Sequence
atgc intronic sequence ATGC exonic sequence...aaggggattaggttcctctcccttttgatattttgaaaatcttgggggagtcttttattttgcctgatactcagagattttgcttttgtgattcttgcagCTTTATTCACAGCCAGGCCTGCAGCTACTCTGGAAATGTTCCCTTCATGGCCAATGAGATTCCAGCAAACCCAAAGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv06s0080g00360.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os05g37170.8 (Oryza sativa), 3'ss of exon 1
-----------------------aaggggattaggt-tcctctcccttttgatattttgaaaa--tcttgggggagtcttttattttgcctgatactcagagattttgcttttgtgattcttgcagCTTTAT---TCACAGCCAGGCCTGCAGCTACTCTGGAAATGTTCCCTTCATGGCCAATGAGATTCCAGCAA-ACCCAAAGA--
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gtgtgatcccacaactcccctacatcttgcttctgtcttctttctttgtctacatttttgcaacctcttgaggaaaagagagcgattgacaaggcctttaa--ttccatttgtatgtatgcagcagCAGGATATCTTGCAGCTAGGCCCCC---CACACTGGAAATCTTCCCTTCATGGCCAATGAGTCATCTACAGGAGCCATACAGT
upper sequence: Vv06s0080g00360.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os05g37170.3 (Oryza sativa), 3'ss of exon 2
--aaggggattaggt-tcctctcccttttgatattttgaaaa--tcttgggggagtcttttattttgcctgatactcagagattttgcttttgtgattcttgcagCTTTAT---TCACAGCCAGGCCTGCAGCTACTCTGGAAATGTTCCCTTCATGGCCAATGAGATTCCAGCAA-ACCCAAAGA--
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acatcttgcttctgtcttctttctttgtctacatttttgcaacctcttgaggaaaagagagcgattgacaaggcctttaa--ttccatttgtatgtatgcagCAGCAGGATATCTTGCAGCTAGGCCCCC---CACACTGGAAATCTTCCCTTCATGGCCAATGAGTCATCTACAGGAGCCATACAGT
upper sequence: Vv06s0080g00360.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os05g37170.5 (Oryza sativa), 3'ss of exon 3
aaggggattaggttcctctcccttttgatattttgaaaa--tcttgggggagtcttttattttgcctgatactcagagattttgcttttgtgattcttgcagCTTTAT---TCACAGCCAGGCCTGCAGCTACTCTGGAAATGTTCCCTTCATGGCCAATGAGATTCCAGCAA-ACCCAAAGA--
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tcttgcttctgtcttctttctttgtctacatttttgcaacctcttgaggaaaagagagcgattgacaaggcctttaa--ttccatttgtatgtatgcagcagCAGGATATCTTGCAGCTAGGCCCCC---CACACTGGAAATCTTCCCTTCATGGCCAATGAGTCATCTACAGGAGCCATACAGT
upper sequence: Vv06s0080g00360.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA12G30990.1 (Glycine max), 3'ss of exon 3
--aaggggattaggttcctctcccttttgatattttgaaaatcttgggggagtcttttattttgcctgatactc--agagattttgcttttgtgattcttgcagCTTTATTCACAGCCAGGCCTGCAGCTACTCTGGAAATGTTCCCTTCATGGCCAATGAGATTCCAGCAAACCCAAAGA
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ctgtcataattgaaagtcctcatggtcttttattttggtaatcttca---actccttcaacttgg-tgatcctcttacagattttgcttttgtgattcttgcagCTTTATTCACAGCCAGACCTGCAGCTACACTGGAAATGTTCCCTTCATGGCCAATGAGATTCCAGCAAACCCCAAGA
upper sequence: Vv06s0080g00360.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA12G09430.3 (Glycine max), 3'ss of exon 3
---aaggggattaggttcctctcccttttgatatt-ttgaaaatcttgggggagtcttttattttgcctgatactcagagattttgcttttgtgattcttgcagCTTTATTCACAGCCAGGCCTGCAGCTACTCTGGAAATGTTCCCTTCATGGCCAATGAGATTCCAGCAAACCCAAAGA
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aaaaggaggataaggttcctccaccttttcatatgattgatgttcataaag----cctttatttttggtgatcctctgagattttccttttgtgattgtagcagCTTTATTCACAGGCAGGCCTTCGGCCACACTGGAAATGTTCCCCTCATGGCCAATGAGATTCCAGCAAACCTCAAGA
upper sequence: Vv06s0080g00360.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA12G09430.2 (Glycine max), 3'ss of exon 2
------aaggggattaggttcctctcccttttgatatt-ttgaaaatcttgggggagtcttttattttgcctgatactcagagattttgcttttgtgattcttgcagCTTTATTCACAGCCAGGCCTGCAGCTACTCTGGAAATGTTCCCTTCATGGCCAATGAGATTCCAGCAAACCCAAAGA
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ttgaaaaggaggataaggttcctccaccttttcatatgattgatgttcataaag----cctttatttttggtgatcctctgagattttccttttgtgattgtagCAGCTTTATTCACAGGCAGGCCTTCGGCCACACTGGAAATGTTCCCCTCATGGCCAATGAGATTCCAGCAAACCTCAAGAMapped 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|161715403|gb|FC065830.1|FC065830EST: AGCAATTGTGCTGCAAGGTGTTAAGATTAGAAATGATGAAGCTAAAACTT CTTTATTCACAGCCAGGCCTGCAGCTACTCTGGAAATGTTCCCTTCATGGC
genomic: AGCAATTGTGCTGCAAGGTGTTAAGATTAGAAATGATGAAGCTAAAACTTgtatgcttct ... attcttgcagCTTTATTCACAGCCAGGCCTGCAGCTACTCTGGAAATGTTCCCTTCATGGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gggagtcttttattttgcctgatactcagagattttgcttttgtgattcttgcagCTTTATTCACAGCCAGGCCTGCAGCTACTCTGGAAATGTTCCCTTCATGGCCAATGAGATTCCAGCAAACCCAAAGA
gcctgat putative branch site (score: 4)
ttcttgc putative PPT
tcttttatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaggggattaggttcctctcccttttgatattttgaaaatcttgggggagtcttttattttgcctgatactcagagattttgcttttgtgattcttgcagCTTTATTCACAGCCAGGCCTGCAGCTACTCTGGAAATGTTCCCTTCATGGCCAATGAGATTCCAGCAAACCCAAAGA
- - - - - - - -ctctccc
- - - - - - - - - - - - - - - - - gaaaatc
- - - - - - - - - - - - - - - - - - - - - -gggggag