Sequence
atgc intronic sequence ATGC exonic sequence...atccaaaagccgcactttctttctttatttttttgctccctcatttttttttctgtaaaaatgtgaattacattttggtttacttaattgtcccgtgcagGAGTTGTTGGAGAAGATTGCGCCTACATGGATGAATGTTTCTTTGAGAATGAAAGATGACCCAGAAACTGATAAAGTATTTGGATGGGTGCTAGAAAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv13s0084g00830.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os01g16600.1 (Oryza sativa), 3'ss of exon 3
-------------------------------------------atccaaaagccgcactttcttt--ctttatttttttgctcc--------------ctcattttt--ttttctgtaaaaatgtgaattacattttggtttacttaattgtcccgtgcagGAGTTGTTGGA----------GAAGATTGCGCCTACATGGATGAATGTTTCTTTGAGAATGAAAGATGACCCAGAAACTGATAAAGTATTTGGATGGGTGCTAGAAAT
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gtaacacatattgcagaattgacgtggtataccttgaagtctcatgcatgaggagtatttccttggattttatttttacattacttacatgccagttgctagttattaatgttttgaattgatgagcttcaatttttaactctatcccttatcatctgaggaaacttttagATACAACTTGAGAAGATTGCCCCTACATGGATGAATGTATCGATTCAAATGAAAGAAGATCAGGAGACAGATAAAGCTTTTGGATGGGTCTTGGAAAT
upper sequence: Vv13s0084g00830.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA15G37490.2 (Glycine max), 3'ss of exon 4
atccaaaagccgcactttctttctttatttttttgctccctcatttttttttctgtaaaaatgtgaattacattttggtttacttaattgtcccgtgcagGAGTTGTTGGAGAAGATTGCGCCTACATGGATGAATGTTTCTTTGAGAATGAAAGATGACCCAGAAACTGATAAAGTATTTGGATGGGTGCTAGAAAT
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aactatcctaactaactagctcccttactaacggacaacttactaactactaatgggtatctactaatggacttctctctcatttttttctttctttcagGATTTGATCGCAAAGATTGCCCCCACATGGATGAATATTTCTTTGAAGATGAAAGAGGACCCAGAGACTGATAAAGCTTTTGGATGGGTGCTAGAAAT
upper sequence: Vv13s0084g00830.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA13G26610.1 (Glycine max), 3'ss of exon 4
atccaaaagccgcactttctttctttatttttttgctccctcatttttttttctgtaaaaatgtgaattacattttggtttacttaattgtcccgtgcagGAGTTGTTGGAGAAGATTGCGCCTACATGGATGAATGTTTCTTTGAGAATGAAAGATGACCCAGAAACTGATAAAGTATTTGGATGGGTGCTAGAAAT
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gcctgcccaactaacctaactaactaattcccttactaacagacacctaactaacaactaatgggtgtctactgatggacttctctatttttttcttcagGATTTGATTGCAAAGATTGCCCCCACATGGATGAATATTTCTTTGAAGATGAAAGAGGATCCAGAGACTGATAAAGCTTTTGGATGGGTGCTAGAAAT
upper sequence: Vv13s0084g00830.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT5G13500.1 (Arabidopsis thaliana), 3'ss of exon 4
------------------------------------------------------------------atccaaaagccgcactttctttctttatttttttgctccctcatttttttttctgtaaaaatgtgaattacattttggtttac-ttaattgtcccgtgcagGAGTTGTTGGAGAAGATTGCGCCTACATGGATGAATGTTTCTTTGAGAATGAAAGATGACCCAGAAACTGATAAAGTATTTGGATGGGTGCTAGAAAT
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gtgagattatctgtgctatactgtttgtatatgtgttatttgacttgggccccaaagattttcagaggcgtttagctagatgtgatgttggtgtccaggaatatgttctgtttgttctgttcatgcattaaaattg-atgttgacatgcatttactttctgatgcagGAATCACTTGAAAAGATTGCTCCTACATGGATGAATGTCTCGCTGACAATGAAAAACGATCCAGAAACTGATAAGGCATTTGGATGGGTGCTGGAAAT
upper sequence: Vv13s0084g00830.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S145_88V6.1 (Physcomitrella patens), 3'ss of exon 3
-------------atccaaaagccgcactttctttctttattt--ttttgctccctcatttttttttctgtaaaaatgt--gaattacattttggttt-------act-taattgtcccgt--------gcagGAGTTGTTGGAGAAGATTGCGCCTACATGGATGAATGTTTCTTTGAGAATGAAAGATGACCCAGAAACTGATAAAGTATTTGGATGGGTGCTAGAAAT
||| || | || | | | | ||| | | | | || | || || | | || | | ||| | |||| | | ||| ||| ||| || |||| | |||||||| || || |||||| | || || | | ||||||||||||||||||||||| |||| |||||| ||||| || |||||
gtacgacgtttttatcaaagacccactgtctaaaccgttaagcgatgtggattactgaacttgcttcttttgaatacttaggaactgtatttccatattatgtgaactctaagtgtgttgttgataaatgcagAGTCAACTAGAGAAGATAGCTCCAACATGGTCTGACGTGTCCATCAAGATGAAAGATGACCCAGAAACTGACAAAGCATTTGGTTGGGTTCTGGAAAT
upper sequence: Vv13s0084g00830.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S48_116V6.1 (Physcomitrella patens), 3'ss of exon 3
------------------------atccaaaagccgcactttctttctttatttttttgctccc-tcatttttttttctgtaaaaatg----tgaatt--acattttggtttacttaattgtcccg--tgcagGAGTTGTTGGAGAAGATTGCGCCTACATGGATGAATGTTTCTTTGAGAATGAAAGATGACCCAGAAACTGATAAAGTATTTGGATGGGTGCTAGAAAT
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gtgccacatttctgtgtcaaggaaactctatgtcgtctattgaataatttagatctttatttctgtcacttttgaatgtcgaggaatggtcctccattcgacgtgaatgctgacactgtggttacgattgcagAGTCAATTAGAGAAGGTAGCCCCAACATGGTCAGACGTGTCCATCAAGATGAAGGATGACCCAGAAACTGACAAAGCATTTGGTTGGGTTTTAGAAATMapped 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|30128013|gb|CB913352.1|CB913352EST: CTGTGACAAATGTTGATCCAATTGGCAACTCTCCTGTAATTATCAAGAGG GAGTTGTTGGAGAAGATTGCGCCTACATGGATGAATGTTTCTTTGAGAATG
genomic: CTGTGACAAATGTTGATCCAATTGGCAACTCTCCTGTAATTATCAAGAGGgtaaagtttc ... tcccgtgcagGAGTTGTTGGAGAAGATTGCGCCTACATGGATGAATGTTTCTTTGAGAATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttttctgtaaaaatgtgaattacattttggtttacttaattgtcccgtgcagGAGTTGTTGGAGAAGATTGCGCCTACATGGATGAATGTTTCTTTGAGAATGAAAGATGACCCAGAAACTGATAAAGTATTTGGATGGGTGCTAGAAAT
acttaat putative branch site (score: 4)
ttgtccc CT-rich tract
taaaaatgtgaattac 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atccaaaagccgcactttctttctttatttttttgctccctcatttttttttctgtaaaaatgtgaattacattttggtttacttaattgtcccgtgcagGAGTTGTTGGAGAAGATTGCGCCTACATGGATGAATGTTTCTTTGAGAATGAAAGATGACCCAGAAACTGATAAAGTATTTGGATGGGTGCTAGAAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - aaaagcc
- - - - - - - - - - - - - - - - -tgctccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaatg