Sequence
atgc intronic sequence ATGC exonic sequencegttggtcattggttttattatagttcttgctatgagcaacatatagctatatggaagcatgctcacattgtcaattgtgaagttccactcattgattgtccaattgaactagaattcgttttgtgcaatcctgttcgtctaatttgaaaaaaaaacatttatttttcctagGTCATGGAAAAGCTCGTAGACATTGTGCATTTCTTACATTTGGAGATCCATAATGCCTTTGGGCGCTCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g65330.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g65330.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G046846_T01 (Zea mays), 3'ss of exon 7
gttggtcattggttttattatagttcttgctatgagcaacatatagctatatggaagcatgctcacattgtcaattgtgaagttccactcattgattgtccaattgaactagaattcgttttgtgcaatcctgttcgtctaatttgaaaaaaaaacatttatttttcctagGTCATGGAAAAGCTCGTAGACATTGTGCATTTCTTACATTTGGAGATCCATAATGCCTTTGGGCGCTCAG
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-----------------------------------------------------cggttttgaccatataatagactatgcactgtcagcaacttgtagctcta-------ggaaaacatt-----caatcctgttgattcaa------aaaataatatttgtttctcctagGTCATGGGAAAGCTTGTGGACATTGTGCACTTCTTACATTTGGAGATCCATAATGTATTTGGGCGTTCAG
upper sequence: LOC_Os01g65330.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G148773_T02 (Zea mays), 3'ss of exon 6
gttggtcattggttttattatagttcttgctatgagcaacatatagctatatggaagcatgctcacattgtcaattgtgaagttccactcattgattgtccaattgaactagaattcgttttgtgcaatcctgttcgtctaatttgaaaaaaaaacatttatttttcctagGTCATGGAAAAGCTCGTAGACATTGTGCATTTCTTACATTTGGAGATCCATAATGCCTTTGGGCGCTCAG
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--------------------------------------------------------tttttaccatataataaacggtgtgctgtcagcaacctgatgctcta-------ggaatgcatc-----caatcctattctactatttc---aaaaaaatatttatttctcctagGTCATGGGAAAGCTTGTGGACATTGTGCACTTCTTACATTTGGAGATCCATAATGCATTTGGGCTTTCAG
upper sequence: LOC_Os01g65330.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA06G16680.1 (Glycine max), 3'ss of exon 5
gttggtcattggttttattatagttcttgctatgagcaacatatagctatatggaagcatgctcacattgtcaattgtgaagttccactcattgattgtccaattgaactagaattcgttttgtgcaatcctgttcgtctaatttgaaaaaaaaacatttatttttcctagGTCATGGAAAAGCTCGTAGACATTGTGCATTTCTTACATTTGGAGATCCATAATGCCTTTGGGCGCTCAG
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-------------------------------------------------------------------tcctctttcctaacaatctaacgtagagaaatcagttttatttaacattaatggagagc--tgagaaaagttgaatttaattcataatc--ttatggattacagGTTATGGAGAAGCTTGTAGACATTGTCCATTTTTTGCATTTGGAGATAAGCAATGCCTTTGGCAATGCAG
upper sequence: LOC_Os01g65330.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv18s0076g00260.t01 (Vitis vinifera), 3'ss of exon 6
gttggtcattggttttattatagttcttgctatgagcaacatatagctatatggaagcatgctcacat-tgtcaattgtgaagttccactcattgattgtccaattgaactagaattcgttttgtgcaatcctgttcgtctaatttgaaaaaaaaacatttatttttcctagGTCATGGAAAAGCTCGTAGACATTGTGCATTTCTTACATTTGGAGATCCATAATGCCTTTGGGCGCTCAG
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--------------gtagca-agtcagtgct----gctttatgtagctcctttttaattttttttaatgtgcataagggaaagttggaaagattg--tatatagtt-acttaga----gctttatgaa----tgttgatttaacctta-----------ttgtctttattagGTAATGGAGAAGCTTGTAGACATTGTGCATTTCTTACATTTGGAGATACATGATGCCTTTGCTACTGCTGMapped 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|29680203|gb|CB676478.1|CB676478EST: ATGTTAAAAGCTTGCAGAAAAAGTCTCTCTGGTCGAAGAATTTGGAAGAG GTCATGGAAAAGCTCGTAGACATTGTGCATTTCTTACATTTGGAGATCCAT
genomic: ATGTTAAAAGCTTGCAGAAAAAGTCTCTCTGGTCGAAGAATTTGGAAGAGgttggtcatt ... tttttcctagGTCATGGAAAAGCTCGTAGACATTGTGCATTTCTTACATTTGGAGATCCAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgttttgtgcaatcctgttcgtctaatttgaaaaaaaaacatttatttttcctagGTCATGGAAAAGCTCGTAGACATTGTGCATTTCTTACATTTGGAGATCCATAATGCCTTTGGGCGCTCAG
gtctaat putative branch site (score: 3)
catttatttttcct putative PPT
taatttgaaaaaaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttggtcattggttttattatagttcttgctatgagcaacatatagctatatggaagcatgctcacattgtcaattgtgaagttccactcattgattgtccaattgaactagaattcgttttgtgcaatcctgttcgtctaatttgaaaaaaaaacatttatttttcctagGTCATGGAAAAGCTCGTAGACATTGTGCATTTCTTACATTTGGAGATCCATAATGCCTTTGGGCGCTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC