Sequence
atgc intronic sequence ATGC exonic sequence...ccattttttgctgtgtattgttttttccaatttttcaatgttgaattctgtgaagcagcttgacttgcagcatcattcatttttaaatgattttatccagGGCAAAGATAAAACAGCCGAAGAGAGAAGGATTGCAATCTGCATCTTTGATGATGTTGCAGAGCAATGTCGTGAAGCGGCTCTTAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv06s0004g00500.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os07g38760.1 (Oryza sativa), 3'ss of exon 13
ccattttttgctgtgtattgttttttccaatttttcaatgttgaattctgtgaagcagcttgacttgcagcatcattcattt-ttaaatgattttatc----cagGGCAAAGATAAAACAGCCGAAGAGAGAAGGATTGCAATCTGCATCTTTGATGATGTTGCAGAGCAATGTCGTGAAGCGGCTCTTAA
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--cttgcatgttttctagtcttagttcta-ttgagctgtgttga-ttatttcttgttttgttgtttactgc-tcattcatttcttgtgtcattttaatttggcagGGAAAAGATAAGACTGCTGAAGAGAGAAGGATAGCTATCTGTATATTTGATGATATTGCAGAGCAATGTCGTGAATCTGCTCTCAA
upper sequence: Vv06s0004g00500.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os03g49420.1 (Oryza sativa), 3'ss of exon 12
ccattttttgctgtgtattgttttttccaatt---tttcaatgttgaattctgtgaagcagcttgacttgcagcatcattcatttttaaatgattttatccagGGCAAAGATAAAACAGCCGAAGAGAGAAGGATTGCAATCTGCATCTTTGATGATGTTGCAGAGCAATGTCGTGAAGCGGCTCTTAA
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-tgtgataaacatagaacatcttattacaaaaaaaatactctgtcaaggacaaaaaagaacctt--ctgcgattataagtattttttttgttaataatattagGCCAAGGACAAAACAGTAGAGGAACGAAGGATTGCCATATGCATTTTTGATGATGTTGCAGAGCACTGTCGCGAAGCAGCTGTCAG
upper sequence: Vv06s0004g00500.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM5G887631_T01 (Zea mays), 3'ss of exon 13
---ccattttttgctgtgtattgttttttccaatttttcaatgttgaattctgtgaagcagcttgacttgcagcatcattcatttttaaatgattttatccagGGCAAAGATAAAACAGCCGAAGAGAGAAGGATTGCAATCTGCATCTTTGATGATGTTGCAGAGCAATGTCGTGAAGCGGCTCTTAA--------------
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gcgtcttttttccattcttaacctgttgtgaggtgcatctattctatatttttttgggt--tttattctatctcatt-ttggtaccttgtggtttatttgcagGGAAAAGATAAAACACCTGAAGAGAGAAGGATAGCTATCTGTATTTTTGATGATGTTGCAGAGCAATGCCGTGAATCAGCTCTGAAGTATTATGACACAT
upper sequence: Vv06s0004g00500.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G033619_T01 (Zea mays), 3'ss of exon 12
------------------------------------------------------------------------------------ccattttttgctgt----gtattgttttttccaatttttcaatgt---tgaattctgtgaagcagcttgacttg-cagcat-cattcatttttaaatgatttt--atccagGGCAAAGATAAAACAGCCGAAGAGAGAAGGATTGCAATCTGCATCTTTGATGATGTTGCAGAGCAATGTCGTGAAGCGGCTCTTAA
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gtaagtgagatgatgaaccattggatttggtgcattttctttgcttgttagggttgtgacttgtgagcactgaacaatacatcacaatttgatgtcactctagatttattacctctgaacatgaaacataaatgcactattgaatattggtaaactaaacaccatatgtacatttttaactttccaccaatttagGGTAAGAATAAATCACCAGAAGAAAGAAGGATTGCCATATGCATTTTTGATGATGTTGCTGAGCATTGCCGTGAAGCAGCAGTTAG
upper sequence: Vv06s0004g00500.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA05G28950.1 (Glycine max), 3'ss of exon 15
ccattttttgctgtgtattgttttttccaatttttcaatgttgaattctgtgaagcagcttgacttgcagcatcattc--attt--ttaaatgatttt-atccagGGCAAAGATAAAACAGCCGAAGAGAGAAGGATTGCAATCTGCATCTTTGATGATGTTGCAGAGCAATGTCGTGAAGCGGCTCTTAA
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-----ttcacgtatcagatacactttttggctctctgatgttgtaccaaacacaactaaaacatgtacgtcattgttttgacttagtttaatgttttggatatagGGAAGGGACAAGACTCCAGAAGAGAGAAGAATTGCAATTTGTATTTTTGATGATGTTGCAGAGCAGTGTCGTGAAGCTGCTGTTAA
upper sequence: Vv06s0004g00500.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA08G12120.1 (Glycine max), 3'ss of exon 13
--ccattttttgctgtgtattgttttttccaatttttcaatgttgaattctgtgaagcagcttgacttgcagcatcattcatttttaaatgatttt-atccagGGCAAAGATAAAACAGCCGAAGAGAGAAGGATTGCAATCTGCATCTTTGATGATGTTGCAGAGCAATGTCGTGAAGCGGCTCTTAA
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acgtatcagatgcactttttggctttctgatgtggtaccaaacacaacc---taagacatgtaggtcattattttgactcttagtttaatgttttggatatagGGAAGGGACAAGACTCCTGAAGAGAGAAGAATTGCAATTTGTATTTTTGATGATGTTGCAGAGCAGTGTCGTGAAGCTGCTATTAA
upper sequence: Vv06s0004g00500.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AT5G19820.1 (Arabidopsis thaliana), 3'ss of exon 13
ccattttttgctgtgtattgttttttccaatttttcaatgttg--aattctgtgaagcagcttgacttgcagcatcattcatttttaaatgattttatccagGGCAAAGATAAAACAGCCGAAGAGAGAAGGATTGCAATCTGCATCTTTGATGATGTTGCAGAGCAATGTCGTGAAGCGGCTCTTAA
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tctggttcaggtgaatgtagtttctaa-attctgtggctgttaccatgtctctggtacaatattagtcttcgttcaccttatgtgtattcgatga-attcagGGAAGAGATAAAACAGCGGAAGAGAGAAGGATTGCTATATGCATTTTTGATGATGTAGCAGAACAATGCCGTGAAGCTGCCTTTAAMapped 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|34547296|gb|CF515528.1|CF515528EST: CTTTCTTGCCATTCTTTGATGAGTTAGCTTCATATCTCACGCCTATGTGG ATCTTAAGATAAAACAGCCGAAGAGAGAAGGATTGCAATCTGCATCTTTGA
genomic: CTTTCTTGCCATTCTTTGATGAGTTAGCTTCATATCTCACACCTATGTGGgtaagttcta ... ttttatccagGGC-AAAGATAAAACAGCCGAAGAGAGAAGGATTGCAATCTGCATCTTTGA
EST:
gi|110690073|gb|EE066851.1|EE066851EST: CTTTCTTGCCATTCTTTGATGAGTTAGCTTCATATCTCACACCTATGTGG GGCAAAGATAAAACAGCCGAAGAGAGAAGGATTGCAATCTGCATCTTTGAT
genomic: CTTTCTTGCCATTCTTTGATGAGTTAGCTTCATATCTCACACCTATGTGGgtaagttcta ... ttttatccagGGCAAAGATAAAACAGCCGAAGAGAGAAGGATTGCAATCTGCATCTTTGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctgtgaagcagcttgacttgcagcatcattcatttttaaatgattttatccagGGCAAAGATAAAACAGCCGAAGAGAGAAGGATTGCAATCTGCATCTTTGATGATGTTGCAGAGCAATGTCGTGAAGCGGCTCTTAA
gcttgac putative branch site (score: 4)
ttttatcc putative PPT
atcattcatttttaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccattttttgctgtgtattgttttttccaatttttcaatgttgaattctgtgaagcagcttgacttgcagcatcattcatttttaaatgattttatccagGGCAAAGATAAAACAGCCGAAGAGAGAAGGATTGCAATCTGCATCTTTGATGATGTTGCAGAGCAATGTCGTGAAGCGGCTCTTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
ccatttt
- - - -ttgctgt
- - - - - - - - - - - - - - - - - -caatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - tgaagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcagca