Sequence
atgc intronic sequence ATGC exonic sequence...ttgcttattcacttctatctttacagatgtgctgcctatttatctcttctcatccctattggccattaaatatatttcttcatatatgttttggttgcagGCTTTTGTCAGTGAATATGCTGTTTGGAGAAGTGATGCAGGTAGAGGAAGTCTACTTGCTTCATTGGCAGAAGCTGCTTTCCTTACTGGACTGGAGAAGA
Basic information
species | Oryza sativa |
transcript | LOC_Os12g03470.5 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g03470.3 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G006130_T05 (Zea mays), 3'ss of exon 12
ttgcttattcacttctatctttacagatgtgct-gcctatttatctcttctcatccctattggccattaaatatatttcttcat-atatgttttggttgcagGCTTTTGTCAGTGAATATGCTGTTTGGAGAAGTGATGCAGGTAGAGGAAGTCTACTTGCTTCATTGGCAGAAGCTGCTTTCCTTACTGGACTGGAGAAGA
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--tctgaagaccctgaaactccagtgattttcttgcttatttatgacatcaccagtaccctgtccatacagtaaaaatgttgctgaaatgattcgaacacagGCCTTTGTGAGCGAGTACGCTGTCTGGAGAAGTGACGCGGGTAGAGGCAGTCTTCTTGCTTCGTTGGCTGAAGCTGCTTTCCTCACTGGTCTGGAGAAGA
upper sequence: LOC_Os12g03470.3 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G077299_T03 (Zea mays), 3'ss of exon 12
ttgcttattcacttctatctttacaga--tgtgc-tgcctatttatctcttctcatccctattggccattaaatatatttcttcatatatgttttggttgcagGCTTTTGTCAGTGAATATGCTGTTTGGAGAAGTGATGCAGGTAGAGGAAGTCTACTTGCTTCATTGGCAGAAGCTGCTTTCCTTACTGGACTGGAGAAGA
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tcgttgattttcttgcttagttacaacatcatacatgtatattgacgtcaccattttctgtttagacagtaaatatcttct---ggatatgattcaaatgcagGCTTTTGTAAGTGAGTACGCTGTTTGGAGAGGTGATGCAGGTAGAGGAAGTCTTCTTGCTTCATTGGCAGAAGCTGCTTTCCTTACTGGACTGGAGAAGA
upper sequence: LOC_Os12g03470.3 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G393002_T01 (Zea mays), 3'ss of exon 22
ttgcttattcacttctatctttacagatgtgctgcctatttatctcttct-catccctattggccattaaatatatttctt-catatatgttttggt--tgcagGCTTTTGTCAGTGAATATGCTGTTTGGAGAAGTGATGCAGGTAGAGGAAGTCTACTTGCTTCATTGGCAGAAGCTGCTTTCCTTACTGGACTGGAGAAGA
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----ctagaaacttgatttattttagtttccttgctcatttgcgaaacccatatcataggtagatggtaaatatgttcctaataaacatgatatgttgatgcagGCTTTTGTCAGCGAGTATGCAGTTTGGAAAACTGACGCCGGTAGAGGAACTCTCCTGGCTGCATTGGCAGAAGCGGCTTTCCTTACTGGACTGGAGAAGA
upper sequence: LOC_Os12g03470.3 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G006130_T04 (Zea mays), 3'ss of exon 13
ttgcttattcacttctatctttacagatgtgct-gcctatttatctcttctcatccctattggccattaaatatatttcttcat-atatgttttggttgcagGCTTTTGTCAGTGAATATGCTGTTTGGAGAAGTGATGCAGGTAGAGGAAGTCTACTTGCTTCATTGGCAGAAGCTGCTTTCCTTACTGGACTGGAGAAGA
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--tctgaagaccctgaagctccagtgattttcttgcttatttatgacatcaccagtaccctgtccatacagtaaaaatgttgctgaaatgattcgaacacagGCTTTTGTGAGCGAGTACGCTGTCTGGAGAAGTGACGCGGGTAGAGGCAGTCTTCTTGCTTCGTTGGCTGAAGCTGCTTTCCTCACTGGTCTGGAGAAGA
upper sequence: LOC_Os12g03470.3 (Oryza sativa), 3'ss of exon 13
lower sequence: AT3G10740.1 (Arabidopsis thaliana), 3'ss of exon 13
ttgcttattcacttctatctttacagatgtgctgcctatttatctcttctcatcccta--ttggccattaaatatatttctt-catatatgttttggttgcagGCTTTTGTCAGTGAATATGCTGTTTGGAGAAGTGATGCAGGTAGAGGAAGTCTACTTGCTTCATTGGCAGAAGCTGCTTTCCTTACTGGACTGGAGAAGA
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--------------gtgcggtaatagattataacaaaacttaattccaacaaacacaagatgaagctttcagcgttttactcactcgtgaactttgtttacagGCTTTTGTCAGTGAATATGCTGTTACTGGAAAAGATGCTGGTACAGGAAGCCTTCTTGCCTCTCTTGCAGAAGCTGCGTTTCTCATTGGTCTTGAAAAGAMapped 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|29667817|gb|CB664092.1|CB664092EST: TGTTTTCGATGAAGAGTGCATTTGATAGATCATCTCGTAATGGGCCCAAG GCTTTTGTCAGTGAATATGCTGTTTGGAGAAGTGATGCANGTAGAGGAAGT
genomic: TGTTTTCGATGAAGAGTGCATTTGATAGATCATCTCGTAATGGGCCCAAGgtatgttgta ... ttggttgcagGCTTTTGTCAGTGAATATGCTGTTTGGAGAAGTGATGCAGGTAGAGGAAGT
EST:
gi|33381874|gb|CF197217.1|CF197217EST: TGTTTTCGATGAAGAGTGCATTTGATAGATCATCTCGTAATGGGCCCAAG GCTTTTGTCAGTGAATATGCTGTTTGGAGNNGTGATGC
genomic: TGTTTTCGATGAAGAGTGCATTTGATAGATCATCTCGTAATGGGCCCAAGgtatgttgta ... ttggttgcagGCTTTTGTCAGTGAATATGCTGTTTGGAGAAGTGATGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttctcatccctattggccattaaatatatttcttcatatatgttttggttgcagGCTTTTGTCAGTGAATATGCTGTTTGGAGAAGTGATGCAGGTAGAGGAAGTCTACTTGCTTCATTGGCAGAAGCTGCTTTCCTTACTGGACTGGAGAAGA
attaaatatatttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgcttattcacttctatctttacagatgtgctgcctatttatctcttctcatccctattggccattaaatatatttcttcatatatgttttggttgcagGCTTTTGTCAGTGAATATGCTGTTTGGAGAAGTGATGCAGGTAGAGGAAGTCTACTTGCTTCATTGGCAGAAGCTGCTTTCCTTACTGGACTGGAGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA