCTGGCTTACTGCTTCTTTATATGAGTGAAGAAGAT
EST: gi|349827061|gb|FQ421334.1|FQ421334
EST:     ATGTTTTGAAGGCATACTCTGTGTATGACAGAGATGTTGGATATGTTCAG                         GGAATGGGATTTTTAGCTGGCTTACTGCTTCTTTATATGAGTGAAGAAGAT
genomic: ATGTTTTGAAGGCATACTCTGTGTATGACAGAGATGTTGGATATGTTCAGgtttggatct ... tgaaatgcagGGAATGGGATTTTTAGCTGGCTTACTGCTTCTTTATATGAGTGAAGAAGAT
EST: gi|349829128|gb|FQ419660.1|FQ419660
EST:     ATGTTTTGAAGGCATACTCTGCGTATGACAGAGATGTTGGATATGTTCAG                         GGAATGGGATTTTTAGCTGGCTTACTGCTTCTTTATATGAGTGAAGAAGAT
genomic: ATGTTTTGAAGGCATACTCTGTGTATGACAGAGATGTTGGATATGTTCAGgtttggatct ... tgaaatgcagGGAATGGGATTTTTAGCTGGCTTACTGCTTCTTTATATGAGTGAAGAAGAT
EST: gi|351038918|gb|FQ457593.1|FQ457593
EST:     ATGTTTTGAAGGCATACTCTGTGTATGACAGAGATGTTGGATATGTTCAG                         GGAATGGGATTTTTAGCTGGCTTACTGCTTCTTTATATGAGTGAAGAAGAT
genomic: ATGTTTTGAAGGCATACTCTGTGTATGACAGAGATGTTGGATATGTTCAGgtttggatct ... tgaaatgcagGGAATGGGATTTTTAGCTGGCTTACTGCTTCTTTATATGAGTGAAGAAGAT
EST: gi|110417184|gb|EC983219.1|EC983219
EST:     ATGTTTTGAAGGCATACTCTGTGTATGACAGAGATGTTGGATATGTTCAG                         GGAATGGGATTTTTAGCTGGCTTACTGCTTCTTTATATGAGTGAAGAAGAT
genomic: ATGTTTTGAAGGCATACTCTGTGTATGACAGAGATGTTGGATATGTTCAGgtttggatct ... tgaaatgcagGGAATGGGATTTTTAGCTGGCTTACTGCTTCTTTATATGAGTGAAGAAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttactgtttgtaggatactgaatgacattggattggtatcgtttgaaatgcagGGAATGGGATTTTTAGCTGGCTTACTGCTTCTTTATATGAGTGAAGAAGATGCATTCTGGTTGATGGTTGCATTACTTAAAGGAGCTGTTCATGCTCCAA
                                           tttgaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttggatctcatgtatctcatcactcttctatttactgtttgtaggatactgaatgacattggattggtatcgtttgaaatgcagGGAATGGGATTTTTAGCTGGCTTACTGCTTCTTTATATGAGTGAAGAAGATGCATTCTGGTTGATGGTTGCATTACTTAAAGGAGCTGTTCATGCTCCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT