Sequence
atgc intronic sequence ATGC exonic sequenceTACTTGACGCCAATCTCAATCCTAAGATCTCGGATTTCGGGCTAGCCAAACTTTATGATGACAAGATGACTCATGTTAGCACAAAAGTTGCTGGTACATTgtaagtatattccatctttgcattttttcttttaaaaaaaataactattttaatggcatgcaagaaataagaggacatcctcttaaggggcaaaaaaaag...
Basic information
species | Oryza sativa |
transcript | LOC_Os04g52640.1 |
intron # | 22 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g52640.1 (Oryza sativa), 5'ss of exon 22
lower sequence: GRMZM2G155837_T02 (Zea mays), 5'ss of exon 18
TACTTGACGCCAATCTCAATCCTAAGATCTCGGATTTCGGGCTAGCCAAACTTTATGATGACAAGATGACTCATGTTAGCACAAAAGTTGCTGGTACATTgtaagtatattccatctttgcattttttcttttaaaaaaaataactattttaatggcatgcaagaaataagaggacatcctcttaaggggcaaaaaaaag
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TGCTTGATGCAAATCTCAACCCTAAGATCTCGGATTTCGGGCTCGCCAAACTTTACGATGACAAGAAGACTCATGTCAGCACCAAAGTTGCGGGTACATTgtaagtgcatttccatattgc----ctcctctacacccaagttatt--ttcaaatgtgagctggtgtcaatttcttactcttctgtgaag----------
upper sequence: LOC_Os04g52640.1 (Oryza sativa), 5'ss of exon 22
lower sequence: GRMZM2G126858_T02 (Zea mays), 5'ss of exon 20
TACTTGACGCCAATCTCAATCCTAAGATCTCGGATTTCGGGCTAGCCAAACTTTATGATGACAAGATGACTCATGTTAGCACAAAAGTTGCTGGTACATTgtaagtatattccatctttgcattttttcttttaaaaaaaataactattttaatggcatgcaagaaataagaggacatcctcttaagg--ggcaaaaaaaag
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TACTTGATGCCACTTTGAACCCTAAGATTTCGGATTTCGGGCTCGCCAAACTTTATGACGATAAAAAGACACATGTTAGCACAAAAGTTGCTGGTACATTgtaagggcatac-------atgtctccccccatatgtttaataattagtttccactaatgtctgagctaatggaagttccttttcactttgatttcttgaag
upper sequence: LOC_Os04g52640.1 (Oryza sativa), 5'ss of exon 22
lower sequence: GRMZM2G031536_T01 (Zea mays), 5'ss of exon 7
TACTTGACGCCAATCTCAATCCTAAGATCTCGGATTTCGGGCTAGCCAAACTTTATGATGACAAGATGACTCATGTTAGCACAAAAGTTGCTGGTACATTgtaagtatattccatctttgcattttttcttttaaaaaaaataactattttaatggcatgcaagaaataagaggacatcctcttaaggggcaaaaaaaag
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TGCTTGACGCAAATTTCAACCCTAAGATCTCAGATTTTGGGCTCGCCAAACTTTATGACGACAAGAAGACTCATGTCAGCACAAAAGTTGCGGGTACATTgtaagtacatttccatcttg-----tgccttttacaagtgcatattattttcaca-tgtgaactaatgccaatttcttgctcttctgtgaag--------
upper sequence: LOC_Os04g52640.1 (Oryza sativa), 5'ss of exon 22
lower sequence: GRMZM2G126858_T01 (Zea mays), 5'ss of exon 20
TACTTGACGCCAATCTCAATCCTAAGATCTCGGATTTCGGGCTAGCCAAACTTTATGATGACAAGATGACTCATGTTAGCACAAAAGTTGCTGGTACATTgtaagtatattccatctttgcattttttcttttaaaaaaaataactattttaatggcatgcaagaaataagaggacatcctcttaaggggcaaaaaaaag----------------------------------------------------------------------------------
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TACTTGATGCCACTTTGAACCCTAAGATTTCGGATTTCGGGCTCGCCAAACTTTATGACGATAAAAAGACACATGTTAGCACAAAAGTTGCTGGTACATTgtaagggcatacatgtctccccccatatgtttaataattagtttccac--taatgtctgagctaatggaagttccttttcactttgatttcttgaagtggctatctttcacctgagtacgccatgagaggtcacatgactgagaaagttgatatttttgcttttggtgtggtcatgttggag
upper sequence: LOC_Os04g52640.1 (Oryza sativa), 5'ss of exon 22
lower sequence: Vv12s0055g00640.t01 (Vitis vinifera), 5'ss of exon 1
TACTTGACGCCAATCTCAATCCTAAGATCTCGGATTTCGGGCTAGCCAAACTTTATGATGACAAGATGACTCATGTTAGCACAAAAGTTGCTGGTACATTgtaagtatatt-----------ccatctttgcattttttcttttaaaaaaaataactattttaatggcatgcaagaaataagaggacatcctcttaaggggcaaaaaaaag
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TGCTTGACTATTATCTCAATCCTAAGATTTCAGATTTTGGTTTGGCCAAACTGTATGATGACACAATGACTCACATAAGCACCCGTGTGGCAGGCACAATgtaagatcctcaaaagtcaaggcccttagttccttgtttattctcttttttgggatttttttcatt-tatccccaaagtttaaaactgggcttttatgttactgaagtag-Mapped 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|29661115|gb|CB657390.1|CB657390EST: CTTTATGATGACAAGATGACTCATGTTAGCACAAAAGTTGCTGGTACATT TGGTTATCTTGCACCTGAGTACGCCATGAGAGGACATATGACTGAGAAAGT
genomic: CTTTATGATGACAAGATGACTCATGTTAGCACAAAAGTTGCTGGTACATTgtaagtatat ... ctctttccagTGGTTATCTTGCACCTGAGTACGCCATGAGAGGACATATGACTGAGAAAGT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TACTTGACGCCAATCTCAATCCTAAGATCTCGGATTTCGGGCTAGCCAAACTTTATGATGACAAGATGACTCATGTTAGCACAAAAGTTGCTGGTACATTgtaagtatattccatctttgcattttttcttttaaaaaaaataactattttaatggcatgcaagaaataagaggacatcctcttaaggggcaaaaaaaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG