Sequence
atgc intronic sequence ATGC exonic sequencegtaaattttctcactattatcatgctgttggagagcagttgctactatgtgaggccattttttttcatttgtttcaagtcttagcacaaaactttgagcattcgtcattcggttacccatttattgaaaagcatgattagtagatgttcttctgatttgaccagGGCAAAGCATGTCTATGGATATGAAGTAGTTCCTGAAGCCATTGCAGATGCTAAAAAGAACGCTAAGCTGAATGGTATCAGCAATGCTACATTTGTTCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g09750.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g09750.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G115198_T01 (Zea mays), 3'ss of exon 6
gtaaattttctcactattatcatgctgttggagagcagttgctacta--tgtgaggccattttttttcatttgtttcaagtcttagcacaaaactttgagcattcgtcattcggttacccatttattgaaaagcatgattagtagatgttcttctgatttgaccagGGCAAAGCATGTCTATGGATATGAAGTAGTTCCTGAAGCCATTGCAGATGCTAAAAAGAACGCTAAGCTGAATGGTATCAGCAATGCTACATTTGTTCAG
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gtagttttttttcaggtgtacatattccgtgaga-cagatatttctggttgtgagagtataattgctttcttggtt--------aacataaacc------cattttctattacaata----ttttatggcaaccatttttagtaaacacttttctgcttggctcagGGCAAAGCACATTTATGGATATGAAGTTGTCCCTGAAGCCATTGAAGATGCGCGAAAGAATGCCAAGTTGAACGGTATCAACAATGCAACATTTGTTCAA
upper sequence: LOC_Os01g09750.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA15G02550.1 (Glycine max), 3'ss of exon 6
gtaaattttctcactattatcatgctgttggagagcagttgctactatgtgaggccattttttttcatttgtttcaagtcttagcacaaaactttgagcattcgtcattcggttacccatttattgaaaagcatgattagtagatgttcttctgattt-gaccagGGCAAAGCATGTCTATGGATATGAAGTAGTTCCTGAAGCCATTGCAGATGCTAAAAAGAACGCTAAGCTGAATGGTATCAGCAA-TGCTACATTTGTTCAG
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-------------------------------------------------------------------gtaatctttgatctccatctgg---ttttagtatt-----ttaggata---aactgtgaaacaatgagattaatttcttgtcttccaattttgaacagTGATAGACATGTTTATGGCTATGAAGTAGTTCCTCAAGCCATCACAGATGCTCATCTTAATGCCAAGATAAATGGAATAAAAAAATGCAACATTT------
upper sequence: LOC_Os01g09750.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA13G42890.1 (Glycine max), 3'ss of exon 7
gtaaattttctcactattatcatgctgttggagagcagttgctactatgtgaggccattttttttcatttgtttcaagtcttagcacaaaactttgagcattcgtcattcggttacccatttattgaaaagcatgattagtagatgttcttctgatt-tgaccagGGCAAAGCATGTCTATGGATATGAAGTAGTTCCTGAAGCCATTGCAGATGCTAAAAAGAACGCTAAGCTGAATGGTATCAGCAATGCTACATTTGTTCAG
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-------------------------------------------------------------------gtaatctttgatctccatctgg---ttttagtatt-----ttaggata---aactgtgaagcaatgagattaatttcttgtcttccaattctgaacagTGTTAGGCATGTTTATGGCTATGAAGTAGTTCCTCAAGCCATCACAGATGCTCGTCTTAATGCCAAGATAAATGGAATACAAAATGCAACATTTGTCCAGMapped 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|27548300|gb|CA766414.2|CA766414EST: CTTGACTTGTTCTGTGGAACCGGAACCATTGGTCTTACCCTTGCTAGAAG GGCAAAGCATGTCTATGGATATGAAGTAGTTCCTGAAGCCATTGCAGATGC
genomic: CTTGACTTGTTCTGTGGAACCGGAACCATTGGTCTTACCCTTGCTAGAAGgtaaattttc ... atttgaccagGGCAAAGCATGTCTATGGATATGAAGTAGTTCCTGAAGCCATTGCAGATGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cggttacccatttattgaaaagcatgattagtagatgttcttctgatttgaccagGGCAAAGCATGTCTATGGATATGAAGTAGTTCCTGAAGCCATTGCAGATGCTAAAAAGAACGCTAAGCTGAATGGTATCAGCAATGCTACATTTGTTCAG
ttctgat putative branch site (score: 3)
atttattgaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaattttctcactattatcatgctgttggagagcagttgctactatgtgaggccattttttttcatttgtttcaagtcttagcacaaaactttgagcattcgtcattcggttacccatttattgaaaagcatgattagtagatgttcttctgatttgaccagGGCAAAGCATGTCTATGGATATGAAGTAGTTCCTGAAGCCATTGCAGATGCTAAAAAGAACGCTAAGCTGAATGGTATCAGCAATGCTACATTTGTTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA