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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGCTAGGAAAAGCTCTTGGGATACCAGAAAACAGTGTGAGGACATATACTGAAGCTGAAATTCGTGCTGGgtatggtaacactttctctttcttaattcctttaaaaatgttgtatttaatgccttatgccgcttagtcaatacagttatattggtagttataaaaccggtattgccatctaactctgcaagggcaaatgttgtttgtag

Basic information

species Vitis vinifera
transcript Vv05s0062g00890.t01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0062g00890.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: LOC_Os12g20150.1 (Oryza sativa), 5'ss of exon 12
ATGCTAGGAAAAGCTCTTGGGATACCAGAAAACAGTGTGAGGACATATACTGAAGCTGAAATTCGTGCTGGgtatggtaacactttctctttcttaattcctttaaaaatgttgtatt-taatgccttatgccgcttagtcaatacagttatattggtagttataaaaccggtattgccatctaactctgcaagggcaaatgttgtttgtag
 |  | || ||||| ||||| |||||||| ||||||||||| || || || || || |||||||||||||||||     |  ||||    | |  | |    |  ||| ||| || || |   ||  ||  |    || | | |       ||    |   ||||   |  |                                        
GTTATTGGGAAAGCCCTTGGAATACCAGATAACAGTGTGAGAACTTACACAGAGGCAGAAATTCGTGCTGGgta-----atccttttctgtacagagtc---tggaaattgtggttttctggagctgtaatcaatctaattattctgaacctaactttttatatatgtctag----------------------------------------

upper sequence: Vv05s0062g00890.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GRMZM2G040968_T03 (Zea mays), 5'ss of exon 6
ATGCTAGGAAAAGCTCTTGGGATACCAGAAAACAGTGTGAGGACATATACTGAAGCTGAAATTCGTGCTGGgtatggtaacactttctctttcttaattcctttaaaaatgttgtatttaatgccttatgccgcttagtcaatacagttatattggtagttataaaaccggt--attgccatctaactctgcaa----gggcaaatgttgtttgtag-
 | || || ||||| ||||| ||||| || |||||||| || ||||| ||||| ||||||||||||||| ||||     |   ||||| |     ||      ||| |    ||  | |  | |   |    | || | | |||| | |||   | |    || || | | |  ||    |||||||| |  |     |    | |||| ||| |   
GTTCTTGGGAAAGCCCTTGGAATACCCGAGAACAGTGTCAGAACATACACTGAGGCTGAAATTCGTGCTAGgta-----atgttttctttggagcaaca----taagagcactgagtgt--tcctgcacattgtttggacgatactgatattaagattaacatcaatctgattcatgtgaatctaactatttagatttgttttagtgttatttttcag

upper sequence: Vv05s0062g00890.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GRMZM2G040968_T01 (Zea mays), 5'ss of exon 6
ATGCTAGGAAAAGCTCTTGGGATACCAGAAAACAGTGTGAGGACATATACTGAAGCTGAAATTCGTGCTGGgtatggtaacactttctctttcttaattcctttaaaaatgttgtatttaatgccttatgccgcttagtcaatacagttatattggtagttataaaaccggtattgccatctaactctgcaagggcaaatgttgtttgtag
 | || || ||||| ||||| ||||| || |||||||| || ||||| ||||| ||||||||||||||| ||||     |   ||||| |     ||      ||| |    ||  | |  | |   |    | || | | |||| | |||   | |    || || | | |     ||| | | |||        | || |||||| |||
GTTCTTGGGAAAGCCCTTGGAATACCCGAGAACAGTGTCAGAACATACACTGAGGCTGAAATTCGTGCTAGgta-----atgttttctttggagcaaca----taagagcactgagtgt--tcctgcacattgtttggacgatactgatattaagattaacatcaatctgat----tcatgtgaatctaactatttagat-ttgttt-tag

upper sequence: Vv05s0062g00890.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA10G44540.1 (Glycine max), 5'ss of exon 11
ATGCTAGGAAAAGCTCTTGGGATACCAGAAAACAGTGTGAGGACATATACTGAAGCTGAAATTCGTGCTGGgtatggtaacactttctctttcttaattcctttaaaaatgttgtatttaatgccttatgccgcttagtcaatacagttatattggtagttataaaaccggtattgccatctaactctgcaagggcaaatgttgtttgtag
|| |||||||||||||| || ||||| ||||||||||| ||||||||||| |||||||| ||||| |||||||||| |||  || | || ||| || ||   ||     |  ||||  | || |||| |||   ||||| || | | || | |    | |||||    |   | ||   |                               
ATACTAGGAAAAGCTCTAGGAATACCTGAAAACAGTGTCAGGACATATACAGAAGCTGAGATTCGAGCTGGgtatgataatgctctatccttcatacttttctt-----ttgtgtacattat-ccttttgcaatttagt-aagataattttttcaagaattatat--tctaaagtgtttt-------------------------------

upper sequence: Vv05s0062g00890.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: AT5G26570.1 (Arabidopsis thaliana), 5'ss of exon 12
ATGCTAGGAAAAGCTCTTGGGATACCAGAAAACAGTGTGAGGACATATACTGAAGCTGAAATTCGTGCTGGgtatggtaa-----cactttctctttcttaattc---ctttaaaaatgttgt-atttaatgccttatgccgcttagtcaatacagtt----atattggtagttataaaaccggtattgccatctaactctgcaagggcaaatgttgtttgtag---
||  ||||||||||||| || || ||||| || ||||| | ||| ||||| ||||| || |||||||||||||| | ||       |||| ||  | ||||  |    |  || ||    | | ||| |||   ||  |    || |   || |  ||    ||  |  || | || |  |   |  ||  || |       | |     || ||| | | |     
ATTTTAGGAAAAGCTCTAGGAATTCCAGAGAATAGTGTCAAGACCTATACAGAAGCAGAGATTCGTGCTGGgtaagttaggcctttacttcctagtacttagcttaaaccatacaagcaatctgattgaatcatttgggaatatttgctgattcttttcttgattattttactcatcatcctctttctgtaattttctctaaccatacttaaggttctgtcttacag

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|29785216|gb|CB342018.2|CB342018
EST:     ATACCAGAAAACAGTGTGAGGACATATACTGAAGCTGAAATTCGTGCTGG                         TGTAATTTTTCAGGTCTCAAAACTTTGTACGCTTCTTTTAAAAGCTGTTAG
genomic: ATACCAGAAAACAGTGTGAGGACATATACTGAAGCTGAAATTCGTGCTGGgtatggtaac ... ttgtttgtagTGTAATTTTTCAGGTCTCAAAACTTTGTACGCTTCTTTTAAAAGCTGTTAG
EST: gi|27578836|gb|CB001531.1|CB001531
EST:     ATACCAGAAAACAGTGTGAGGACATATACTGAAGCTGAAATTCGTGCTGG                         TGTAATTTTTCAGGTCTCAAAACTTTGTACGCTTCTTTTAAAAGCTGTTAG
genomic: ATACCAGAAAACAGTGTGAGGACATATACTGAAGCTGAAATTCGTGCTGGgtatggtaac ... ttgtttgtagTGTAATTTTTCAGGTCTCAAAACTTTGTACGCTTCTTTTAAAAGCTGTTAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGCTAGGAAAAGCTCTTGGGATACCAGAAAACAGTGTGAGGACATATACTGAAGCTGAAATTCGTGCTGGgtatggtaacactttctctttcttaattcctttaaaaatgttgtatttaatgccttatgccgcttagtcaatacagttatattggtagttataaaaccggtattgccatctaactctgcaagggcaaatgttgtttgtag

- - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA