Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttcactattaatgctacacatgtattgggaaactggcttgtgttgtaatggtctaagatccatacatcttccaaatgtcatccatgacatgaaatcttgggagcccaggagtggattatatcttaattgtttgccatgtgtctgtctgaagtgattattctactcttgcagGTATCAGAAGCGGGTCTCAAACATAATAGATGATGTTCTTGAGTGGTCACCAAGATTGGCTTTGTCTGGAATGATGGAGAAGCAGCAACCAGTAGTTGAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv06s0004g02280.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os02g23890.2 (Oryza sativa), 3'ss of exon 5
gtaagtttcactattaatgctacacatgtattgggaaactggcttgtgttgtaatggtctaagatccataca-tcttccaaatgtcatccatgacatgaaatcttgggagcccaggagtggattatatcttaattgtttgccatgtgtctgtctgaagtgattattctactcttgcagGTATCAGAAGCGGGTCTCAAACATAATAGATGATGTTCTTGAGTGGTCACCAAGATTGGCTTTGTCTGGAATGATGGAGAAGCA-GCAACCAGTAGTTGAT
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----------------------------------------------------------------tgcacggagtgtgctgaagcttgtgtgcaa-atgatatgtt-----ctccattctatatcatattctatcagttgagtaatcatttctctt------ttttcctgttact--agGTACCAGAAGAAGGTTTCGAACATAATTGATGATGTTCTTGAGTGGTCTCCAAAGTTAGCTTTGTCTGGGATGATGGAAAAACATACTGGGACTAATGCA-
upper sequence: Vv06s0004g02280.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G45020.1 (Glycine max), 3'ss of exon 4
gtaagtttcactattaatgctacacatgtattgggaaactggcttgtgttgtaatggtctaag---atccatacatcttccaaatgtcatccatgacatgaaatcttgggagcccaggagtggattatatcttaattgtttgccatgtgtctgtctgaagtgattattctactcttgcagGTATCAGAAGCGGGTCTCAAACATAATAGATGATGTTCTTGAGTGGTCACCAAGATTGGCTTTGTCTGGAATGATGGAGAAGCAGCAACCAGTAGTTGAT
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-------------------------------------gcaagtcctaaatatagtggatggaatttatccatccattttcagcttaaattcctttctagttggatctataaacccataaagggaa--------aactgtttgtagttggtttttctaactgttacatgttgct-ttgcagGTACCAGAAGAGGGTATCTAACATCATTGATGATGTTCTTGAATGGTCTCCGACTCTAGCCTTGTCTGGGATGATGGATAAGCAACAAAATGTGGCTAAT
upper sequence: Vv06s0004g02280.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA18G07900.1 (Glycine max), 3'ss of exon 4
gtaagtttcactattaatgctacacatgtattgggaaactggcttgtgttgtaatggtctaagatccatacatcttccaaatgtcatccatgacatgaaatcttgggagcccaggagtggattatatcttaattgtttgccatgtgtctgtctgaagtgattattctactcttgcagGTATCAGAAGCGGGTCTCAAACATAATAGATGATGTTCTTGAGTGGTCACCAAGATTGGCTTTGTCTGGAATGATGGAGAAGCAGCAACCAGTAGTTGAT
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gtaagtc-catagttgatgaaatttatcctttc----actttcttgc-taagaataatcatatgctcaaac-tctgcttaatttcctttctagttgga---tctataaacccataaagggaaaac-tgtttgtagtttgtctt---tctaactgttacaac-atgttgct-ttgcagGTACCAGAAGAGGGTATCTAACATCATTGATGATGTTCTTGAATGGTCTCCGACTTTAGCCTTGTCTGGGAGGATGGAAAAGCAACAAAATGTGGCTAATMapped 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|37190643|gb|CF609992.1|CF609992EST: TTTATATTGTTGCTGAGGCACCATGCCCCTGATGAAGCTGCAAGAGCCAG GTATCAGAAGCGGGTCTCAAACATAATAGATGATGTTCTTGAGTGGTCACC
genomic: TTTATATTGTTGCTGAGGCACCATGCCCCTGATGAAGCTGCAAGAGCCAGgtaagtttca ... actcttgcagGTATCAGAAGCGGGTCTCAAACATAATAGATGATGTTCTTGAGTGGTCACC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatatcttaattgtttgccatgtgtctgtctgaagtgattattctactcttgcagGTATCAGAAGCGGGTCTCAAACATAATAGATGATGTTCTTGAGTGGTCACCAAGATTGGCTTTGTCTGGAATGATGGAGAAGCAGCAACCAGTAGTTGAT
tcttaat putative branch site (score: 3)
ttctactctt putative PPT
ttaattgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtttcactattaatgctacacatgtattgggaaactggcttgtgttgtaatggtctaagatccatacatcttccaaatgtcatccatgacatgaaatcttgggagcccaggagtggattatatcttaattgtttgccatgtgtctgtctgaagtgattattctactcttgcagGTATCAGAAGCGGGTCTCAAACATAATAGATGATGTTCTTGAGTGGTCACCAAGATTGGCTTTGTCTGGAATGATGGAGAAGCAGCAACCAGTAGTTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC