Sequence
atgc intronic sequence ATGC exonic sequencegtacgtacgcatgctactagtagcaaggcgccattgtattcgttcagcttgttcttcacttgttcgtcgtgtcgtcgtttgcatatgctcttgcttgttgtgttgatttgtttcgctgccaatgtcgttggtcattccgtgtgcagTGACGGGCCTGGGGAGCCTGTGCTTCGACTACAGGAGCAGCATGGAGCCGGAGCCGGGGCGGTGCCGGCGCACGGACGGCAAGAAGTGGCGGTGCTCGCG
Basic information
species | Oryza sativa |
transcript | LOC_Os04g48510.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g48510.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G045977_T01 (Zea mays), 3'ss of exon 2
gtacgtacgcatgctactagtagcaaggcgccattgtattcgttcagcttgttcttcacttgttcgtcgtgtcgtcgtttgcatatgctcttgcttgttgtgttgat-ttgtttcgctgccaatgtcgttggtcattccgtgtgcagTGACGGGCCTGGGGAGCCTGTGCTTCGACTACAGGAGCAGCATGGAGCCGGAGCCGGGGCGGTGCCGGCGCACGGACGGCAAGAAGTGGCGGTGCTCGCG
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-----------------------------------gtaagcactaagcac---cgacaacagcttcagccgcccccggccg-atttctatttgttt-ttgcgtttgtactgtcttgccg----tatcg--aatgaacgtgt-tgcagTGATGGGCCTGGGGAGCCTGTGCTTCGACTACCGCAGCAGCATGGAGCCGGAGCCCGGGCGGTGCCGGCGCACGGACGGCAAGAAGTGGCGGTGCTCCCG
upper sequence: LOC_Os04g48510.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G124566_T01 (Zea mays), 3'ss of exon 2
----gtacgtacgcatgctactagtagcaag-gcgccattgtattcgttcagcttgttcttcacttgttcgtcgtgtcgtcgtttgcatatgctcttgcttgttgtgttgatttgtttcgctgccaatgtcgttggtcattccgtgtgcagTGACGGGCCTGGGGAGCCTGTGCTTCGACTACAGGAGCAGCATGGAGCCGGAGCCGGGGCGGTGCCGGCGCACGGACGGCAAGAAGTGGCGGTGCTCGCG
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gtaagcaccggcagaagct-ccaataccttgtgtttttttgtttgtttttgttttgcttttctactgttcggcacgt-acgaggtacgaccggcgtcgtggaggaggctgtttggaatgaatgaacgaatgaatgaatgtct----tgcagTGATGGGCCTGGGCAGCCTGTGCTTCGACTACCGCAGCAGCATGGAGCCGGAGCCCGGGCGGTGCCGGCGCACGGACGGCAAGAAGTGGCGGTGCTCCCG
upper sequence: LOC_Os04g48510.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ24024 (Selaginella moellendorffii), 3'ss of exon 2
gtacgtacgcatgctactagtagcaaggcgccattgtattcgttcagcttgttcttcacttgttcgtcgtgtcgtcgtttgcatatgctcttgcttgttgtgttgatttgtttcgctgccaatgtcgttggtcattccgtgtgcagTGACGGGCCTGGGGAGCCTGTGCTTCGACTACAGGAGCAGCATGGAGCCGGAGCCGGGGCGGTGCCGGCGCACGGACGGCAAGAAGTGGCGGTGCTCGCG---
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----------------------gtgagtgcctgctgcctttctcccttcacttcactgctcgactgcctcctcgctgttctca---------gcaccttgcacc-actggcaactctaaagatctccttgc---tttcctgtgcagTG---GGCTGGGGAAACTTCCACCTTGGAATTCCGAACAATCCCGACCCGGAGCCTGGTCGGTGCCGACGAACAGACGGCAAGAAGTGGAGGTGCTCCAGGGA
upper sequence: LOC_Os04g48510.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ24588 (Selaginella moellendorffii), 3'ss of exon 2
gtacgtacgcatgctactagtagcaaggcgccattgtattcgttcagcttgttcttcacttgttcgtcgtgtcgtcgtttgcatatgctcttgcttgttgtgttgatttgtttcgctgccaatgtcgttggtcattccgtgtgcagTGACGGGCCTGGGGAGCCTGTGCTTCGACTACAGGAGCAGCATGGAGCCGGAGCCGGGGCGGTGCCGGCGCACGGACGGCAAGAAGTGGCGGTGCTCGCG---
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----------------------gtgagtgcctgctgcctttctcccttcacttcactgctcgactgcctcctcgccgttctca---------gcaccttgcacc-actggcaactctaaagatctccttgc---tttcctgtgcagTG---GGCTGGGGAAACTTTCACCTTGGAATTCCGAACAATCCCGACCCGGAGCCTGGTCGGTGCCGACGAACAGACGGCAAGAAGTGGAGGTGCTCCAGGGAMapped 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|88325930|gb|CI649781.1|CI649781EST: GAACAGCATCGCCGCCGCCTCCTCGTTCGGCCCGCAAAGCTTTCCCTCCC TGACGGGCCTGGGG
genomic: GAAGAGCATCGCCGCCGCCTCCTCGTTCGGCCCGCAAAGCTTTCCCTCCCgtacgtacgc ... ccgtgtgcagTGACGGGCCTGGGG
EST:
gi|88573639|gb|CI665408.1|CI665408EST: GAAGAGCATCGCCGCCGCCTCCTCGTTCGGCCCGCAAAGCTTTCCCTCCC TGACGGGCCTGGGGAGCCTGTGCTTCGACTACAGGAGCAGCATGGAGCC
genomic: GAAGAGCATCGCCGCCGCCTCCTCGTTCGGCCCGCAAAGCTTTCCCTCCCgtacgtacgc ... ccgtgtgcagTGACGGGCCTGGGGAGCCTGTGCTTCGACTACAGGAGCAGCATGGAGCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcttgttgtgttgatttgtttcgctgccaatgtcgttggtcattccgtgtgcagTGACGGGCCTGGGGAGCCTGTGCTTCGACTACAGGAGCAGCATGGAGCCGGAGCCGGGGCGGTGCCGGCGCACGGACGGCAAGAAGTGGCGGTGCTCGCG
tgttgat putative branch site (score: 4)
tcattcc putative PPT
atttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgtacgcatgctactagtagcaaggcgccattgtattcgttcagcttgttcttcacttgttcgtcgtgtcgtcgtttgcatatgctcttgcttgttgtgttgatttgtttcgctgccaatgtcgttggtcattccgtgtgcagTGACGGGCCTGGGGAGCCTGTGCTTCGACTACAGGAGCAGCATGGAGCCGGAGCCGGGGCGGTGCCGGCGCACGGACGGCAAGAAGTGGCGGTGCTCGCG
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