Sequence
atgc intronic sequence ATGC exonic sequence...cacaaactaatcaccaattaagctagctagctagccaaaatgataatcttgcttgcatgcgctaatggtgtgtgtgatgatggtggtgtcacgcatgcagGCACGCAGGAGGAGGCGGCGGAGGCGTACGACATCGCGGCGATCAAGTTCCGGGGGCTCAACGCCGTCACCAACTTCGACATGAGCCGCTACGACGTCAA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g67410.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g67410.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G141638_T01 (Zea mays), 3'ss of exon 7
cacaaactaat-caccaattaagctagctagctagccaaaatgataatctt--gcttgcatgcgctaatggtgtgtgtgatgatggtggtgtcacgcatgcagGCACGCAGGAGGAGGCGGCGGAGGCGTACGACATCGCGGCGATCAAGTTCCGGGGGCTCAACGCCGTCACCAACTTCGACATGAGCCGCTACGACGTCAA
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catgcatgcatgcatgcaccgtgc--acgacgaaagcgaaacgctcgttctcggaatatttgaactgacgaagc-cgagtgcaaccttccgtcgtggatgcagGCACCCAGGAGGAGGCAGCGGAGGCGTACGACATCGCGGCGATCAAGTTCCGCGGCCTCAACGCCGTCACCAACTTCGACATGAGCCGCTACGACGTGAA
upper sequence: LOC_Os01g67410.1 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S131_139V6.1 (Physcomitrella patens), 3'ss of exon 5
------------------------------------------------------------------------------------------------cacaaac-taatcaccaattaagctagctagcta-gccaaaatgataatcttgcttgcatgcgctaa-tggtgtgtgtgatgatggtggtgtcacgc-atgcagGCACGCAGGAGGAGGCGGCGGAGGCGTACGACATCGCGGCGATCAAGTTCCGGGGGCTCAACGCCGTCACCAACTTCGACATGAGCCGCTACGACGTCAA
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gtgagtgccggtttcacatgaatttgtaaacattagtggattaccctcgctgcaaatcctggtcgtttctcctgataggacttctgatatcgattccggagacatcagcatattctgggtctcgttgcaatgttgaaaggatttcgcagggtgcccatgttacctaatggttaaaatga-actggctttgtatgactcagGCACACAAGAGGAAGCAGCAGAGGCCTACGACATTGCCGCGATAAAATTCCGTGGAATCAATGCCGTCACAAACTTCGACATGTCTCGTTACAATGCTGC
upper sequence: LOC_Os01g67410.1 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S66_282V6.1 (Physcomitrella patens), 3'ss of exon 6
-----------------------------------------------cacaaactaatcaccaattaagctagctagctagccaaaatgataatcttgcttgcatgcgctaatggtgtgtgtgatgatggtggtgtcacgcatgcagGCACGCAGGAGGAGGCGGCGGAGGCGTACGACATCGCGGCGATCAAGTTCCGGGGGCTCAACGCCGTCACCAACTTCGACATGAGCCGCTACGACGTCAA
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gtgagtggcagtttgacttgggggtttgcagaggaggagggggtttgtatgtgttgttgggatgtggagggagatgtgcagttgcag---cagacgtggggatctgatccaacggtcggcgtggcg-tgggtgtgt-gtgagt-cagGCACGCAGGAGGAAGCAGCAGAGGCATACGACCTGGCGGCGATAAAATTCCGTGGAATCAACGCCGTGACAAACTTCGACATCTCTCGGTACGACGCCGGMapped 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|86850648|gb|CI309460.1|CI309460EST: AAGGATAGGAAGAGTTGCAGGGAACAAGGACCTCTACTTGGGCACCTTCA GCACGCAGGAGGAGGCGGCGGAGGCGTACGACATCGCGGCGATCAAGTTCC
genomic: AAGGATAGGAAGAGTTGCAGGGAACAAGGACCTCTACTTGGGCACCTTCAgtaagtacaa ... acgcatgcagGCACGCAGGAGGAGGCGGCGGAGGCGTACGACATCGCGGCGATCAAGTTCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcttgcttgcatgcgctaatggtgtgtgtgatgatggtggtgtcacgcatgcagGCACGCAGGAGGAGGCGGCGGAGGCGTACGACATCGCGGCGATCAAGTTCCGGGGGCTCAACGCCGTCACCAACTTCGACATGAGCCGCTACGACGTCAA
cgctaat putative branch site (score: 3)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cacaaactaatcaccaattaagctagctagctagccaaaatgataatcttgcttgcatgcgctaatggtgtgtgtgatgatggtggtgtcacgcatgcagGCACGCAGGAGGAGGCGGCGGAGGCGTACGACATCGCGGCGATCAAGTTCCGGGGGCTCAACGCCGTCACCAACTTCGACATGAGCCGCTACGACGTCAA
- -aaactaa
- - - - - - - - - - - - - - - - -gccaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - gcatgcg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtggtg