Sequence
atgc intronic sequence ATGC exonic sequencegtgaactactaaacttgttttttttacaagttaaccattcatatatataaataacttcctgtaacaattttctttattagATACAATCATCTCATGGAGGGATCCAGAAGTAGCAACAGAATTAGCGTTGAGCTTTCAGGAAGCTGCTGGGTGCTCATACATATG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g23590.3 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g23590.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G435675_T01 (Zea mays), 3'ss of exon 3
gtgaactactaaacttgttttttttacaagttaaccattcatata-tataaataacttcctgtaacaattttctttattagATACAATCATCTCATGGAGGGATCCAGAAGTAGCAACAGAATTAGCGTTGAGCTTTCAGGAAGCTGCTGGGTGCTCATACATATG---------------
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gtgagctaacacagt--atcattttatgtttgcgctattttttttctttttgcaaatttctaataca-ttttctttgttagAAACAATCATTTCATGGAGAGATCGTGAAGCAGCAACAGACTTAGCGTTAAGCTTTCAGGAAGCTGCTGGATGCTCCTACATATGGTGATGGATGCAAGA
upper sequence: LOC_Os01g23590.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA17G03570.1 (Glycine max), 3'ss of exon 3
------------------------------------------gtgaactactaaacttgtttt---ttttacaagttaaccattcatatatataaataacttcctgtaacaattttctttattagATACAATCATCTCATGGAGGGATCCAGAAGTAGCAACAGAATTAGCGTTGAGCTTTCAGGAAGCTGCTGGGTGCTCATACATATG
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gtagttggtagcttttatctttccttcctctctttctcaataaagagctgttgtctttcatttacgcttgaaatataaatgggtcatggtgtttatcagtttgatg-gattcttttgttcttcagATACAATCATCTCATGGAGAGATCCAGAATATGCTACTGAACTGGCACTTAGCTTTCAAGAGCCTAGCGGCTGCTCTTACATATG
upper sequence: LOC_Os01g23590.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA07G37040.1 (Glycine max), 3'ss of exon 1
------------------------------------gtgaactactaaacttgttttttttacaagtt-------aaccattcatatatataaataacttcctgtaacaattttctttattagATACAATCATCTCATGGAGGGATCCAGAAGTAGCAACAGAATTAGCGTTGAGCTTTCAGGAAGCTGCTGGGTGCTCATACATATG
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gtagttggtagcttttatccttcctccctctctttttcaataaagggaatttgtctttcatttatgcttgaataaaaggggtcatggtgtttatcagtttgatg-gatgcttttgttcttcagATACAATCATCTCATGGAGAGATCCAGAATATGCTACAGAACTGGCACTTAGCTTTCAAGAGCCTAGTGGCTGCTCTTACATATG
upper sequence: LOC_Os01g23590.2 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S112_103V6.1 (Physcomitrella patens), 3'ss of exon 2
---------------------------------------------------------------------------------------------------------gtgaactactaaacttgttttttttacaagttaaccattcatatatataaataacttcctgtaacaattttctttattagATACAATCATCTCATGGAGGGATCCAGAAGTAGCAACAGAATTAGCGTTGAGCTTTCAGGAAGCTGCTGGGTGCTCATACATATG
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gtattgtcatgcattttatgcctagatatgctcagttttgcagatcatggttactaatgctgtgattgttgcctaataagttgttatgtggatagtcgagaagttctagatggtttagtatatttttgtgtttcgcttcttttgagtttctgaactggatcttacttgcctctgatctctat-agACACTATCATCTCATGGACGGATCCAGAAGTGGCAACAGATTTGGCTCTCAGTTTTCAAGAGACAATGGGTTGTTCCTTCATATG
upper sequence: LOC_Os01g23590.2 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S60_97V6.1 (Physcomitrella patens), 3'ss of exon 3
---------------------gtgaactactaaacttgtttttttta-caagttaaccattcatatatataaataacttcctgtaacaattttctttattagATACAATCATCTCATGGAGGGATCCAGAAGTAGCAACAGAATTAGCGTTGAGCTTTCAGGAAGCTGCTGGGTGCTCATACATATG
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agtattgttgttcctaagcttgtgaactacaggttgtaccttctttggcaggtttcacgttattttctgagtgtaatttaacatgagcagtttgtt--tcagATACAATCATATCATGGACGGATCCAGAAGTGGCAACAGATCTAGCCCTCAGTTTCCAAGAAACTATGGGTTGTACTTTCATATGMapped 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|29681402|gb|CB677677.1|CB677677EST: ATTGCTCATGCACAACATTACTTCTGAAGATATCTACAGAAAGCAAGAAG ATACAATCATCTCATGGAGGGATCCAGAAGTAGCAACAGAATTAGCGTTGA
genomic: ATTGCTCATGCACAACATTACTTCTGAAGATATCTACAGAAAGCAAGAAGgtgaactact ... tctttattagATACAATCATCTCATGGAGGGATCCAGAAGTAGCAACAGAATTAGCGTTGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acaagttaaccattcatatatataaataacttcctgtaacaattttctttattagATACAATCATCTCATGGAGGGATCCAGAAGTAGCAACAGAATTAGCGTTGAGCTTTCAGGAAGCTGCTGGGTGCTCATACATATG
ttttctttatt CT-rich tract
ttaaccattcatatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaactactaaacttgttttttttacaagttaaccattcatatatataaataacttcctgtaacaattttctttattagATACAATCATCTCATGGAGGGATCCAGAAGTAGCAACAGAATTAGCGTTGAGCTTTCAGGAAGCTGCTGGGTGCTCATACATATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT