Sequence
atgc intronic sequence ATGC exonic sequence...agtacgtagtacgtgccatattaggtttagcgcattataagtatgccaactgaaattaacctaagcagcttattaatcaactaattattactgcgtgcagGGAGGTGTCCGAGGAGTACGGGAGAGAGGTGATCAAGCTGTGCGAGCGGCTGATGAGGTTGCTGTCAGCGAGCCTGGGGCTGGACGAGACGCGGTTCCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g61610.3 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g61610.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G058024_T02 (Zea mays), 3'ss of exon 2
-agtacgtagtacgtgccatattaggtttagcgcattataagtatgccaactgaaattaacctaagcagcttattaatcaactaat---tattactgcgtgcagGGAGGTGTCCGAGGAGTACGGGAGAGAGGTGATCAAGCTGTGCGAGCGGCTGATGAGGTTGCTGTCAGCGAGCCTGGGGCTGGACGAGACGCGGTTCCAG
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tagtagaccttgt-tcctacactag-ctagctgcatgcaaag--tgccaaattggctggccgggctcgttgtgtatattgatgtgtgtgcattatattatacagGGATGTGTCGGAGGAGTACGGGCGCGAGGTGGTGCGGCTGTGCGAGCTGCTGATGCGGGTGCTGTCCGTGAGCCTAGGGCTGGACGAGGCGCACCTCCAG
upper sequence: LOC_Os01g61610.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G122280_T02 (Zea mays), 3'ss of exon 2
---agtacgta-gtacgtgccatattaggtttagcgcattataagtatgccaactgaaattaacctaagcagcttattaatcaactaattattactgcgtgcagGGAGGTGTCCGAGGAGTACGGGAGAGAGGTGATCAAGCTGTGCGAGCGGCTGATGAGGTTGCTGTCAGCGAGCCTGGGGCTGGACGAGACGCGGTTCCAG
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actgacatgcacgtacgtacaacagtatagctagta-gctagcggctcatgtactgta-ttgatgtgtatacatcat--gtgcgtgtatatatgctatatacagGGAGGTGTCCGAGGAGTACGGACGCGAGGTGGTGCGGCTGTGCGAGCTGCTGATGCGGGTGATGTCAGTGAGCCTAGGGCTGGACGAGGCGCACCTTCAGMapped 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|58689249|gb|CK077936.1|CK077936EST: GCCGCCAAGAGCCCGGCCAAATACTGGCCGGCCAATCCCGGCATCTGCAA GGAGGTGTCCGAGGAGTACGGGAGAGAGGTGATCAAGCTGTGCGAGCGGCT
genomic: GCCGCCAAGAGCCCGGCCAAATACTGGCCGGCCAATCCCGGCATCTGCAAgtaagcacta ... ctgcgtgcagGGAGGTGTCCGAGGAGTACGGGAGAGAGGTGATCAAGCTGTGCGAGCGGCT
EST:
gi|58607588|gb|CK035621.1|CK035621EST: GCCGCCAAGAGCCCGGCCAAATACTGGCCGGCCAATCCCGGCATCTGCAA GGAGGTGTCCGAGGAGTACGGGAGAGAGGTGATCAAGCTGTGCGAGCGGCT
genomic: GCCGCCAAGAGCCCGGCCAAATACTGGCCGGCCAATCCCGGCATCTGCAAgtaagcacta ... ctgcgtgcagGGAGGTGTCCGAGGAGTACGGGAGAGAGGTGATCAAGCTGTGCGAGCGGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccaactgaaattaacctaagcagcttattaatcaactaattattactgcgtgcagGGAGGTGTCCGAGGAGTACGGGAGAGAGGTGATCAAGCTGTGCGAGCGGCTGATGAGGTTGCTGTCAGCGAGCCTGGGGCTGGACGAGACGCGGTTCCAG
aactaat putative branch site (score: 2)
ttattaatcaactaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agtacgtagtacgtgccatattaggtttagcgcattataagtatgccaactgaaattaacctaagcagcttattaatcaactaattattactgcgtgcagGGAGGTGTCCGAGGAGTACGGGAGAGAGGTGATCAAGCTGTGCGAGCGGCTGATGAGGTTGCTGTCAGCGAGCCTGGGGCTGGACGAGACGCGGTTCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA