Sequence
atgc intronic sequence ATGC exonic sequence...aggcatgcatgcagtactatcttttgttagtattgatgataaagactttgaaatgtaatgacgtattaacatgcaaagattcaaccttgaaactgtgcagTATCTGGATGAGAACAAGCAGCTGATCCTGGCCATCCTTGACAACCAGAACAATGGGAAGGTGGAAGAGTGCGCTCG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g52320.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g52320.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G180246_T01 (Zea mays), 3'ss of exon 1
aggcatgcatgcagtactatcttttgttagtattgatgataaagactttgaaatgtaatg--acgtattaacatgcaaagattcaaccttgaaactgtgcagTATCTGGATGAGAACAAGCAGCTGATCCTGGCCATCCTTGACAACCAGAACAATGGGAAGGTGGAAGAGTGCGCTCG
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--gggtgagagaaagtaaatgctcagtcaacggtggatacaaagcgtctacactggaatgtgacatacttaacaatacgtttttgatcatgaaactgtgcagTACCTGGACGAGAACAAGCAGCTGATCCTGGCCATCCTCGACAACCAGAACAATGGCAAGGCGGAGGAGTGCGAACG
upper sequence: LOC_Os03g52320.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S107_190V6.1 (Physcomitrella patens), 3'ss of exon 1
aggcatgcatgcagtactatcttttgttagtattgatgataaagactttgaa--atgtaatgacgtatt---aacatgcaaagattcaaccttgaaactg---tgcagTATCTGGATGAGAACAAGCAGCTGATCCTGGCCATCCTTGACAACCAGAACAATGGGAAGGTGGAAGAGTGCGCTCG
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------gtctactctatcttttttattt--ttctgaaaagaagcaccttgtaggacacaatcccccactttgacctttttctgattgtgtgtcttaattgacgtgcagTATCTGGACGAGAACAAGCAGCTTATCCTCGCGATTCTTGACAATCAAAACCTTGGAAAGCTGAACGAATGCGCTAT
upper sequence: LOC_Os03g52320.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ18273 (Selaginella moellendorffii), 3'ss of exon 1
-------------aggcatgcatgcagtactatcttttgttagtattgatgataaagactttgaaatgtaatgacgtattaacatgcaaagattcaaccttgaaactgtgcagTATCTGGATGAGAACAAGCAGCTGATCCTGGCCATCCTTGACAACCAGAACAATGGGAAGGTGGAAGAGTGCGCTCG
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tttgggttttaggagaggagcataaagtg--atctctcac-agttttg----taaggcc----aaagctcacttttttttgctcttttctcttttggatttggtgct--gcagTACTTGGACGAGAACAAGCAGCTCATACTTGCAATCCTTGACAACCAGAACCTCGGCAAGCTTAATGAATGCGCGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttgaaatgtaatgacgtattaacatgcaaagattcaaccttgaaactgtgcagTATCTGGATGAGAACAAGCAGCTGATCCTGGCCATCCTTGACAACCAGAACAATGGGAAGGTGGAAGAGTGCGCTCG
tattaac putative branch site (score: 1)
aaatgtaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aggcatgcatgcagtactatcttttgttagtattgatgataaagactttgaaatgtaatgacgtattaacatgcaaagattcaaccttgaaactgtgcagTATCTGGATGAGAACAAGCAGCTGATCCTGGCCATCCTTGACAACCAGAACAATGGGAAGGTGGAAGAGTGCGCTCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - -tgcatgc
- - - - - - - - - - cttttgt
- - - - - - - - - - - - - - - - ttgatga
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgtaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acatgca