Sequence
atgc intronic sequence ATGC exonic sequence...cagagaatttttttccgatcttgattttgatttatatctgagtatttgaaatgaaaaacttctagatgtaagtatgaccagaagtattatgatttgacagGTTGCAACTGCTTGCGCTGTGGCAGCATTCAAGCTGCGGCGCCCAGTTCGAATGTACCTCGATCGCAAGACGGACATGATAATGGCGGGAGGGCGGCATC
Basic information
species | Oryza sativa |
transcript | LOC_Os10g04860.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os10g04860.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G899851_T01 (Zea mays), 3'ss of exon 5
---------------------------cagagaatttt-tttccgatcttgattttgatttatatctgagtatttgaaatgaaaaactt----ctagatgt---aagtatgaccagaagtattatgatttgacagGTTGCAACTGCTTGCGCTGTGGCAGCATTCAAGCTGCGGCGCCCAGTTCGAATGTACCTCGATCGCAAGACGGACATGATAATGGCGGGAGGGCGGCATC
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gtaagtactaataaactagagttaatgttgaaatttttatttttgattaccaatccactgccaactaatattcataatgtgatcagattgagacaaattgtgcaacggataactatcaattttctc-tttgttagGTTGCATGTGCATGTGCAGTTGCTGCATTGAAGCTACAACGTCCAGTTCGGATGTACCTCGATCGCAAGACAGACATGATAATGGCAGGCGGGCGGCATC
upper sequence: LOC_Os10g04860.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G141535_T01 (Zea mays), 3'ss of exon 5
---------------------------------cagagaatttt---tttccgat-----cttgattttgatttatatctgagtatttgaaatgaaaaacttctagatgtaagtatgaccagaagt-attatga---------tttgacagGTTGCAACTGCTTGCGCTGTGGCAGCATTCAAGCTGCGGCGCCCAGTTCGAATGTACCTCGATCGCAAGACGGACATGATAATGGCGGGAGGGCGGCATC
| | ||||| ||| | || || ||| | | || | | | |||||| |||| | ||||| || | |||| | || ||| |||| ||| |||| ||| || || | || || |||||||||||||| |||||| | ||||||||||||||||||||||||||||||||||| |||||| | ||||
gtaagtcctgcctgtaactagagcttcagttcactcaatattttgtgttttcaattgccactgtattgtcaattgaacttcatgatttgaccaaaaaactgttgagatgcaaatggtgttagaaatgatcatggattttcctctttgtcagACTGCATGTGCATGTGCCCTTGCTGCCTTCAAGCTGCGGCGTCCAGTTAGGATGTACCTCGATCGCAAGACGGACATGATAATGGCTGGAGGGAGACATC
upper sequence: LOC_Os10g04860.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G141473_T01 (Zea mays), 3'ss of exon 5
-------------------------------cagagaatttttttccgatcttgattttgatttatatctgagtat-ttgaaatgaaaaacttctagatgtaagtatgaccagaagtattatgattt-----gacagGTTGCAACTGCTTGCGCTGTGGCAGCATTCAAGCTGCGGCGCCCAGTTCGAATGTACCTCGATCGCAAGACGGACATGATAATGGCGGGAGGGCGGCATC
|| | | ||| | | || | | | | || || | || | || | | || | | | | | ||||| | ||||||||| ||| || || || || ||||||||||||||||| |||||||| |||||||| ||||||||||| |||||||||||||| || || |||||||
gtaagtcttaaaaataactagtgcttatgctcaacttttctattttcagttacgaatgtagtgcgtgcgaactgatattcatgtggtcagattgagaaaaaatgtgttattatagatgactggatttcctctgtcagGTTGCATGTGCATGTGCGGTTGCTGCATTCAAGCTGCGGCGTCCAGTTCGGATGTACCTGGATCGCAAGACAGACATGATAATGGCAGGCGGTCGGCATC
upper sequence: LOC_Os10g04860.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G019799_T01 (Zea mays), 3'ss of exon 5
-cagagaatttttttcc-gatcttgattttgatttatatctgagtatttgaaatgaaa----aacttctagatgtaagtatgaccagaagtattatgatttgacagGTTGCAACTGCTTGCGCTGTGGCAGCATTCAAGCTGCGGCGCCCAGTTCGAATGTACCTCGATCGCAAGACGGACATGATAATGGCGGGAGGGCGGCATC
| || | | || ||| |||| | | ||| | |||||| | || | || | ||||| || ||| ||| | | | | ||| ||| ||||| ||| ||||| || || ||||||||||| | ||| || ||| |||||||| ||||||||||||||||||||||| ||||| ||||| || |
gtaagtcataactaactagagcttttctttgctaaacatc-gtctatttgtattgccatccaaagtggatgatgtgag-atg-ccaagaatctcctc-cttgtcagATTGCATGTGCATGCGCCGTTGCCGCATTCAAGCTACAGCGTCCTGTTAAGATGTACCTTGATCGCAAGACGGACATGATAATAGCGGGTGGGCGACACCMapped 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|88350174|gb|CI622105.1|CI622105EST: GTTTCGGTGGAAAGGCAATGAAAGCAACACAT GTTGCAACTTGCTTGCGCTGTGTGCAGCATTCAAGCTGCGGCGCCCAGTTC
genomic: GTTTCGGTGGAAAGGCAATGAAAGCAACACATgtaagaacct ... gatttgacagGTTGCAACT-GCTTGCGCTGTG-GCAGCATTCAAGCTGCGGCGCCCAGTTC
EST:
gi|2431129|gb|C73549.1|C73549EST: CGAGAAGAGTTGGAGGAGGTTTCGGTGGAAAGGCAATGAAAGCAACACAT GTTGCAACTGCTTGCGCTGTGGCAGCATTCAAGCTGCGGCGCCCAGTTCGA
genomic: CGAGAAGAGTTGGAGGAGGTTTCGGTGGAAAGGCAATGAAAGCAACACATgtaagaacct ... gatttgacagGTTGCAACTGCTTGCGCTGTGGCAGCATTCAAGCTGCGGCGCCCAGTTCGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgaaatgaaaaacttctagatgtaagtatgaccagaagtattatgatttgacagGTTGCAACTGCTTGCGCTGTGGCAGCATTCAAGCTGCGGCGCCCAGTTCGAATGTACCTCGATCGCAAGACGGACATGATAATGGCGGGAGGGCGGCATC
aagtattatgattt 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 |
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cagagaatttttttccgatcttgattttgatttatatctgagtatttgaaatgaaaaacttctagatgtaagtatgaccagaagtattatgatttgacagGTTGCAACTGCTTGCGCTGTGGCAGCATTCAAGCTGCGGCGCCCAGTTCGAATGTACCTCGATCGCAAGACGGACATGATAATGGCGGGAGGGCGGCATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - atgaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - accagaa