Sequence
atgc intronic sequence ATGC exonic sequence...tgttatctgaagcattccatggtttgttaaactatttagatgccctttttgttacaccaacttacttaccttttgctttgtttcgctggtgaatgtccagGGTGTTGGCCATAATGATGACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g04814.4 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g04814.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G088834_T01 (Zea mays), 3'ss of exon 3
------tgttatctgaagcattccatggtttgttaaactat---ttagatgccctttttgttacaccaacttacttaccttttgctttgtttcgctggtgaatgtccagGGTGTTGGCCATAATGATGACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAG
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ttctccgtttgtttagaggact---tgttttcttaatctcagcattctatgccttctttgatgt-taaactgacatgat-----catattttctgtacttgattcccagGGTGTTGGTCACAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACGCCATATGCTCTGGACCAG
upper sequence: LOC_Os01g04814.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G126860_T01 (Zea mays), 3'ss of exon 3
----tgttatctg---aagcattccatggtttgtta-aactat-ttagatgccctttt--tgttacaccaacttacttaccttttgctttgtttcgctggtgaatgtccagGGTGTTGGCCATAATGATGACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAG
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aatacactatctggctaccaataccataattaatcagaactgtattctaagcccttttcatgttagactgacaa---taattttttctgtacct--------gattcccagGGTGTTGGTCATAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACGCCATATGCTCTGGACCAG
upper sequence: LOC_Os01g04814.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA11G19120.1 (Glycine max), 3'ss of exon 3
tgttatctgaagcattccatggtttgttaaactatttagatgccctttttgttacaccaacttacttaccttttgctttgtttcgctggtgaatgtc-cagGGTGTTGGCCATAATGATGACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAG
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-attttttcggaagatccaaggtttccaacagctttggcgtcaattttcattttcgcgtttgttcctaatcataatgtagtttatccacttcacattgtagGGTGTGGGACACAATGATCAGAAAGTTCTTGTTCTTGCAGCTACAAATACACCTTATGCTCTAGACCAG
upper sequence: LOC_Os01g04814.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA12G09300.1 (Glycine max), 3'ss of exon 3
tgttatctgaagcattccatggtttgttaaactatttagatgccctttttgttacaccaacttact--taccttttgctttgtttcgctggtgaatgtc-cagGGTGTTGGCCATAATGATGACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAG
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-cctaattcagaagatccaaggtt--tccaacagctttggtgtcaattttctttttcgtgtttgttcctaatcataatgtagtttgtccgctttacattgtagGGTGTTGGACACAATGATCAGAAAGTTCTTGTTCTAGCAGCTACAAATACACCTTATGCTCTAGACCAGMapped 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|300215967|gb|HO088593.1|HO088593EST: AGAGTGAAGCTTCTAGGAGAATCAAAACTGAACTTCTTGTGCAAATGCAG GGTGTTGGCCATAATGATGACAAAGTACTGGTTCTTGCTGCTACAAACACG
genomic: AGAGTGAAGCTTCTAGGAGAATCAAAACTGAACTTCTTGTGCAAATGCAGgtgaatttta ... gaatgtccagGGTGTTGGCCATAATGATGACAAAGTACTGGTTCTTGCTGCTACAAACACG
EST:
gi|33381146|gb|CF196489.1|CF196489EST: AGAGTGAAGCTTCTAGGAGAATCAAAACTGAACTTCTTGTGCAAATGCAG GGTGTTGGCCATAATGATGACAAAGTACTGGTTCTTGCTGCTACAAACACG
genomic: AGAGTGAAGCTTCTAGGAGAATCAAAACTGAACTTCTTGTGCAAATGCAGgtgaatttta ... gaatgtccagGGTGTTGGCCATAATGATGACAAAGTACTGGTTCTTGCTGCTACAAACACG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttgttacaccaacttacttaccttttgctttgtttcgctggtgaatgtccagGGTGTTGGCCATAATGATGACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAG
tacttac putative branch site (score: 1)
ttactta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgttatctgaagcattccatggtttgttaaactatttagatgccctttttgttacaccaacttacttaccttttgctttgtttcgctggtgaatgtccagGGTGTTGGCCATAATGATGACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT