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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggctaaattataaagaatgcctaaacaatgtaggagtcacatgtgctttgcacttctggcagttttgttgccttcatgtgttcacgttgttcttgtgtagGTTATAGTCTCTGCGAGGAAGCCAGAGTTCTTCCAAATGTCACACCCATTGTATGAGGTGGTGACAGATGAGGGTCTAATGCGTCCATGCTTCAAGGCTT

Basic information

species Vitis vinifera
transcript Vv05s0020g00880.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g00880.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os01g14810.3 (Oryza sativa), 3'ss of exon 10
------ggctaaattataaagaat-gcctaaacaatgtaggagtcacatgtgctttgcacttctggcagttttgttgccttcatgtgttcacgttgttcttg-tgtagGTTATAGTCTCTGCGAGGAAGCCAGAGTTCTTCCAAATGTCACACCCATTGTATGAGGTGGTGACAGATGAGGGTCTAATGCGTCCATGCTTCAAGGCTT
|| || | | | ||| | | | || | ||| | ||| | ||| | ||| || | || ||||| ||||||||||||||||||| |||||||||||||| |||||||| || || || || || ||||| || ||| |||| || |||||||||| || || || |||
gtgagtaatcaagttgctggttctagattgaactgtttgtcattcgttgcttgcctgccatgctgaaaactttactaagatcacttgat----ttattcttactgtagGTTATAGTCTCTGCAAGGAAGCCAGAGTTTTTCCAAATCTCTCATCCGTTATACGAGGTTGTAACAAATGATGGATTAATGCGTCCCTGTTTTAAAGCTA

upper sequence: Vv05s0020g00880.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G044819_T02 (Zea mays), 3'ss of exon 9
ggctaaattataaagaatgcctaa--acaatgtaggagtcacatgtgctttgcacttctggca------gttttgttgccttcat--gtgttcac--gttgttcttg-tgtagGTTATAGTCTCTGCGAGGAAGCCAGAGTTCTTCCAAATGTCACACCCATTGTATGAGGTGGTGACAGATGAGGGTCTAATGCGTCCATGCTTCAAGGCTT
||| || | | | ||| | || | | | || | || || ||| | | || || |||||| | | || || || || | ||||||||||||||||| ||||||||||| || ||||| | ||||| |||||||||||||| || |||||||| || || |||||||| || || || |
--gtaagtttttatctctcccttataccagttttgtagaagtgtctgtttggcagtcattgcttacaacacactggaaacttcattaatatccattaattctttttactatagGTTATAGTCTCTGCAAGGAAGCCAGAATTTTTCCAGCTTTCACATCCATTGTATGAGGTTGTAACAGATGATGGACTGATGCGTCCCTGTTTTAAAGTAA

upper sequence: Vv05s0020g00880.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA15G21240.1 (Glycine max), 3'ss of exon 9
-------------------ggctaaattataaag--aatgcctaaacaatgtaggagtca----catgtgctttgcacttctggcagttttgttgcc-------ttcatgtgttcacgttgttcttgt------gtagGTTATAGTCTCTGCGAGGAAGCCAGAGTTCTTCCAAATGTCACACCCATTGTATGAGGTGGTGACAGATGAGGGTCTAATGCGTCCATGCTTCAAGGCTT
|| | ||| ||| | || | | || |||| | | | |||| | ||| |||||| | || || | || | ||| || |||||| || ||||| || | || ||||| |||||||||||||||||||| ||||||||||||||||||| ||||| || |||||||||||||| ||||||
gtaagttcttgtagataatcaatacaatatgaagttatcctcttgatagtggaggaatgaaaaatacatgctattattctctttactttttgtgaaataagcaatgcacaaattgatgtggctctcgttcatgagtagGTAATTGTCTCGGCAAACAAACCAGAATTCTTCCAAATGTCACACCCCATGTATGAGGTGGTGACAGAAGAGGGCCTGATGCGTCCATGCTTTAAGGCTC

upper sequence: Vv05s0020g00880.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA13G17950.1 (Glycine max), 3'ss of exon 10
----------------------------------------------------------------------ggctaaattataaagaatgcctaaacaatgtaggagtcacatgtgctttgcacttctggcagttttg---ttgccttc----atgtgttcacg---ttgttcttgtgtagGTTATAGTCTCTGCGAGGAAGCCAGAGTTCTTCCAAATGTCACACCCATTGTATGAGGTGGTGACAGATGAGGGTCTAATGCGTCCATGCTTCAAGGCTT
|| ||| | | | | | || || | | | | | || | || || | ||| | || || | |||||| || ||||| |||||||| || || || |||||||||||||||| |||||| || ||||||| ||||| |||| ||||| || ||||||||||||||||| |||
gtaagttcatgtaaattatttcttccatatttttattcttgaagaaaattaatgagacattctcgacattggaggaataaaatacactatctccacgtcattatttttccctaaattaacaaccttatcttattatgaaataaactttggataaatggacatggttttgttcatggatagGTAATAGTCTCAGCAAGAAAACCAGAGTTCTTCCAAACGTCACATCCCATGTATGAAGTGGTCACAGGCGAGGGCCTTATGCGTCCATGCTTCAAAGCTC

upper sequence: Vv05s0020g00880.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA17G04580.1 (Glycine max), 3'ss of exon 10
----------------------------------------------------------------------ggctaaattataaagaatgcctaaacaatgtag---------gagtcacatgtgctttgcacttctggcagttttgttgccttcatgtgttcacgttgttcttgtgtagGTTATAGTCTCTGCGAGGAAGCCAGAGTTCTTCCAAATGTCACACCCATTGTATGAGGTGGTGACAGATGAGGGTCTAATGCGTCCATGCTTCAAGGCTT
|| ||| | | | | | ||| || | | | | | || || | | |||| | ||| | || ||| || ||||| |||||||| || || || |||||||||||||||| ||||| || ||||||| ||||| |||| ||||| || |||||||||||||||| |||
gtaagttcatgtaaattatttcttccatatttttattcttgaggaaaattactgaaacattctcgacattggaggaatgaaatacactatctacacgtcattattttgccctaaattgacaaccttatcttattatgaaataaattttgcataaatggatatggttttttcatggatagGTAATAGTCTCAGCAAGAAAACCAGAGTTCTTCCAAACATCACATCCCATGTATGAAGTGGTCACAGGCGAGGGCCTTCTGCGTCCATGCTTCAAAGCTC

upper sequence: Vv05s0020g00880.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT5G48960.1 (Arabidopsis thaliana), 3'ss of exon 10
--ggctaaattataaagaatgcctaaacaatg--taggagtcacatgtgctttgcacttctggcagttttgttgccttcatgtgttcacgt---tgttcttgtgtagGTTATAGTCTCTGCGAGGAAGCCAGAGTTCTTCCAAATGTCACACCCATTGTATGAGGTGGTGACAGATGAGGGTCTAATGCGTCCATGCTTCAAGGCTT
| ||| || | || | || | | || ||| || | | | || | || ||| || | |||| ||||| ||||| ||||||||||| |||||||||||||| ||||| ||||| | |||||||| ||||| | |||||| | |||||||||||||||||||||
gtgagcaaacgtaaatttgtttctgcattttgattgtaaatctgttgtttttcagagagtagtttgcattag-actttactgtttttgaattcatgtttccacatagGTGATAGTTTCTGCGAGGAAACCAGAGTTCTTCCAGATGTCGCACCCTCTATATGAGGTTGTGACTGGAGAGGGTTTGATGCGTCCATGCTTCAAGGCTG

upper sequence: Vv05s0020g00880.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: EFJ30141 (Selaginella moellendorffii), 3'ss of exon 9
ggctaaattataaagaatgcctaaacaatgtaggagtcacatgtgctttgcacttctggcagttttgttgccttcatgtgttcacgttgttcttgtgtagGTTATAGTCTCTGCGAGGAAGCCAGAGTTCTTCCAAATGTCACACCCATTGTATGAGGTGGTGACAGATGAGGGTCTAATGCGTCCATGCTTCAAGGCTT
|| | || | | | ||| || | || | | | ||| | |||| || || || ||||| ||||||||||| |||||||||||||| || ||||| ||| | || || | || || | ||||||||||| ||||| ||
------------------------------------------gtaacatacaat----gtaccttttttattctgat-ttctgtccttgggagcttacagGTGATTGTGTCAGCGAGAAAGCCAGAGTTTTTCCAAATGTCACATCCCTTGTACGAGATCGTTACCAAGGATGGCTTGATGCGTCCATGTTTCAAAGCAA

upper sequence: Vv05s0020g00880.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: EFJ08324 (Selaginella moellendorffii), 3'ss of exon 9
ggctaaattataaagaatgcctaaacaatgtaggagtcacatgtgctttgcacttctggcagttttgttgccttcatgtgttcacgttgttcttgtgtagGTTATAGTCTCTGCGAGGAAGCCAGAGTTCTTCCAAATGTCACACCCATTGTATGAGGTGGTGACAGATGAGGGTCTAATGCGTCCATGCTTCAAGGCTT
|| | || | | | ||| || | || | | | ||| | |||| || || || ||||| ||||||||||| |||||||||||||| || ||||| ||| | || || | || || | ||||||||||| ||||| ||
------------------------------------------gtaacatacaat----gtaccttttttattctgat-ttctgtccttggaagcttacagGTGATTGTGTCCGCGAGAAAGCCAGAGTTTTTCCAAATGTCACATCCCTTGTACGAGATCGTTACCAAGGATGGCTTGATGCGTCCATGTTTCAAAGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttgcacttctggcagttttgttgccttcatgtgttcacgttgttcttgtgtagGTTATAGTCTCTGCGAGGAAGCCAGAGTTCTTCCAAATGTCACACCCATTGTATGAGGTGGTGACAGATGAGGGTCTAATGCGTCCATGCTTCAAGGCTT
                                         ttgttctt  CT-rich tract
 ttttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggctaaattataaagaatgcctaaacaatgtaggagtcacatgtgctttgcacttctggcagttttgttgccttcatgtgttcacgttgttcttgtgtagGTTATAGTCTCTGCGAGGAAGCCAGAGTTCTTCCAAATGTCACACCCATTGTATGAGGTGGTGACAGATGAGGGTCTAATGCGTCCATGCTTCAAGGCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - gaatgcc
- - - - - - - - - - - aaacaat
- - - - - - - - - - - - - - - - - - tcacatg
- - - - - - - - - - - - - - - - - - - - - -tgctttg
- - - - - - - - - - - - - - - - - - - - - - - - - - -ttctggc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgttc