Sequence
atgc intronic sequence ATGC exonic sequence...gttattgggggctcaagtcttcaatcagctctgcaagacaaaatttatctttcacctttgtatttgaaatttgattgtaatttttacctttcacctgcagATTTTATGTAGCAGAGGTCCTCTTAGCTCTAGAATACCTCCACATGCTTGGGATTGTCTACCGAGATCTTAAGCCGGAAAATGTTCTGGTGAGGGATGAC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv10s0116g00440.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os09g08420.1 (Oryza sativa), 3'ss of exon 2
gttattgggggctcaagtcttcaatcagctctgcaagacaaaatttatctttcacctttgtatttgaaatttg-attgtaattt--ttacct--ttcacctgcagATTTTATGTAGCAGAGGTCCTCTTAGCTCTAGAATACCTCCACATGCTTGGGATTGTCTACCGAGATCTTAAGCCGGAAAATGTTCTGGTGAGGGATGAC
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----gtgtctgccctggttttctggtatcatggagtgatagtactaaacctt-gctcaagtctaagagagtcatgttgatgtttggttgattaattcttttgcagGTTTTATGTGGCTGAGGTGCTTCTTGCTCTAGAATACCTGCATATGCTTGGCATCATATATCGGGACCTTAAGCCAGAAAATGTTCTTGTGAGAGAAGAT
upper sequence: Vv10s0116g00440.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AC217842.3_FGT001 (Zea mays), 3'ss of exon 1
---------gttattgggggctcaagtcttcaatcagctctgcaagacaaaatttatctttcacctttgtatttgaaatttgattgtaatttttacctttcacctgcagATTTTATGTAGCAGAGGTCCTCTTAGCTCTAGAATACCTCCACATGCTTGGGATTGTCTACCGAGATCTTAAGCCGGAAAATGTTCTGGTGAGGGATGAC
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atatttagcatgataggctgccctgattgtcatgtcatttgcaactgcaagaagccttaatcaaatctat----gaacttatgttgacatcaaaaa-----atatgcagGTTTTATGTAGCAGAGGTGCTTCTTGCTCTGGAATACCTGCACATGCTTGGTATCATATACCGTGACTTAAAGCCAGAGAATGTTCTTGTGAGGGAAGAT
upper sequence: Vv10s0116g00440.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G026065_T01 (Zea mays), 3'ss of exon 2
gttattgggggctcaagtcttcaatcagctctgcaagacaaaatttatctttcacctttgtatttgaa-atttgattgtaatttt----tacctttcacctgcagATTTTATGTAGCAGAGGTCCTCTTAGCTCTAGAATACCTCCACATGCTTGGGATTGTCTACCGAGATCTTAAGCCGGAAAATGTTCTGGTGAGGGATGAC
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----tttctgacctat-ttataaactagatttgtgctattatctgtcttcattaaaacgactttaaattatttggcattgattatctaataccttgatgtttcagGTTCTATGTGGCAGAGGTACTCCTTGCATTGGAATACCTGCATATGCTTGGGATTATATACCGTGATCTTAAACCAGAAAATGTCCTCGTTCGGGAAGAT
upper sequence: Vv10s0116g00440.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA15G12760.1 (Glycine max), 3'ss of exon 2
gttattgggggctcaagtcttcaatcagctctgcaagacaaaatttatctttcacctttgtatttgaaat--ttgattgtaatttttacctttcacctgcagATTTTATGTAGCAGAGGTCCTCTTAGCTCTAGAATACCTCCACATGCTTGGGATTGTCTACCGAGATCTTAAGCCGGAAAATGTTCTGGTGAGGGATGAC
| ||| | | || | | | ||| | | | || |||||| | | || | ||| | | | || |||||||||||||| ||||||||||| | ||| | || || || ||||||||||||||||||||||| || |||||||| ||||||||||| || ||||||||
-tgatttcttttcttgctttgcatttttgggttttttgcctggtttggcaattatgttatgatttgatggtatccactgctaatttc-cttgtaacttgcagATTTTATGTGGCAGAGGTCCTACTGGCTTTGGAGTATCTTCACATGCTTGGGATTGTCTACCGTGACCTTAAGCCAGAAAATGTTCTTGTTAGGGATGAT
upper sequence: Vv10s0116g00440.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA09G01800.1 (Glycine max), 3'ss of exon 2
gttattgggggctcaagtcttcaatcagctctgcaagacaaaatttatctttcacctttgtatttgaaatttgattgtaatt--tttacctttcacctgcagATTTTATGTAGCAGAGGTCCTCTTAGCTCTAGAATACCTCCACATGCTTGGGATTGTCTACCGAGATCTTAAGCCGGAAAATGTTCTGGTGAGGGATGAC
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-ttatttcttttcttgcttttgaattttgggtattttgcccggtttggcaattatgtt-atgattggatgctaaccactgctaatttccttgtaacttgcagATTTTATGTGGCAGAGGTCCTACTGGCTTTGGAGTATCTTCACATGCTTGGGATTGTCTACCGTGACCTTAAGCCAGAAAATGTCCTTGTTCGGGATGAC
upper sequence: Vv10s0116g00440.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G47750.1 (Arabidopsis thaliana), 3'ss of exon 2
----------------------------------------------gttattgggggctcaagtcttcaatcagctctgcaagacaaa---atttatctttcacctttgtatttgaa-----atttgattgtaatttttacctttcacctg---cagATTTTATGTAGCAGAGGTCCTCTTAGCTCTAGAATACCTCCACATGCTTGGGATTGTCTACCGAGATCTTAAGCCGGAAAATGTTCTGGTGAGGGATGAC
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gtgagtcatttttccttcgtctgtcaagattagcatttcctttgattttatcgtatttcaaagtattgggtagatgacaaaagacatactcatttcggctgaagcagagcattcttattctcatctcactaaagattttgttttcaatgtgtggcagATTTTACATAGCAGAGTCATTGTTAGCTTTGGAATACCTGCACATGCTTGGGATTGTGTATCGAGATCTTAAGCCTGAAAACGTTCTAGTTCGAGAAGACMapped 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|110720084|gb|EE095697.1|EE095697EST: ACTCTTAGACAGAGGCAGCCAGGGAAACATTTTACTGAGCAAGCAGTGAA ATTTTATGTAGCAGAGGTCCTCTTAGCTCTAGAATACCTCCACATGCTTGG
genomic: ACTCTTAGACAGAGGCAGCCAGGGAAACATTTTACTGAGCAAGCAGTGAAgtatgctatc ... tcacctgcagATTTTATGTAGCAGAGGTCCTCTTAGCTCTAGAATACCTCCACATGCTTGG
EST:
gi|30301014|gb|CB977808.1|CB977808EST: ACTCTTAGACAGAGGCAGCCTGGGAAACATTTTACTGAGCAAGCAGTGAA ATTTTATGTAGCAGAGGTCCTCTTAGCTCTAGAATACCTCCACATGCTTGG
genomic: ACTCTTAGACAGAGGCAGCCAGGGAAACATTTTACTGAGCAAGCAGTGAAgtatgctatc ... tcacctgcagATTTTATGTAGCAGAGGTCCTCTTAGCTCTAGAATACCTCCACATGCTTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatctttcacctttgtatttgaaatttgattgtaatttttacctttcacctgcagATTTTATGTAGCAGAGGTCCTCTTAGCTCTAGAATACCTCCACATGCTTGGGATTGTCTACCGAGATCTTAAGCCGGAAAATGTTCTGGTGAGGGATGAC
atttgat putative branch site (score: 5)
tttttacctttcacct putative PPT
tttgtatttgaaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttattgggggctcaagtcttcaatcagctctgcaagacaaaatttatctttcacctttgtatttgaaatttgattgtaatttttacctttcacctgcagATTTTATGTAGCAGAGGTCCTCTTAGCTCTAGAATACCTCCACATGCTTGGGATTGTCTACCGAGATCTTAAGCCGGAAAATGTTCTGGTGAGGGATGAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - ttggggg
- - - - - - tcaagtc
- - - - - - - - - - tcaatca
- - - - - - - - - - - - - -gctctgc
- - - - - - - - - - - - - - - - - - gacaaaa