Sequence
atgc intronic sequence ATGC exonic sequence...gttccaaggtatacttagttattacgtcattggatgtttaataagtttagtgttcatgataactgcctgtgatctaacacttccagtatacaatatgtagGTATCAAGCCCTGAGACCAGCCTGGTGGCTAGATGTCGTAGAGTTTATGCTCATGCTCACGACTATCATATCAATTCTATTTCAAATAATAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 6
-------------------------gttccaaggtatacttagttattacgtcattggatgtttaataagtttagt-gttcatgataactgcc-tgtgatctaacac---ttccagtatacaatatgtagGTATCAAGCCCTGAGACCAGCCTGGTGGCTAGATGTCGTAGAGTTTATGCTCATGCTCACGACTATCATATCAATTCTATTTCAAATAATAG
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gtaagctatactcgacaacttatatattattaactttagcatttgaaattgtacttgtataacttttaagtgaaattatgcaaaactgcagctatttagtccaactcatttctctttcgaccatatgcagGTTACCAGTCTAGAAGCAAACCCTGTTGCTAGATGTCGACGTGTATTTGCTCATGCTCACGATTACCATATAAATTCTATTTCAAATAATAG
upper sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G142334_T01 (Zea mays), 3'ss of exon 5
------------------------------------------------------------------------------------------gttccaaggtatactt-agttattacgtcattggatgt-ttaataagtttagtgttcatgataactgcctgtgat-ctaacacttccagtatacaatatgtagGTATCAAGCCCTGAGACCAGCCTGGTGGCTAGATGTCGTAGAGTTTATGCTCATGCTCACGACTATCATATCAATTCTATTTCAAATAATAG
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gctgtacttaactcagtttcatttattcacctggcaaaaagcatattctaattatttagaaccattatgccattacctggaatttatgcagcgggaaaatgcattttagtcgattcatcgtccttcctgtctatgtaaccaactttttttttcacaatttgttacactgacccagtc--taaactgtaaacagGTTACAACCCAAGAAACAAGCCTTGCTGCGAGTTGCCGAAGAGTATATGCTCATGCACATGACTATCATATAAATTCAATATCAAATAACAG
upper sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 5
---------------------------------------------------------------------------------------------gttccaaggtatactt-agttattacgtcattggatgt-ttaataagtttagtgttcatgataactgcctgtgat-ctaacacttccagtatacaatatgtagGTATCAAGCCCTGAGACCAGCCTGGTGGCTAGATGTCGTAGAGTTTATGCTCATGCTCACGACTATCATATCAATTCTATTTCAAATAATAG
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gtagctgtacttaactcagtttcatttattcacctggcaaaaagcatattctaattatttagaaccattatgccattacctggaatttatgcagcgggaaaatgcattttagtcgattcatcgtccttcctgtctatgtaaccaactttttttttcacaatttgttacactgacccagtc--taaactgtaaacagGTTACAACCCAAGAAACAAGCCTTGCTGCGAGTTGCCGAAGAGTATATGCTCATGCACATGACTATCATATAAATTCAATATCAAATAACAG
upper sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 5
-----gttccaaggtatacttagttattacgtcattggatgtttaataagtttagtgttcatgataactgcctgtgatctaacacttccagtatacaatatgtagGTATCAAGCCCTGAGACCAGCCTGGTGGCTAGATGTCGTAGAGTTTATGCTCATGCTCACGACTATCATATCAATTCTATTTCAAATAATAG
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atttttgtatgtagtggagctagttttcaagcctt--gacaattacttgtttgaaactttgtagt---ttagtgagtgctaacacattgattgtaaaatatgtagGTAACCAGCCATGAGACCAGTTTGGTGGCTCGATGTCGTAGAGTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAG
upper sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA08G20830.1 (Glycine max), 3'ss of exon 5
-----gttccaaggtatacttagttattacgtcattggatgtttaataagtttagtgttcatgataactgcctgtgatctaacacttccagtatacaatatgtagGTATCAAGCCCTGAGACCAGCCTGGTGGCTAGATGTCGTAGAGTTTATGCTCATGCTCACGACTATCATATCAATTCTATTTCAAATAATAG
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attttagtatgtagtggagctagttttcaagcctt--gacaattacttgtttgaaactttgtagt---ttagcgagttctaacacgttgattgtaaaatatgtagGTAACCAGCCATGAGACCAGTTTGATGGCTCGATGCCGTAGAGTATATGCCCATGCTCATGATTATCATATTAATTCTATTTCAAATAACAG
upper sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 5
--gttccaaggtatacttagttattacgtcattggatgtttaataagtttagtgttcatgataactgcctgtgatctaacacttccagtatacaatatgtagGTATCAAGCCCTGAGACCAGCCTGGTGGCTAGATGTCGTAGAGTTTATGCTCATGCTCACGACTATCATATCAATTCTATTTCAAATAATAG
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agagaagaaagaatttgaagtggttgaagttctttcttttcaaacccacaattgcttgtt-tgagaatctgtagtacta-acctgtgttgtaaaatatgtagGTAAGTAGCCATGAAACCAGTTTAGTTGCTCGATGTCGTAGAGTGTATGCACACGCTCATGATTATCACATCAATTCTATTTCAAATAACAG
upper sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 5
--------gttccaaggtatacttagttattacgtcattggatgtttaataagtttagtgttcatgataactgcctgtgatctaacacttccagtatacaatatgtagGTATCAAGCCCTGAGACCAGCCTGGTGGCTAGATGTCGTAGAGTTTATGCTCATGCTCACGACTATCATATCAATTCTATTTCAAATAATAG
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gaagaaagaattggaagtggttgaagttctttctttttcaaac-tttgacaatt---gcttttttgagaatt---tgtagtacta-acctgtgttttaaaatatgtagGTAAGTAGCCATGAAACCAGCTTAGTTGCCCGATGCCGTAGAGTGTATGCGCATGCTCATGATTATCACATCAATTCTATTTCAAATAACAG
upper sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 7
gttccaaggtatacttagttattacgtc--attggatgtttaataagtttagtgttcatgataactgcc----tgtgatctaacacttccagtatacaatatgtagGTATCAAGCCCTGAGACCAGCCTGGTGGCTAGATGTCGTAGAGTTTATGCTCATGCTCACGACTATCATATCAATTCTATTTCAAATAATAG
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----catggccttcactaccactgattaggaattgattcttaagtcatgcaatattacttaatattgctcatttgtagactaatagttc--atttgacatatacagGTAACTAGCCATGAGTCGAGCCCTGTGGCTAGATGTCGAAGAGTATATGCTCATGCTCATGATTATCATATTAATTCAATCTCAAATAACAGMapped 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|161714603|gb|FC064207.1|FC064207EST: ATTTTTCCTTCCCTCCAGGGGGCATTCCATCTCTACGGTTGCCTACGGTA GTATCAAGCCCTGAGACCAGCCTGGTGGCTAGATGTCGTAGAGTTTATGCT
genomic: ATTTTTCCTTCCCTCCAGGGGGCATTCCATCTCTACGGTTGCCTACGGTAgttgtactca ... caatatgtagGTATCAAGCCCTGAGACCAGCCTGGTGGCTAGATGTCGTAGAGTTTATGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttagtgttcatgataactgcctgtgatctaacacttccagtatacaatatgtagGTATCAAGCCCTGAGACCAGCCTGGTGGCTAGATGTCGTAGAGTTTATGCTCATGCTCACGACTATCATATCAATTCTATTTCAAATAATAG
atctaac putative branch site (score: 2)
tatacaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttccaaggtatacttagttattacgtcattggatgtttaataagtttagtgttcatgataactgcctgtgatctaacacttccagtatacaatatgtagGTATCAAGCCCTGAGACCAGCCTGGTGGCTAGATGTCGTAGAGTTTATGCTCATGCTCACGACTATCATATCAATTCTATTTCAAATAATAG
- - - - - - - - - - - - - - - tggatgt
- - - - - - - - - - - - - - - - - - - - - - - - - -gttcatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actgcct