Sequence
atgc intronic sequence ATGC exonic sequencegtaaggctattcaccaacttttctcccttgcatgtcccaatatacggaaaatcttgtgaactgattgtatttattttatatattagTTTGAGGCCTTGGCTTTTGGAAGCACGGCAATGTGTGGAAAAGCTACCTTCTGGTATTGGTTCATTGCTGCTGTCCCATTTTACTGCGCAACCTGGGAAC
Basic information
species | Oryza sativa |
transcript | LOC_Os02g02750.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g02750.4 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G466281_T02 (Zea mays), 3'ss of exon 6
gtaaggctattcaccaacttttctcccttgcatgtcccaatatacggaaaatcttgtgaactgattgtatttattttatatattagTTTGAGGCCTTGGCTTTTGGAAGCACGGCAATGTGTGGAAAAGCTACCTTCTGGTATTGGTTCATTGCTGCTGTCCCATTTTACTGCGCAACCTGGGAAC
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gtaagaccacctgtcaatattttttattt-caagtgcaatgattttcaagtcgttgtgagct-----cattttttttatatactagTTTGAATCCTTGGCTTTTGGAAGCACGGCGATGTGTGGAAAGGCTACCTTCTGGTTTTGGTTCATTTCAGCTGTCCCATTTTACTTCGCAACCTGGGAAC
upper sequence: LOC_Os02g02750.4 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA12G08720.1 (Glycine max), 3'ss of exon 7
gtaaggctattcaccaacttttctcccttgcatgtcccaatatacggaaaatcttgtgaactgattgtatttattttatatattagTTTGAGGCCTTGGCTTTTGGAAGCACGGCAATGTGTGGAAAAGCTACCTTCTGGTATTGGTTCATTGCTGCTGTCCCATTTTACTGCGCAACCTGGGAAC
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gtatgtctctt-gttgctttggctattatttttaaatcattg-aaagagaatagagacagtcatctatgataacttctttt--cagTTTGAAGCATTGGCTTTTGGGAGCACAGCCATGTGTGGAAGAACTACTTTCTGGTGGTGGTTAATATCTGCAATTACATTTTATGGTGCAACCTGGGAGC
upper sequence: LOC_Os02g02750.4 (Oryza sativa), 3'ss of exon 6
lower sequence: AT1G13560.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaaggctattcaccaacttttctcccttgcatgtcccaatatacggaaaatcttgtgaactgattgtatttattttat----atattagTTTGAGGCCTTGGCTTTTGGAAGCACGGCAATGTGTGGAAAAGCTACCTTCTGGTATTGGTTCATTGCTGCTGTCCCATTTTACTGCGCAACCTGGGAAC
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gtatg-ctatt-atcaatcctttaatctttc-ttttttaattcagtactcgtcttg-gagtcgattatgaaggttttaccctaaaaacagTTTGAAGCCATGGCATTTGGAAGCACTGCAATGTGTGGAAGAGATACTTTCTGGTTCTGGGTTATTTCAGCTATTCCATTTTATGGAGCTACATGGGAACMapped 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|2431249|gb|C73669.1|C73669EST: CGGATGTGATGCGCTTGCATGTGCT TTTGAGGCCTTGGCTTTTGGAAGCACGGCAATGTGTGGAAAAGCTACCTTC
genomic: CGGATGTGATGCGCTTGCATGTGCTgtaaggctat ... tatatattagTTTGAGGCCTTGGCTTTTGGAAGCACGGCAATGTGTGGAAAAGCTACCTTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgtcccaatatacggaaaatcttgtgaactgattgtatttattttatatattagTTTGAGGCCTTGGCTTTTGGAAGCACGGCAATGTGTGGAAAAGCTACCTTCTGGTATTGGTTCATTGCTGCTGTCCCATTTTACTGCGCAACCTGGGAAC
aactgat putative branch site (score: 3)
tttatttt putative PPT
tgaactgattgtattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggctattcaccaacttttctcccttgcatgtcccaatatacggaaaatcttgtgaactgattgtatttattttatatattagTTTGAGGCCTTGGCTTTTGGAAGCACGGCAATGTGTGGAAAAGCTACCTTCTGGTATTGGTTCATTGCTGCTGTCCCATTTTACTGCGCAACCTGGGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT