Sequence
atgc intronic sequence ATGC exonic sequenceCACAGAGAAGGGGATTAGTGGAGATGATTCAGATTTGACTGCAAGACGAAATGCATTTGGATCGAATACATACCCTCGTAAGAAAGGAAGAAGCTTCCTGgtatgctgactgctgagaattctttaatatttgtatagcattttttccctttttgatgctcattattggtgtactgacacttttgtttag
Basic information
species | Oryza sativa |
transcript | LOC_Os04g51610.3 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G140328_T02 (Zea mays), 5'ss of exon 5
CACAGAGAAGGGGATTAGTGGAGATGATTCAGATTTGACTGCAAGACGAAATGCATTTGGATCGAATACATACCCTCGTAAGAAAGGAAGAAGCTTCCTGgtatgctgactgctgagaattctttaatatttgtatagcattttttccctttttga--tgctcattattggtgtactgacacttttgtttag
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TTCGGAGAAGGGCATTAGTGGAGATGACTCAGATTTGATAGCAAGGAAAAATACATTTGGTTCAAACACATATCCTCGTAAGAAAGGAAGAAGTTTTTTGgtatgctaa-------ggtttcgtttatg---atatagtacttctcttttctctgggttagtcacacctgctg-attgaacatcttgtttag
upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G391042_T02 (Zea mays), 5'ss of exon 5
CACAGAGAAGGGGATTAGTGGAGATGATTCAGATTTGACTGCAAGACGAAATGCATTTGGATCGAATACATACCCTCGTAAGAAAGGAAGAAGCTTCCTGgtatgctgactgctgagaattctttaatatttgtatagcattttttccctttttgatgctcattattggtgtactgacacttttgtttag
||| |||||||||||||||||||||| ||||||||| ||||| ||||||||||||||| || ||||| ||||||||||||||||||||||| ||||||| | | || | |||| |||| ||| | || | | | ||| | || || |||| | | |||||
TACACAGAAGGGGATTAGTGGAGATGACTCAGATTTGCTGGCAAGGAAAAATGCATTTGGATCAAACACATATCCTCGTAAGAAAGGAAGAAGCTTTTTGgtatgttaa--------ggtttcctgatata-gtat---gtttcctttctctgggtttgtcacttctgctg-actgtacatcatatttag
upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA08G23760.1 (Glycine max), 5'ss of exon 7
CACAGAGAAGGGGATTAGTGGAGATGATTCAGATTTGACTGCAAGACGAAATGCATTTGGATCGAATACATACCCTCGTAAGAAAGGAAGAAGCTTCCTGgtatgctgactgctgagaattctttaatatttgtatagcattttttccctttttgatgctcattattggtgtactgacacttttgtttag
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TCCGGATAAAGGTGTTAGTGGAGATGATGCTGATCTGTTAAAAAGGAAAAATGCATTTGGAACTAATACATATCCTCGGAAAAAAGGAAGAAGTTTCTGGgtatatt---cttaatgacttattctacatatatatttttctaaaattataattgatg--aattaattgtcatttgtgattgtt--tcag
upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA07G00630.1 (Glycine max), 5'ss of exon 7
CACAGAGAAGGGGATTAGTGGAGATGATTCAGATTTGACTGCAAGACGAAATGCATTTGGATCGAATACATACCCTCGTAAGAAAGGAAGAAGCTTCCTGgtatgctgactgctgagaattctttaatatttgtatagcattttttccctttttgat--gctcattattggtgtactgacacttttgtttag
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TCCGGATAAAGGTATTAGTGGAGATGATGCTGATCTGTTAAAAAGGAAAAATGCATTTGGAACTAATACATATCCTCGGAAAAAAGGAAGAAGTTTCTGGgtatatt---cttaatgacttcatcattctacatatatatttttctgaaattataattgatgaactaattgtgatttgtgattgtt--ttagMapped 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|58600052|gb|CK010580.1|CK010580EST: TGCATTTGGATCGAATACATACCCTCGTAAGAAAGGGAAGAAGCTTCCTG GCTTTCTTATGGGATGCTTGTAAAGATTTGACACTTATCATTCTCATGGTT
genomic: TGCATTTGGATCGAATACATACCCTCGTAAGAAAGG-AAGAAGCTTCCTGgtatgctgac ... ttttgtttagGCTTTCTTATGGGATGCTTGTAAAGATTTGACACTTATCATTCTCATGGTT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CACAGAGAAGGGGATTAGTGGAGATGATTCAGATTTGACTGCAAGACGAAATGCATTTGGATCGAATACATACCCTCGTAAGAAAGGAAGAAGCTTCCTGgtatgctgactgctgagaattctttaatatttgtatagcattttttccctttttgatgctcattattggtgtactgacacttttgtttag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC