Sequence
atgc intronic sequence ATGC exonic sequence...atataactgcataaactatcaagcttttcgctgttttgattgtatataatctaatcttgtgaaatgatttcataaagttagtggttacttcatttttcagAATTCCTAGAACAATTGGGGTAGCAATTCCAATGAAAGCAACTTTCTTCATATCTTACATAATGGTTGATGGATGGGCTGGCATAGCAGCAGAGATTTTA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv10s0116g00940.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os01g35050.3 (Oryza sativa), 3'ss of exon 9
-ata-taactgcataaactatcaagcttttcgctgttttgattgtatataatctaatcttgtgaaatgatttcataaagttagtggttacttcatttttcagAATTCCTAGAACAATTGGGGTAGCAATTCCAATGAAAGCAACTTTCTTCATATCTTACATAATGGTTGATGGATGGGCTGGCATAGCAGCAGAGATTTTA
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catgctcttcatttgtgctacaatttcctattgtatttcctttctttttcgaagaaactcttatactccttttcaactgtacttatttgcctc--tttgcagAATACCAAGGACAATTGGTGAAGCAATTCCAATGAAAGCAACCTTTTTTATAACATATGTAATGGTTGATGGTTGGGCTGGGGTAGCTGGTGAAATTTTA
upper sequence: Vv10s0116g00940.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA07G39320.1 (Glycine max), 3'ss of exon 9
---atataactgca-taaactatcaagcttttcgctgttttgattgtatataatcta-atcttgtgaa-atgatttcataaagttagtggttacttcatttttcagAATTCCTAGAACAATTGGGGTAGCAATTCCAATGAAAGCAACTTTCTTCATATCTTACATAATGGTTGATGGATGGGCTGGCATAGCAGCAGAGATTTTA
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actttatgattttggctatttacgaaccatgatgttagtgctcttgtct-taatttacaccgtgttaatatgatta---agaattctttttatattcatgt--cagATATCCTATTACAATTGGCACTGCAATTCCTTTGAAAGCAAGTTTCTTCATCACTTATATAATGGTTGATGGATGGGCTGGTATAGCTGCAGAGGTTTTG
upper sequence: Vv10s0116g00940.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA17G01400.1 (Glycine max), 3'ss of exon 8
---atataactgca-taaactatcaagcttttcgctgttttgattgtatataatcta-atcttgtgaa-atgatttcataaagttagtggttacttcatttttcagAATTCCTAGAACAATTGGGGTAGCAATTCCAATGAAAGCAACTTTCTTCATATCTTACATAATGGTTGATGGATGGGCTGGCATAGCAGCAGAGATTTTA
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actttttaattttagctatttacgaaccatgatgttagtgctcttgtct-taatttacaccatgttaatatgatta---agaattctttttatattcatgt--cagATATCCCATAACAATTGGCACTGCAATTCCTTTGAAAGCAAGTTTCTTCATCACTTATATAATGGTTGATGGATGGGCTGGTATAGCTGCAGAGGTTTTG
upper sequence: Vv10s0116g00940.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA20G16230.2 (Glycine max), 3'ss of exon 4
atataactgcataaactatcaagcttttcgctgttttgatt--gtatataatctaatcttgtgaaatgatttcataaagttagtggttacttca-----tttttcagAATTCCTAGAACAATTGGGGTAGCAATTCCAATGAAAGCAACTTTCTTCATATCTTACATAATGGTTGATGGATGGGCTGGCATAGCAGCAGAGATTTTA
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-----tccttttaatcaacaatatttttaacattattgatcaagaatttgtctttaatttatgcaatg--ctgataaaattaagcactcttgtaatacttttggcagATATCCTGTAACAATTGGCACTGCTATTCCTTTAAAAGCAAGTTTTTTCATTACTTATATAATGGTTGATGGATGGGCCAGTATAGCTGCAGAGGTTTTG
upper sequence: Vv10s0116g00940.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA13G10490.1 (Glycine max), 3'ss of exon 9
atataactgcataaactatcaagcttttcgctgtt-ttgatt--gtatataatctaatcttgtgaaatgatttcataaagttagtggttacttca-----tttttcagAATTCCTAGAACAATTGGGGTAGCAATTCCAATGAAAGCAACTTTCTTCATATCTTACATAATGGTTGATGGATGGGCTGGCATAGCAGCAGAGATTTTA
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------tccttttaatcaacagtatatttaccattattgatcaagaatttgccttaaatttatgcaacg--tggataaaattaagcactcttgtaatacttttggcagATATCCTGTAACAATTGGCACTGCTATTCCTTTAAAAGCAAGTTTCTTCATTACTTATATAATGATTGATGGATGGGCCAGTATAGCTGCAGAGGTTTTGMapped 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|110360195|gb|EC922969.1|EC922969EST: GGAAGTGCACTTGAACAACTAAATACCTTTATGAAGCAGTCGCCAAATCA AATTCCTAGAACAATTGGGGTAGCAATTCCAATGAAAGCAACTTTCTTCAT
genomic: GGAAGTGCACTTGAACAACTAAATACCTTTATGAAGCAGTCGCCAAATCAgtaagttatc ... catttttcagAATTCCTAGAACAATTGGGGTAGCAATTCCAATGAAAGCAACTTTCTTCAT
EST:
gi|351028550|gb|FQ444831.1|FQ444831EST: GGAAGTGCACTTGAACAACTAAATACCTTTATGAAGCAGTCGCCAAATCA AATTCCTAGAACAATTGGGGTAGCAATTCCAATGAAAGCAACTTTCTTCAT
genomic: GGAAGTGCACTTGAACAACTAAATACCTTTATGAAGCAGTCGCCAAATCAgtaagttatc ... catttttcagAATTCCTAGAACAATTGGGGTAGCAATTCCAATGAAAGCAACTTTCTTCAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataatctaatcttgtgaaatgatttcataaagttagtggttacttcatttttcagAATTCCTAGAACAATTGGGGTAGCAATTCCAATGAAAGCAACTTTCTTCATATCTTACATAATGGTTGATGGATGGGCTGGCATAGCAGCAGAGATTTTA
atctaat putative branch site (score: 3)
ttacttcatttttc putative PPT
aaatgatttcataaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atataactgcataaactatcaagcttttcgctgttttgattgtatataatctaatcttgtgaaatgatttcataaagttagtggttacttcatttttcagAATTCCTAGAACAATTGGGGTAGCAATTCCAATGAAAGCAACTTTCTTCATATCTTACATAATGGTTGATGGATGGGCTGGCATAGCAGCAGAGATTTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - -cataaac
- - - - - - - - - tcaagct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cataaag