Sequence
atgc intronic sequence ATGC exonic sequence...ctatttttggttacagaaaccccttctaattttttggttacataaactccttctaattgagattcaaagcatggatttaacaagtttctgttctttttagGTTGTTCGCTGGGGAAGGTCTGTCTATGCAAATATTCAGAAATTCATCCAGTTTCAGCTTACTGTTAATGTTGCCGCACTCGTGATTAATGTTGTTGCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os08g40530.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g40530.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G132712_T03 (Zea mays), 3'ss of exon 27
ctatttttggttacagaaaccccttctaattt-----tttggttacataaactccttctaattgagattcaaagcatggatttaacaa-gtttctgttcttttt-agGTTGTTCGCTGGGGAAGGTCTGTCTATGCAAATATTCAGAAATTCATCCAGTTTCAGCTTACTGTTAATGTTGCCGCACTCGTGATTAATGTTGTTGCAG
||||| || | | ||||| | | | ||| || || || | ||||||| | | | ||||| | | | |||| ||| |||||||||| |||||| | |||||||| || ||||| ||||||||||| ||||| ||||| || || |||||||| ||||| || |||||||| ||||| |
-----tttgggtataatgtgcatttctaggctataattcttgttgcagaag--tctacctggtgagattttacgatagaatttatggatatatacattctctttcagGTTGTTCGTTGGGGACGATCTGTCTACGCTAATATCCAGAAATTCATTCAGTTCCAGCTCACCGTCAATGTTGCTGCACTTGTCATTAATGTGGTTGCTG
upper sequence: LOC_Os08g40530.1 (Oryza sativa), 3'ss of exon 11
lower sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 22
ctatttttggttacagaaaccccttctaattttttggttacataaactccttctaattgagattcaaagcatggatttaacaagtttctgttctttttagGTTGTTCGCTGGGGAAGGTCTGTCTATGCAAATATTCAGAAATTCATCCAGTTTCAGCTTACTGTTAATGTTGCCGCACTCGTGATTAATGTTGTTGCAG
| || | | | | | | | | | | || ||||||| |||||||| |||| || ||||| ||||||||||| || |||||||| ||||| ||||| ||||||| || || || | || || || || |
--------------------------------------------------gtaagataacagcttttggtgcgagtctga-aggatcgaaattcttgcagGTTGTACGCTGGGGTCGGTCCGTGTATGCCAATATTCAGAAGTTTATCCAGTTCCAGCTGACTGTAAATGTTGTTGCGCTGGTTCTCAACGTCGTGGCCG
upper sequence: LOC_Os08g40530.1 (Oryza sativa), 3'ss of exon 11
lower sequence: EFJ25508 (Selaginella moellendorffii), 3'ss of exon 23
ctatttttggttacagaaaccccttctaattttttggttacataaactccttctaattgagattcaaagcatggatttaacaagtttctgttctttttagGTTGTTCGCTGGGGAAGGTCTGTCTATGCAAATATTCAGAAATTCATCCAGTTTCAGCTTACTGTTAATGTTGCCGCACTCGTGATTAATGTTGTTGCAG
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--------------------------------------------------gtaagataacagcttttggtgcgagtctga-aggatcgaaattcttgcagGTTGTACGCTGGGGTCGGTCCGTGTATGCCAATATTCAGAAGTTTATCCAGTTCCAGCTGACTGTAAATGTAGTTGCGCTGGTTCTCAACGTCGTGGCCGMapped 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|29665351|gb|CB661626.1|CB661626EST: AAAGTTCTGACATTATAATCTTGGATGACAACTTCACATCAGTTGTGAAG GTTGTTCGCTGGGGAAGGTCTGTCTATGCAAATATTCAGAAATTCATCCAG
genomic: AAAGTTCTGACATTATAATCTTGGATGACAACTTCACATCAGTTGTGAAGgtttgttttt ... ttctttttagGTTGTTCGCTGGGGAAGGTCTGTCTATGCAAATATTCAGAAATTCATCCAG
EST:
gi|29681421|gb|CB677696.1|CB677696EST: AAAGTTCTGACATTATAATCTTGGATGACAACTTCACATCAGTTGTGAAG GTTGTTCGCTGGGGAAGGTCTGTCTATGCAAATATTCAGAAATTCATCCAG
genomic: AAAGTTCTGACATTATAATCTTGGATGACAACTTCACATCAGTTGTGAAGgtttgttttt ... ttctttttagGTTGTTCGCTGGGGAAGGTCTGTCTATGCAAATATTCAGAAATTCATCCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actccttctaattgagattcaaagcatggatttaacaagtttctgttctttttagGTTGTTCGCTGGGGAAGGTCTGTCTATGCAAATATTCAGAAATTCATCCAGTTTCAGCTTACTGTTAATGTTGCCGCACTCGTGATTAATGTTGTTGCAG
tttctgttcttttt CT-rich tract
atttaacaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctatttttggttacagaaaccccttctaattttttggttacataaactccttctaattgagattcaaagcatggatttaacaagtttctgttctttttagGTTGTTCGCTGGGGAAGGTCTGTCTATGCAAATATTCAGAAATTCATCCAGTTTCAGCTTACTGTTAATGTTGCCGCACTCGTGATTAATGTTGTTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT