Sequence
atgc intronic sequence ATGC exonic sequence...ttttgttactctctggctactatataatcatatttgtcaaatttatttatttgtccctaatgaacttgagttgtgatctgaaattcaatgatccctccagCTTCATCTTCAAGAAGGTGGTCTCCATGCTGATATTAACGGAGATGGGGTTCTAGATCATGTCCAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv04s0023g02750.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os02g01070.1 (Oryza sativa), 3'ss of exon 8
------ttttgttactctctggctactatataatcatatttgtcaaatttatttatttgtccctaatgaacttgagttgtgatctgaaattcaatgatccctccagCTTCATCTTCAAGAAGGTGGTCTCCATGCTGATATTAACGGAGATGGGGTTCTAGATCATGTCCAG
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taaggaaatcataattcacgtgtgcgcata-atttacatgtctgtaatcccatcatacaacttttctgtctttgttttctgatttttttttccat-----ttccagCTTCATTTAACAGAAGGAGGCCTTCATGCAGATATTAATGGAGATGGGGTTCTAGACCATGTTCAG
upper sequence: Vv04s0023g02750.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA01G37580.1 (Glycine max), 3'ss of exon 10
ttttgttactctctggct--actatataatcatatttg---tcaaatttattta-tttgtccctaatgaacttgagttgtgatctgaaattcaatgatccctccagCTTCATCTTCAAGAAGGTGGTCTCCATGCTGATATTAACGGAGATGGGGTTCTAGATCATGTCCAG
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------tatcctgtggttgtactatttagccaaaattctatttaactccatttaattctttcacaaactttttcatgtctaatgtaatgacatttgtttatttcagCTTCATCTCCAGGAAGGTGGTCTACATGCTGATATTAATGGTGATGGAGTTCTAGATCATGTGCAG
upper sequence: Vv04s0023g02750.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA11G07720.1 (Glycine max), 3'ss of exon 10
ttttgttactctctggctactatataatcatatttgtcaaatttattta--tttgtccctaatgaacttgagttgtgatctgaaattcaatgatccctccagCTTCATCTTCAAGAAGGTGGTCTCCATGCTGATATTAACGGAGATGGGGTTCTAGATCATGTCCAG
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-cccgtgattgtactattcagcttaaattttatttagctccttcatttaattctttcattaactattatgtcttatgtaatgataaatt-tgtttatttcagTTTCATCTCCAGGAAGGTGGTCTACATGCTGATGTTAATGGTGATGGAGTTCTAGATCATGTGCAG
upper sequence: Vv04s0023g02750.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: PP1S11_162V6.1 (Physcomitrella patens), 3'ss of exon 10
---ttttgttactctctggctactatataatcatatttgtcaaatttatttatttgtccctaatgaacttgagttgtgatctgaaattcaatgatccctccagCTTCATCTTCAAGAAGGTGGTCTCCATGCTGATATTAACGGAGATGGGGTTCTAGATCATGTCCAG
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tcaactgggtactttc--gtaagcgtctcttc-tgtcagtgaaattttcaaaccacgtcgactttgtcctctcacatcacgcattattggtgcatttttgtagCTGTATCTACCCGAAGGAGGTCTTCATGCAGATATCAACGGCGATGGGGTTCTGGATCACGTCCAGMapped 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|110709284|gb|EE084611.1|EE084611EST: AGCTGTTCACTTGCCCACTGGTCGCACTATCTGTAAG CTTCATCTTCAAGAAGGTGGTCTCCATGCTGATATTAACGGAGATGGGGTT
genomic: AGCTGTTCACTTGCCCACTGGTCGCACTATCTGTAAGgtgaatatca ... atccctccagCTTCATCTTCAAGAAGGTGGTCTCCATGCTGATATTAACGGAGATGGGGTT
EST:
gi|33403432|gb|CF209059.1|CF209059EST: GGGAAGGAATAGAAGCTGTTCACTTGCCCACTGGTCGCACTATCTGTAAG CTTCATCTTCAAGAAGGTGGTCTCCATGCTGATATTAACGGAGATGGGGTT
genomic: GGGAAGGAATAGAAGCTGTTCACTTGCCCACTGGTCGCACTATCTGTAAGgtgaatatca ... atccctccagCTTCATCTTCAAGAAGGTGGTCTCCATGCTGATATTAACGGAGATGGGGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttatttgtccctaatgaacttgagttgtgatctgaaattcaatgatccctccagCTTCATCTTCAAGAAGGTGGTCTCCATGCTGATATTAACGGAGATGGGGTTCTAGATCATGTCCAG
ccctaat putative branch site (score: 3)
tccctcc putative PPT
aaattcaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttgttactctctggctactatataatcatatttgtcaaatttatttatttgtccctaatgaacttgagttgtgatctgaaattcaatgatccctccagCTTCATCTTCAAGAAGGTGGTCTCCATGCTGATATTAACGGAGATGGGGTTCTAGATCATGTCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - ctctggc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatgaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaattcaa