Sequence
atgc intronic sequence ATGC exonic sequencegttgctgataacctgaaaaccatgtttactttttccatccaacatgctattctacaacttgccaactgaacactgtgctgattttttgcagGAAAGTTCAGACATTTGCCTGTTGTAGAGAATGGGGAGGTCATTGCTTTACTAGACATAGCAAAGTGTTTATATGATGCTATTGCTCGAATGGAGAGGGC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv17s0000g01200.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g69900.1 (Oryza sativa), 3'ss of exon 3
gttgctgataacctgaaaaccatgtttactttttccatccaacatgctattctacaacttgccaactgaacactgtgctgattttttgcagGAAAGTTCAGACATTTGCCTGTTGTAGAGAATGGGGAGGTCATTGCTTTACTAGACATAGCAAAGTGTTTATATGATGCTATTGCTCGAATGGAGAGGGC
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gtgggtgaagtcccaaacactatctctggtcccttgttt----gcacttctcttgattttcctga--gaa---tgtatcacttcattccagGTAAGTTCAGACATTTACCTGTCGTGGAGAACGGTGAAGTCATTGCACTGCTCGACATAGCCAAGTGCCTGTATGATGCTATTGCGCGAATGGAAAGGGC
upper sequence: Vv17s0000g01200.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G133621_T02 (Zea mays), 3'ss of exon 3
-gttgctgataacctgaaaaccatgtttactttttccatccaacatgctattctacaacttgccaactgaacactgtgctgattttttgcagGAAAGTTCAGACATTTGCCTGTTGTAGAGAATGGGGAGGTCATTGCTTTACTAGACATAGCAAAGTGTTTATATGATGCTATTGCTCGAATGGAGAGGGC
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gtccgtgaatgctctgaagatt---tctgcgcgccttacctatagtcatcttcta-atgttgcctgatggaaggtatcct--ttggttccagGTAAGTTCAGACATCTGCCTGTTGTTGAGAATGGTGAAGTCATTGCAATTCTGGACATAGCCAAGTGCCTATATGATGCTATTGCACGGATGGAAAGGGC
upper sequence: Vv17s0000g01200.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G171622_T01 (Zea mays), 3'ss of exon 3
gttgctgataacctgaaaaccatgtttactttttccatccaacatgctattctacaacttgccaactgaacactgtgctgattttttgcagGAAAGTTCAGACATTTGCCTGTTGTAGAGAATGGGGAGGTCATTGCTTTACTAGACATAGCAAAGTGTTTATATGATGCTATTGCTCGAATGGAGAGGGC
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--gtctgtgaatgctcccacggtttctgtgcgcctcacctatattcatcttttaatgttccctgatgaaac---gtatccttcggttccagGTAAGTTCAGGCATCTGCCTGTCGTGGAGAATGGCGAGGTCATTGCAATTCTGGACATAGCCAAGTGCCTATATGATGCTATTGCACGGATGGAAAGGGC
upper sequence: Vv17s0000g01200.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA04G37370.3 (Glycine max), 3'ss of exon 4
gttgctgataacctgaa-aaccatgtttactttttccatccaacatgctattctacaacttgccaactgaacactgtgctgat---tttttgcagGAAAGTTCAGACATTTGCCTGTTGTAGAGAATGGGGAGGTCATTGCTTTACTAGACATAGCAAAGTGTTTATATGATGCTATTGCTCGAATGGAGAGGGC
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---gttggtagtgtatatagagaaacacaacttttcaagttagt-tacttttctgtatcctgccttttgaatacatggctgatatatgttgacagGGAAATTCAGACATTTACCTGTGGTGGAGAATGGAGAAGTTTTGGCTTTACTAGACATAGCAAAGTGTTTGCATGATGCCATTGCCCGTATGGAAAGGGC
upper sequence: Vv17s0000g01200.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA05G38140.1 (Glycine max), 3'ss of exon 3
gttgctgataacctgaaaaccatgtttactttttccatccaacatgctattctacaacttgccaactgaacactgtgctgatttt--ttgcagGAAAGTTCAGACATTTGCCTGTTGTAGAGAATGGGGAGGTCATTGCTTTACTAGACATAGCAAAGTGTTTATATGATGCTATTGCTCGAATGGAGAGGGC
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gttggtattacacggagataggcacatgctaattac---tatttcggtacggtgccctttg---aataaatacaaagatgattatgttttcagGGAGGTTCAGACATTTACCTGTGGTGGAGAATGGAGAAGTAGTTGCCATACTTGACATAGCAAAGTGTTTGTATGATGCCATTGCCCGTATGGAAAGGGC
upper sequence: Vv17s0000g01200.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G01470.1 (Glycine max), 3'ss of exon 2
gttgctgataacctgaaaaccatgtttactttttccatccaacatgctattctacaacttgccaactgaacactgtgctgattt---tttgcagGAAAGTTCAGACATTTGCCTGTTGTAGAGAATGGGGAGGTCATTGCTTTACTAGACATAGCAAAGTGTTTATATGATGCTATTGCTCGAATGGAGAGGGC
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gttggtattactcggagataggcacatgctaatt---tctatttctgtatggtgccattgg---aataagtacaaagatcatttatgttttcagGGAGGTTCAGACATTTACCTGTGGTGGAGAATGGAGAAGTTGTTGCCATACTTGACATAGCAAAGTGTTTGTATGATGCCATTGCCCGTATGGAAAGGAA
upper sequence: Vv17s0000g01200.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G63490.1 (Arabidopsis thaliana), 3'ss of exon 4
-gttg-ctgataacctgaaaaccatgtttactt--tttccatccaacatgctat-tctacaac-ttgccaa--ctgaacactgtgctgattttttgcagGAAAGTTCAGACATTTGCCTGTTGTAGAGAATGGGGAGGTCATTGCTTTACTAGACATAGCAAAGTGTTTATATGATGCTATTGCTCGAATGGAGAGGGC
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gtttgtctcattgtttttaagctagagaaacttgatgtttatctgat-tgctgtgtctagatccttaatgaggctatatcttaaccttacctactgcagGAAAATTCAGACATTTGCCGGTTGTTGAAAATGGCGAAGTTATTGCTTTATTAGATATAGCAAAGTGTTTGTATGATGCAATTGCTCGTATGGAGAGGGC
upper sequence: Vv17s0000g01200.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G50530.1 (Arabidopsis thaliana), 3'ss of exon 4
gttgctgataacctgaaaaccatgtttactttttccatccaacatgctattctacaacttgccaactgaacactgtgctgattttttgcagGAAAGTTCAGACATTTGCCTGTTGTAGAGAATGGGGAGGTCATTGCTTTACTAGACATAGCAAAGTGTTTATATGATGCTATTGCTCGAATGGAGAGGGC
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-----------------gtttgttatttcttgttcttttataagttctttgttg-gtcttggtacttgagctgactagtggatat--gcagGCAAGTTTAGACATTTGCCGGTGGTGGAGAATGGAGAAGTTATCGCGCTTCTCGATATTGCAAAGTGTTTGTATGATGCTATTGCCCGCATGGAAAGATC
upper sequence: Vv17s0000g01200.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ29517 (Selaginella moellendorffii), 3'ss of exon 2
gttgctgataacctgaaaaccatgtttactttttccatccaacatgctattctacaacttgccaactgaacactgtgctgattttttgcagGAAAGTTCAGACATTTGCCTGTTGTAGAGAATGGGGAGGTCATTGCTTTACTAGACATAGCAAAGTGTTTATATGATGCTATTGCTCGAATGGAGAGGGC
| | | || | || || | || | || | | | | | |||| |||||||||||||||| |||||||| ||||| ||||| ||||| ||||| | ||||||| | ||||| | ||||| ||||| | || |||||| || |
----------------------------gtatgttgatttgctgtttcatccttgtatctg--atctagagatatcg--gttgttttacagGAAAGTTCAGACACTTGCCTGTCGTAGACAATGGCGAGGTGATTGCACTTTTAGACATCACGAAGTGCCTGTATGACGCTATAGTGCGCATGGAGCGGTC
upper sequence: Vv17s0000g01200.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ28088 (Selaginella moellendorffii), 3'ss of exon 2
gttgctgataacctgaaaaccatgtttactttttccatccaacatgctattctacaacttgccaactgaacactgtgctgattttttgcagGAAAGTTCAGACATTTGCCTGTTGTAGAGAATGGGGAGGTCATTGCTTTACTAGACATAGCAAAGTGTTTATATGATGCTATTGCTCGAATGGAGAGGGC
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----------------------------gtatgttgatttgctgtttcatccttgtatctg--atctagagattat-cggttgttttacagGAAAGTTCAGACACTTGCCTGTCGTAGACAATGGCGAGGTGATTGCACTTTTAGACATCACGAAGTGCCTGTATGACGCTATAGTGCGCATGGAGCGGTCMapped 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|26264368|gb|CA815431.1|CA815431EST: TGCTC-TTCTGATACTCTTGCTGTGGAAGCCCTGCAAAAGATGGTGCAAG GAAAGTTCAGACATTTGCCTGTTGTAGAGAATGGGGAGGTCATTGCTTTAC
genomic: TGTTCTTTCTGATACTCTTGCTGTGGAAGCCCTGCAAAAGATGGTGCAAGgttgctgata ... ttttttgcagGAAAGTTCAGACATTTGCCTGTTGTAGAGAATGGGGAGGTCATTGCTTTAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atccaacatgctattctacaacttgccaactgaacactgtgctgattttttgcagGAAAGTTCAGACATTTGCCTGTTGTAGAGAATGGGGAGGTCATTGCTTTACTAGACATAGCAAAGTGTTTATATGATGCTATTGCTCGAATGGAGAGGGC
tgctgat putative branch site (score: 3)
ttttttgc CT-rich tract
tgatttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgctgataacctgaaaaccatgtttactttttccatccaacatgctattctacaacttgccaactgaacactgtgctgattttttgcagGAAAGTTCAGACATTTGCCTGTTGTAGAGAATGGGGAGGTCATTGCTTTACTAGACATAGCAAAGTGTTTATATGATGCTATTGCTCGAATGGAGAGGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG