Sequence
atgc intronic sequence ATGC exonic sequence...gccttccaggcagcacattagtcttgcaggataccctgttcatcaactctgaaactattgttttagtgttcactatgcctgtgacttttttttaatgcagGTTCGCAGCTCACCTGACCATGGCTTATGTTTTCACATTTTGGACATGCTATGTGCTGTTACGGGAGTATGAAATAGTGGCAACAATGCGTCTGCGCTTT
Basic information
species | Oryza sativa |
transcript | LOC_Os01g35050.3 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g35050.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G021194_T01 (Zea mays), 3'ss of exon 3
---gccttccaggcagcacattagtcttgcaggataccctgttcatcaactctgaaactattgttttagtgttcactatgcctg-tgacttttttttaatgcagGTTCGCAGCTCACCTGACCATGGCTTATGTTTTCACATTTTGGACATGCTATGTGCTGTTACGGGAGTATGAAATAGTGGCAACAATGCGTCTGCGCTTT
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cagagtttacaatcaatacaccttgtcattaaaattagggattg--cagttttgagttcata--ttgactgctcatgagtcctaaccaatttctctttgtgaagGTTTATAGCCCACTTGGCAATGGCGTATGTTTTCACATTTTGGACCTGCTATGTACTGTTACGTGAGTATGAAGTAGTTGCAAAGATGAGACTGCGATTT
upper sequence: LOC_Os01g35050.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G163334_T01 (Zea mays), 3'ss of exon 2
---gccttccaggcagcacat-tagtcttgcaggataccctgttcatcaactctgaaactattgttttagtgttcactatgcctg-tgacttttttttaatgcagGTTCGCAGCTCACCTGACCATGGCTTATGTTTTCACATTTTGGACATGCTATGTGCTGTTACGGGAGTATGAAATAGTGGCAACAATGCGTCTGCGCTTT
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cagattttacaatcaatacaccttgtcattcaaattag---ggattgcagttttgagttcata--ttgactgctcatgagtcctaaccaatttctctttgtgaagGTTTATAGCCCACTTGGCAATGGCGTATGTTTTCACATTTTGGACCTGCTATGTACTATTACGTGAGTATGAAGTAGTTGCAAAGATGAGACTGCGATTTMapped 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|58609230|gb|CK037263.1|CK037263EST: AGTGATATTGACAAACTTTCAATATCCAACATACCTGTAGGGTCAAAGAG GTTCGCAGCTCACCTGACCATGGCTTATGTTTTCACATTTTGGACATGCTA
genomic: AGTGATATTGACAAACTTTCAATATCCAACATACCTGTAGGGTCAAAGAGgttagtacca ... tttaatgcagGTTCGCAGCTCACCTGACCATGGCTTATGTTTTCACATTTTGGACATGCTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actctgaaactattgttttagtgttcactatgcctgtgacttttttttaatgcagGTTCGCAGCTCACCTGACCATGGCTTATGTTTTCACATTTTGGACATGCTATGTGCTGTTACGGGAGTATGAAATAGTGGCAACAATGCGTCTGCGCTTT
ttttaat putative branch site (score: 3)
ctttttttt CT-rich tract
tgacttttttttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gccttccaggcagcacattagtcttgcaggataccctgttcatcaactctgaaactattgttttagtgttcactatgcctgtgacttttttttaatgcagGTTCGCAGCTCACCTGACCATGGCTTATGTTTTCACATTTTGGACATGCTATGTGCTGTTACGGGAGTATGAAATAGTGGCAACAATGCGTCTGCGCTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT