Sequence
atgc intronic sequence ATGC exonic sequence...cgttaagatgaattagtgtgtcattatgacgtgtagcttagcaggtgtattttgtttggcgcattgtgtttttggtaaccatacccctcatgttttgcagTTGACATCATTTCTGCTATTGAGTTTGACAAAACTGGAGACCATCTTGCGACTGGTGATCGTGGGGGACGGGTGGTTTTATTTGAAAGGACAGACAAGAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 1
----cgttaagatgaattagtgtgtcattatgacgtgtagcttagcaggtgtattttgtttggcgcattgtgtttttggtaaccatacccctcatgttttgcagTTGACATCATTTCTGCTATTGAGTTTGACAAAACTGGAGACCATCTTGCGACTGGTGATCGTGGGGGACGGGTGGTTTTATTTGAAAGGACAGACAAGAG
| ||| || | | | | | | ||||| ||| | | | || | || || ||| || ||||| ||||||||||||| ||||| ||||||||||||||| | || ||||||||||| ||||| ||| | || || || || ||||||||||||||||| ||| ||
ttgcccgaaagttgtgtcaaatgacttgagcattgcttttttcacaaggtggttttgatatcatgatatgcatcttaatta--catgtgtttcttgttt--cagTTGACATCATCTCTGCAATTGAGTTTGACAAATCCGGTGACCATCTTGCCACTGGAGATAGAGGTGGTCGTGTAGTTTTATTTGAAAGGACTGACTCCAG
upper sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 1
-------cgttaagatgaattagtgtgtcattatgacgtgtagcttagcaggtgtatt-ttgtttggcgcattgtgtttttggtaaccatacccctcatgttttgcagTTGACATCATTTCTGCTATTGAGTTTGACAAAACTGGAGACCATCTTGCGACTGGTGATCGTGGGGGACGGGTGGTTTTATTTGAAAGGACAGACAAGAG
| ||||||| | | ||| ||| | | || || | ||| ||| | |||||| || | | || | | ||||| ||||||||||||| ||||| ||||||||||| ||| |||| || |||||||| || || || | || ||||| || |||||||||||||||||||| |
tatccatttcttagatgaaggatttcttca--atgctagacaagt--acaaatgcacaattggttgcttctttgtgtgtt-gatctttatgctgttt-tgttt--cagTTGACATCATCTCTGCAATTGAGTTTGATAAATCTGGTGATCATCTTGCCACCGGAGACAGAGGAGGACGTGTTGTTTTATTTGAAAGGACAGATGCTCG
upper sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 2
-cgttaagatgaattagtgtgtcatta-tgacgtgtagcttagcaggtgtattttgtttggcgcattgtgtttttggtaaccatacccctcatgttttgcagTTGACATCATTTCTGCTATTGAGTTTGACAAAACTGGAGACCATCTTGCGACTGGTGATCGTGGGGGACGGGTGGTTTTATTTGAAAGGACAGACAAGAG
| || | | | | || | ||| | | | | ||| | | | || ||| ||| | || | | | || | || | ||| ||||||||||||| ||||| ||||| ||||||||| |||| ||||||||||| ||||| ||| || ||||| ||||||||||||||||||||||| |
ttccacacctgctctgctctttaataagtgaggaatttcacttcgtgtgagtgtagaatgtcgccttgcatgttgattta--acactcttctttgttttcagTTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCACTGGGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCG
upper sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 1
-----cgttaagatgaattagtgtgtcattatgacgtgtagcttagcaggtgtattttgtttggcgcattgtgtttttggtaaccatacccctcatgttttgcagTTGACATCATTTCTGCTATTGAGTTTGACAAAACTGGAGACCATCTTGCGACTGGTGATCGTGGGGGACGGGTGGTTTTATTTGAAAGGACAGACAAGAG
|| | | | || || ||| || |||| | | | | ||| | || | ||| | | | | | || | ||||||| |||| ||||| || ||||| ||||||||||||||| |||| | |||||||| ||||| ||| | || ||||| |||||||| || ||||| |||||||
tttagtgtcttgttcatttcacttgatatt-tgttgtgtcggcttg-atttgttcgccagctaaatcagtttgtatcttg-atcagtatgctacatgttt--cagTGGACATAATATCTGCAATTGAGTTTGACAAATCTGGGAATCATCTTGCTACTGGAGATAGAGGTGGACGTGTGGTTTTGTTCGAAAGAACAGACATTGC
upper sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S425_2V6.1 (Physcomitrella patens), 3'ss of exon 1
cgttaagatgaattagtgtgtcattatgacgtgtagcttagcaggtgtattttgtttggcgcattgtgtttttggtaaccatacccctcatgttt-tgcagTTGACATCATTTCTGCTATTGAGTTTGACAAAACTGGAGACCATCTTGCGACTGGTGATCGTGGGGGACGGGTGGTTTTATTTGAAAGGACAGACAAGAG
| | | | ||| | | || ||| || | || || | | | | | || | | || || |||||||||||| || |||||||||||||| || ||||||||||| || | |||||||| || | || ||||| || || | ||||| || || || ||
-ggaagggatagttaatccgccaacatggatctcgttttcatactcgtgttcgatgatgtgaaattcaaattaattcatttcacattgttggtgaatgcagTTGACATTATCTCTGCTATTGAGTTCGATAAAACTGGAGAACACTTGGCGACTGGCGACAGAGGAGGACGTGTTGTGCTTTTTGAGAGAACCGATGGCAG
upper sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S10_312V6.1 (Physcomitrella patens), 3'ss of exon 1
----cgttaaga---tgaattagtgtgtcattatgacgtgtagcttagcaggtgtattttgtttggcgcattgtgtttttggtaaccatacccctcatgttttgcagTTGACATCATTTCTGCTATTGAGTTTGACAAAACTGGAGACCATCTTGCGACTGGTGATCGTGGGGGACGGGTGGTTTTATTTGAAAGGACAGACAAGAG
| ||| || ||||| | || | || || || | | | | | | |||| | | || || || || ||| | | | ||||||||||||||||| |||||||| || ||||||||||| || ||| | || || |||||||| || || || || ||||| || ||||| || || ||
agcttctcaagcccttggattaggggaccaacgt-acatgcagagt--ctgatctgatctgttgaagtcttcgtcttattataaagtata----ttgaatgtggcagTTGACATCATTTCCGCTATTGAATTCGACAAAACTGGGGAGCATTTAGCAACAGGTGATCGAGGCGGTCGTGTCGTTTTGTTCGAAAGAACTGATGGCAG
upper sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S100_124V6.1 (Physcomitrella patens), 3'ss of exon 1
cgttaagatgaattagtgtgtcattatgacgtgtagcttagcaggtgtattttgtttggcgcattgtgtttttggtaaccatacccctcatgttt---tgcagTTGACATCATTTCTGCTATTGAGTTTGACAAAACTGGAGACCATCTTGCGACTGGTGATCGTGGGGGACGGGTGGTTTTATTTGAAAGGACAGACAAGAG
| | | || | | | | | || || || | || || | || |||| | | || || | ||| | ||||||||||||||| ||||||||||||||||| ||||||||||| ||| | |||||||| || || || ||||| || || | ||||| ||||| || ||
-gcccatgtttgtttatct-tggcgagggcgatagtatttgctgttggggattcatatatgc-ttgtttctcaaatataaattgttttgttgtatgaatgcagTTGACATCATCTCTGCTATTGAGTTTGATAAAACTGGAGAGCATTTGGCGACTGGAGACCGAGGAGGACGAGTTGTGCTGTTTGAGAGGACGGATGGCAGMapped 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|27755257|gb|CB036012.1|CB036012EST: GTTCTCTCAGGTGTTCGGGGAGCGGACGGCGGGGGAGGAAGTTCAGGAAG TTGACATCATTTCTGCTATTGAGTTTGACAAAACTGGAGACCATCTTGCGA
genomic: GTTCTCTCAGGTGTTCGGGGAGCGGACGGCGGGGGAGGAAGTTCAGGAAGgtatatatcg ... tgttttgcagTTGACATCATTTCTGCTATTGAGTTTGACAAAACTGGAGACCATCTTGCGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtattttgtttggcgcattgtgtttttggtaaccatacccctcatgttttgcagTTGACATCATTTCTGCTATTGAGTTTGACAAAACTGGAGACCATCTTGCGACTGGTGATCGTGGGGGACGGGTGGTTTTATTTGAAAGGACAGACAAGAG
tggtaac putative branch site (score: 2)
cccctcat putative PPT
tttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cgttaagatgaattagtgtgtcattatgacgtgtagcttagcaggtgtattttgtttggcgcattgtgtttttggtaaccatacccctcatgttttgcagTTGACATCATTTCTGCTATTGAGTTTGACAAAACTGGAGACCATCTTGCGACTGGTGATCGTGGGGGACGGGTGGTTTTATTTGAAAGGACAGACAAGAG
- - aagatgaa
- - - - - - - - - - - - - - - -tgtagct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcgcatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtaacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acccctc