Sequence
atgc intronic sequence ATGC exonic sequence...gggcttcaggttcttcttctgtctgtagtgtagagttatcacagcccttttctgtagttccaaagaaaagcaatcatccatatcacttaccttttttcagTCACTCCCGGTTGCTTTTGGTATGGAAACTGCAAAGTGGATATGTGTAGGAGCGATTGACATAACTCAATTATCCGTTGCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os05g28200.2 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g28200.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G162672_T02 (Zea mays), 3'ss of exon 11
gggcttcaggttcttcttctgtctgtagtgtagagttatcacagcccttttctgtagttccaaagaaaagcaatcatccatatcacttaccttttttcagTCACTCCCGGTTGCTTTTGGTATGGAAACTGCAAAGTGGATATGTGTAGGAGCGATTGACATAACTCAATTATCCGTTGCAG
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----gttatactctttttttttgtgtaaatatttatcattaacgtgcttctcaata-----acagtttcactttttttaaaaatgttttaaattttgtagTCACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGGAGCAATTGATATCACTCAATTATCTGTTGCAG
upper sequence: LOC_Os05g28200.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA18G43310.1 (Glycine max), 3'ss of exon 11
---gggcttcag-gttcttcttctgtctgtagt-gtagagttatcacagcccttttct-gtagttccaaagaaaagcaatcatcca---------------------tatcacttacctttttt---cagTCACTCCCGGTTGCTTTTGGTATGGAAACTGCAAAGTGGATATGTGTAGGAGCGATTGACATAACTCAATTATCCGTTGCAG
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ggtatactctattgtcctttgcctttcaataacagtactctgagcttattcatgttttagaaattctaatcatgtacagtcattgaagtagcttctactgacttttctattggctaccttctttgagtaGTCTCTTCCAGTTGCTTTTGGTGCTGAAACTGCAAAGTGGATCTGTGTTGGCGCTATTGACATTACACAATTATCTGTAGCG-
upper sequence: LOC_Os05g28200.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA16G19390.1 (Glycine max), 3'ss of exon 3
--gggcttcag-gttcttcttctgtctgtagt-gtagagttatcacagcccttttct-gtagttccaaagaaaagcaatcatcca---------------------tatcacttacctttttt---cagTCACTCCCGGTTGCTTTTGGTATGGAAACTGCAAAGTGGATATGTGTAGGAGCGATTGACATAACTCAATTATCCGTTGCAG
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gtctactctattgtcctttgcctttcaataacagtactctgaactcattcatgttttagaaattctaatcatgtacagtcattaaagtagcttctactgacttttgtattggctaccttctttgagtagTCTCTTCCAGTTGCTTTTGGTGCTGAAACTGCAAAGTGGATATGTGTTGGCGCTATTGACATTACACAATTATCTGTAGCTG
upper sequence: LOC_Os05g28200.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA07G18470.1 (Glycine max), 3'ss of exon 11
gggcttcaggttcttcttctgtctgtagtgtagagttatcacagcccttttctgt------agttccaaagaaaagcaatcatcca---------------------tatcacttacctttttt---cagTCACTCCCGGTTGCTTTTGGTATGGAAACTGCAAAGTGGATATGTGTAGGAGCGATTGACATAACTCAATTATCCGTTGCAG
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-gtctactctattgtcctttgcctttcaataagagtactctgaactcattcatgttttagaaattctaatcatgtacagtcattaaagtagcttctactgacttttgtattggctaccttctttgagtagTCTCTTCCAGTTGCTTTTGGTTCTGAAACTGCAAAGTGGATATGTGTTGGCGCTATTGACATTACACAATTATCTGTAGCTGMapped 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|86907178|gb|CI292792.1|CI292792EST: CCCTTACTCCTGATATTGTTGTCCTGACTTCTTTGTATAGCATAGCTGGG TCACTCCCGGTTGCTTTTGGTATGGAAAC
genomic: CCCTTACTCCTGATATTGTTGTCCTGACTTCTTTGTATAGCATAGCTGGGgtatatcttc ... cttttttcagTCACTCCCGGTTGCTTTTGGTATGGAAAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccttttctgtagttccaaagaaaagcaatcatccatatcacttaccttttttcagTCACTCCCGGTTGCTTTTGGTATGGAAACTGCAAAGTGGATATGTGTAGGAGCGATTGACATAACTCAATTATCCGTTGCAG
cacttac putative branch site (score: 2)
tcacttaccttttttc CT-rich tract
aaagaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gggcttcaggttcttcttctgtctgtagtgtagagttatcacagcccttttctgtagttccaaagaaaagcaatcatccatatcacttaccttttttcagTCACTCCCGGTTGCTTTTGGTATGGAAACTGCAAAGTGGATATGTGTAGGAGCGATTGACATAACTCAATTATCCGTTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- gcttcag
- - - - - - - - - ctgtctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catccat