Sequence
atgc intronic sequence ATGC exonic sequence...cattattcttccttatatatctaatgtacttatttgaattatgaaagatcatttacatctgtcatgaaccgcacaatctaagtgctgaattacattgcagATATGACCTCCTGCATAATGCACATCTTAACCTTGAAGGTTTGGAAGAGCTTTTCAAAGTTGCTCAAGTAAGGAACCTTAACGTTCTGTACTTCCATTTG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g48300.3 |
intron # | 23 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g48300.3 (Oryza sativa), 3'ss of exon 23
lower sequence: GRMZM2G022997_T01 (Zea mays), 3'ss of exon 3
-----cattat-tcttccttatatatctaatgtacttatttgaattatgaaagatcatttacatctgtcatgaaccgcacaatctaagtgctgaattacattgcagATATGACCTCCTGCATAATGCACATCTTAACCTTGAAGGTTTGGAAGAGCTTTTCAAAGTTGCTCAAGTAAGGAACCTTAACGTTCTGTACTTCCATTTG
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ttgttgatgatgtctttcttaaaaaatatgaacatttacat-aattatagtaatacaattctgt-tggcatataactcctaaactaa----tggagtaaattgcagGTATGACCTTTTGCATAATGCTCATCTCAATCTTAAGGGTTTGGAAGAGCTATTCAAAGTTGCTCAA---------------------------------
upper sequence: LOC_Os03g48300.3 (Oryza sativa), 3'ss of exon 23
lower sequence: GLYMA18G49000.1 (Glycine max), 3'ss of exon 23
----cattattcttccttatatatctaatgtacttatttgaattatgaaagatcatttacatctgtcatgaaccgcacaatctaagtgctgaattacattgcagATATGACCTCCTGCATAATGCACATCTTAACCTTGAAGGTTTGGAAGAGCTTTTCAAAGTTGCTCAAGTAAGGAACCTTAACGTTCTGTACTTCCATTTG
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acttaatcaatatgaagaaaaaat-tggcagtttcatttaaattatgtagctttttttattccttttgt---ttgagatgttaacatttactttcacattacagATATGATCTCTTGCATAATGCCCATCTTAATCTAGAAGGATTGGATGAGCTTTTCAAGGTTGCTCAG---------------------------------
upper sequence: LOC_Os03g48300.3 (Oryza sativa), 3'ss of exon 23
lower sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 21
cattattcttccttatatatctaatgtac----ttatttgaattatgaaagatcatttacatctgtcatgaaccgcacaatctaagtgctgaattacattgcagATATGACCTCCTGCATAATGCACATCTTAACCTTGAAGGTTTGGAAGAGCTTTTCAAAGTTGCTCAAGTAAGGAACCTTAACGTTCTGTACTTCCATTTG
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acttagtcaatatga-agagaaaatgggcagtttcatttaaattatgtagtttcttttattcctttcgt---ttgagatgttaacatttactttcacattacagATATGATCTCTTGCATAATGCTCATCTTAATCTAGAAGGATTGGATGAGCTTTTCAAGGTTGCTCAG---------------------------------
upper sequence: LOC_Os03g48300.3 (Oryza sativa), 3'ss of exon 23
lower sequence: GLYMA13G05060.1 (Glycine max), 3'ss of exon 37
---cattattcttccttatatatctaatgtacttatttgaattatgaaagatcatttacatctgtcatgaaccgcacaatctaagtgctgaattacattgcagATATGACCTCCTGCATAATGCACATCTTAACCTTGAAGGTTTGGAAGAGCTTTTCAAAGTTGCTCAAGTAAGGAACCTTAACGTTCTGTACTTCCATTTG
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ttcaacaaccaagccttgtcccactagatgccctggaggtttcatttaaactatgtgatttttattcttttctg-acgaatttaatgtttactt--attgcagATATGATCTCTTGCACAATGCACATCTTAATCTAGAAGGACTTCATGAGCTTTTCAAAGTTGCTCAG---------------------------------
upper sequence: LOC_Os03g48300.3 (Oryza sativa), 3'ss of exon 23
lower sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 21
-cattattcttccttatatatcta-atgtact---tatttgaattatgaaagatcatttacatctgtcatgaaccgcacaatctaagtgctgaattacattgcagATATGACCTCCTGCATAATGCACATCTTAACCTTGAAGGTTTGGAAGAGCTTTTCAAAGTTGCTCAAGTAAGGAACCTTAACGTTCTGTACTTCCATTTG
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caacaaccaagccttgtcccactagatgccctggacgtttcatttaaactacgtgatttttattcttttctgacagtaag---ttaatgtttactt--attacagATATGATCTCTTGCACAATGCACATCTTAATCTAGAAGGACTTGATGAGCTTTTCAAAGTTGCTCAG---------------------------------
upper sequence: LOC_Os03g48300.3 (Oryza sativa), 3'ss of exon 23
lower sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 23
--cattattcttccttatatatctaatgtacttatttgaattatgaaagatcatttacatctgtcatgaaccgcacaatctaagtgctgaattaca---ttgcagATATGACCTCCTGCATAATGCACATCTTAACCTTGAAGGTTTGGAAGAGCTTTTCAAAGTTGCTCAAGTAAGGAACCTTAACGTTCTGTACTTCCATTTG
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agtgttctattaacaaaaaagctccttgctcttatatgagtcctttatgttc---tatg-ctaacattgcttgtgct-tttgattgttgacctgccaattcacagATATGATCTCTTGCACAATGCACATCTTAATCTAGAAGATCTGGATGAGCTTTTCAAAGTTGCTCAG---------------------------------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|33675067|gb|CF303306.1|CF303306EST: CCGATTTGACATTACACAAATCCCAGATGTCTATGACTCCTGCAA ATATGACCTCCTGCATAATGCACATCTTAACCTTGAAGGTTTGGAAGAGCT
genomic: CCGATTTGACATTACACAAATCCCAGATGTCTATGACTCCTGCAAgtaagtgaac ... tacattgcagATATGACCTCCTGCATAATGCACATCTTAACCTTGAAGGTTTGGAAGAGCT
EST:
gi|29622332|gb|CB627343.1|CB627343EST: CCGATTTGACATTACACAAATCCCAGATGTCTATGACTCCTGCAA ATATGACCTCCTGCATAATGCACAT
genomic: CCGATTTGACATTACACAAATCCCAGATGTCTATGACTCCTGCAAgtaagtgaac ... tacattgcagATATGACCTCCTGCATAATGCACAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agatcatttacatctgtcatgaaccgcacaatctaagtgctgaattacattgcagATATGACCTCCTGCATAATGCACATCTTAACCTTGAAGGTTTGGAAGAGCTTTTCAAAGTTGCTCAAGTAAGGAACCTTAACGTTCTGTACTTCCATTTG
aattacatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cattattcttccttatatatctaatgtacttatttgaattatgaaagatcatttacatctgtcatgaaccgcacaatctaagtgctgaattacattgcagATATGACCTCCTGCATAATGCACATCTTAACCTTGAAGGTTTGGAAGAGCTTTTCAAAGTTGCTCAAGTAAGGAACCTTAACGTTCTGTACTTCCATTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -catctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgaa