Sequence
atgc intronic sequence ATGC exonic sequence...ctcagatgtattactagaaaaaccatgcttaaatatttgtgcatcagttcagcatttcaaagatatctagtgttactcatcggtctatctatctggttagGTGTGGTCACTGCAAGAAGCTTGCCCCTGAGTATGAAAAGCTTGGTGCAAGTTTCAAGAAAGCCAAATCTGTCTTTATTGCAAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g23740.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g23740.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G128171_T03 (Zea mays), 3'ss of exon 1
ctcagatgtattactagaaaaaccatgc-ttaaatatttgtg-catcagttcagcatttcaaagatatctagtgttactcatcggtct-atctatctggttagGTGTGGTCACTGCAAGAAGCTTGCCCCTGAGTATGAAAAGCTTGGTGCAAGTTTCAAGAAAGCCAAATCTGTCTTTATTGCAAAG
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--gtaacatagaactgtacttggaatttattatttctctgcatcagcaggtcaacgtttcataaat-tctggttttaatcatctgcttgatttgtttgtttagGTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAGTTTTAAGAAAGCTAAATCTGTCTTGATTGCTAAG
upper sequence: LOC_Os01g23740.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA10G01820.1 (Glycine max), 3'ss of exon 2
ctcagatgtattactagaaaaaccatgcttaaatatttgtgcatcagttcagcatttcaaagatatctagtgttac--tcatcggtctatctatctggttagGTGTGGTCACTGCAAGAAGCTTGCCCCTGAGTATGAAAAGCTTGGTGCAAGTTTCAAGAAAGCCAAATCTGTCTTTATTGCAAAG
| | | | | || | ||| | | | | | | | | | || |||| ||| | | | | ||||||||| |||||||| |||||||| || || ||||||||||||||| || |||||||||||||||||||| || |||| |||
--taaccaattcattgtactaattacttagtaatttccttatgttattatgttcactaatatgtcattatgtttacgatcacttccttttttgttgtaatagGTGTGGACACTGCAAAAAGCTTGCTCCAGAATATGAAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAG
upper sequence: LOC_Os01g23740.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA02G01750.1 (Glycine max), 3'ss of exon 1
ctcagatgtattactagaaaaaccatgcttaaatatttgtgcatcagttcagcatttcaaagatatctagtgttactcatcggtctatctatctggt--tagGTGTGGTCACTGCAAGAAGCTTGCCCCTGAGTATGAAAAGCTTGGTGCAAGTTTCAAGAAAGCCAAATCTGTCTTTATTGCAAAG
| | | | | | || | || | | || ||| | | || | |||| ||| | ||| | | || ||||||||| |||||||| |||||||| || || ||||||||||||||| || |||||||||||||||||||| || || | |||
-ttaacctattcattgtagtaattactaagtaacttccttatattagtat-gtacactaatatgtcattatgtttacgatcacttcctctttgttgtaatagGTGTGGACACTGCAAAAAGCTTGCTCCAGAATATGAAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATCGGCAAG
upper sequence: LOC_Os01g23740.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT2G47470.3 (Arabidopsis thaliana), 3'ss of exon 1
------ctcagatgtattactagaaaaaccatgcttaaatatttgtgc-atcagttcagcatttcaaagatatctagtgttactcatcggtctatctatctggttagGTGTGGTCACTGCAAGAAGCTTGCCCCTGAGTATGAAAAGCTTGGTGCAAGTTTCAAGAAAGCCAAATCTGTCTTTATTGCAAAG
| | |||| ||||| ||| ||||| || ||||| | || | | | || | | | || ||| | | || || |||||||||||||||||||| ||||| || |||||||||||||| || ||||| |||||||| || || ||||| || |||||||||
tttcgatttatatgttttactgagaaattagagcttactgatgtgtgctgttgaatctg-actaattgcatttatggaattggacatggttttaataat------agGTGTGGTCACTGCAAGAAACTTGCTCCAGAGTATGAAAAGCTAGGGGCAAGCTTCAAGAAGGCTAAGTCTGTGTTGATTGCAAAGMapped 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|88354765|gb|CI614043.1|CI614043EST: AAGGAGGTCGGCCAGGACCGCGGCGCCCTCGTCGAGTTCTACGCGCCCTG GTGTGGTCACTGCAAGAAGCTTGCCCCTGAGTATGAAAAGCTTGGTGCAAG
genomic: AAGGAGGTCGGCCAGGACCGCGGCGCCCTCGTCGAGTTCTACGCGCCCTGgttcgttctc ... atctggttagGTGTGGTCACTGCAAGAAGCTTGCCCCTGAGTATGAAAAGCTTGGTGCAAG
EST:
gi|58598802|gb|CK009330.1|CK009330EST: AAGGAGGTCGGCCAGGACCGCGGCGCCCTCGTCGAGTTCTACGCGCCCTG GTGTGGTCACTGCAAGAAGCTTGCCCCTGAGTATGAAAAGCTTGGTGCAAG
genomic: AAGGAGGTCGGCCAGGACCGCGGCGCCCTCGTCGAGTTCTACGCGCCCTGgttcgttctc ... atctggttagGTGTGGTCACTGCAAGAAGCTTGCCCCTGAGTATGAAAAGCTTGGTGCAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttcagcatttcaaagatatctagtgttactcatcggtctatctatctggttagGTGTGGTCACTGCAAGAAGCTTGCCCCTGAGTATGAAAAGCTTGGTGCAAGTTTCAAGAAAGCCAAATCTGTCTTTATTGCAAAG
tctatct CT-rich tract
atttcaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctcagatgtattactagaaaaaccatgcttaaatatttgtgcatcagttcagcatttcaaagatatctagtgttactcatcggtctatctatctggttagGTGTGGTCACTGCAAGAAGCTTGCCCCTGAGTATGAAAAGCTTGGTGCAAGTTTCAAGAAAGCCAAATCTGTCTTTATTGCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - -agaaaaa
- - - - - - - - - - - - -tgcttaa
- - - - - - - - - - - - - - - - - - - gtgcatc
- - - - - - - - - - - - - - - - - - - - - - - -ttcagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaagata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttact