Sequence
atgc intronic sequence ATGC exonic sequence...attcaattttatttctctatcctgtgttgtatgtgcttctcatattggcatcgggctttgtcatattttaatgggtttatttactctctctcttttgcagACAACACATGTTGCAGCACAATATGGTCAAACTGCTTTCCTATACCACGTTGTTACAAAATGGAATGCTGATCCTGATGTTCCTGATAATGATGGAAGAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv11s0118g00470.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os02g09130.1 (Oryza sativa), 3'ss of exon 2
---attcaattttatttctctatcctgtgttgt-atgtgcttctcatattggcatcgggctttgtcatattttaatgggtttatttactctctctcttttgcagACAACACATGTTGCAGCACAATATGGTCAAACTGCTTTCCTATACCACGTTGTTACAAAATGGAATGCTGATCCTGATGTTCCTGATAATGATGGAAGAA
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ccggtttgatcttaaaagttgggcagaaaaagtcaagagtcagtca-gttaccttgtatttgaagtatttctgacggaatccatctgttgt---tataccacagACTACACATGTTGCAGCACAGTATGGTCAAACATCATATCTTTATCATATTGTTGCAAAATGGAATGCTGATCCTGATGTCCCTGATAATGATGGAAGAA
upper sequence: Vv11s0118g00470.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os06g43680.1 (Oryza sativa), 3'ss of exon 2
attcaattttatttctctatcctgtgttgtatgtgcttctcatattggcatcgggctttgtcatattttaatgggtttatt---tactct---ctctcttttgcagACAACACATGTTGCAGCACAATATGGTCAAACTGCTTTCCTATACCACGTTGTTACAAAATGGAATGCTGATCCTGATGTTCCTGATAATGATGGAAGAA
||||| | | | || || | | || || | || | |||||| ||| | || ||| || ||||| || ||||||| |||||||||||||||| || ||||| || || || || | || || ||||| | || |||||||||||||| ||||| |||||||||||||||||||
----aatttaacctatgaattctctaggtaaaatgaaaagca-agaatcaacaacttttgtc-tatggcagtgaatttgttaaaaactctatactgctgtttgcagGCAACACATGTTGCAGCGCAGTATGGCCAGACAGCATTTATTTATCATATTGTTGCGAAGTGGAATGCTGATCCAGATGTCCCTGATAATGATGGAAGAA
upper sequence: Vv11s0118g00470.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G087806_T01 (Zea mays), 3'ss of exon 2
attcaattttatttctctatcctgtgttgta---tgtgcttctcatattggcatcg----ggctttgtcatattttaatgggtttatttactctctctcttttgcagACAACACATGTTGCAGCACAATATGGTCAAACTGCTTTCCTATACCACGTTGTTACAAAATGGAATGCTGATCCTGATGTTCCTGATAATGATGGAAGAA
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---tcatgtgattgttctgtgttaagggaaaaaaagaataattgaagttgattatgcagagaatttgtcacagctctttatttcgatatact-tctgtgtt---cagGCCACGCATGTTGCAGCACAGTATGGTCAGACTGCATTCATTTACCACATTGTTGCAAAATGGAATGCTGATCCAGATATCCCTGATAATGATGGAAGGA
upper sequence: Vv11s0118g00470.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G024437_T01 (Zea mays), 3'ss of exon 2
attcaattttatttctctatcct-gtgttgtatgtgcttctcatattggcatc---gggctttgtcatattttaatgggtttatttactctctctcttttgcagACAACACATGTTGCAGCACAATATGGTCAAACTGCTTTCCTATACCACGTTGTTACAAAATGGAATGCTGATCCTGATGTTCCTGATAATGATGGAAGAA
| || | ||| || || | | | | | | | | ||| || | ||| ||| | | | || || || | ||| | || ||| | ||||||||||||||||| |||||||| ||||| ||| | |||| | ||||| | ||||||||||||||||| ||| | |||||||||||||| || |
ttgtcatgtgattgttccatgttagggaaaaaagaaccagtgaagttgttatgcagagaatttttcacagctctttaagtaaatatatt-tctgtgtt---cagGCCACACATGTTGCAGCACAGTATGGTCAGACTGCATTCATTTACCGCATTGTTGCGAAATGGAATGCTGATCCAGATATCCCTGATAATGATGGGAGGA
upper sequence: Vv11s0118g00470.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA17G11600.1 (Glycine max), 3'ss of exon 2
attca-attttatttctctatcctgtgttgtatgtgcttctcatattggcatcgggctttgtcatattttaatgggtttatttactctct-ctcttttgcagACAACACATGTTGCAGCACAATATGGTCAAACTGCTTTCCTATACCACGTTGTTACAAAATGGAATGCTGATCCTGATGTTCCTGATAATGATGGAAGAA
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-tacatatgctaatttggtagtttgggttct-tgttttacttgaagcacaggtgtgcagctgtaaatgctaattttactaattatgatttgcttggatgcagACAACACATGTTGCTGCACAATATGGTCAGACAGCTTTCCTTTACCACATTGTTTCAAAATGGAATGCTGACCCTGATGTTCCTGATAATGATGGAAGAA
upper sequence: Vv11s0118g00470.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA13G23230.1 (Glycine max), 3'ss of exon 3
attcaatt-ttatttctctatcctgtgttgtatgtgcttctcatattggcatcgggctttgtcatattttaatgggtttatttactctct-ctcttttgcagACAACACATGTTGCAGCACAATATGGTCAAACTGCTTTCCTATACCACGTTGTTACAAAATGGAATGCTGATCCTGATGTTCCTGATAATGATGGAAGAA
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--acatctgctaatttggtagtttgggattcttgttttacttgaagcacaagcgtgtggctgtaaatgttaattttactaattatgatttgcttggacacagACAACGCATGTTGCTGCACAATATGGTCAGACAGCTTTCCTTTACCACATTGTTTCAAAATGGAATGCTGACCCTGATGTTCCTGATAATGATGGAAGAA
upper sequence: Vv11s0118g00470.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G20350.1 (Arabidopsis thaliana), 3'ss of exon 2
-------------attcaattttatttctctatcctgtgttgtatgtgcttctcatattggcatcgggctttgtcatattttaatgggtttat--------ttactctctctct-tttgcagACAACACATGTTGCAGCACAATATGGTCAAACTGCTTTCCTATACCACGTTGTTACAAAATGGAATGCTGATCCTGATGTTCCTGATAATGATGGAAGAA
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gttcatatctcttctttaactacgcgtccatgttctctgctg-acttctatcaaatttcccttcttttcttgtttagttctcaatgggtgtatgttaatacttaattttgaactgcttgtagGCAACACATGTTGCCGCACAGTATGGCCAGACTGCTTTTCTTTGTCACGTTGTCTCAAAGTGGAATGCTGATCCTGACGTGCCTGATAATGATGGAAGAAMapped 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|161721152|gb|FC071027.1|FC071027EST: TACTCCAAGAGGGTGCTCGGGTTAACACAGCTGATATGTATGGCTATCAG ACAACACATGTTGCAGCACAATATGGTCAGACTGCTTTCCTATACCACGTT
genomic: TACTCCAAGAGGGTGCTCGGGTTAACACAGCTGATATGTATGGCTATCAGgttggtttca ... tcttttgcagACAACACATGTTGCAGCACAATATGGTCAAACTGCTTTCCTATACCACGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggcatcgggctttgtcatattttaatgggtttatttactctctctcttttgcagACAACACATGTTGCAGCACAATATGGTCAAACTGCTTTCCTATACCACGTTGTTACAAAATGGAATGCTGATCCTGATGTTCCTGATAATGATGGAAGAA
ttttaat putative branch site (score: 3)
tttatttactctctct putative PPT
atattttaatgggttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attcaattttatttctctatcctgtgttgtatgtgcttctcatattggcatcgggctttgtcatattttaatgggtttatttactctctctcttttgcagACAACACATGTTGCAGCACAATATGGTCAAACTGCTTTCCTATACCACGTTGTTACAAAATGGAATGCTGATCCTGATGTTCCTGATAATGATGGAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - -tctatcc
- - - - - - - - - - - - - - -tatgtgc