Sequence
atgc intronic sequence ATGC exonic sequencegtacgtgcccttgtctgacgtttcttggaaccgaagatggctgcggctgatgagaccgcatgttggttgtatttggcgcggcgaatgcgcgtgcagTGGAGGCGCTGATCGCCATCAGGCAGGGGCTGGTCGACCCGCACGGCGTGCTGAACAACTGGGACGAGGACTCCGTCGACCCCTGCAGCTGGGCCATGGT
Basic information
species | Oryza sativa |
transcript | LOC_Os08g34380.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g34380.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G151955_T01 (Zea mays), 3'ss of exon 1
gta-cgtgcccttgt-ctgacgtttcttggaaccgaagatggctgcggctgatgagaccgcatgttggttgtatt-tggcgcggcgaatgcgcgtgcagTGGAGGCGCTGATCGCCATCAGGCAGGGGCTGGTCGACCCGCACGGCGTGCTGAACAACTGGGACGAGGACTCCGTCGACCCCTGCAGCTGGGCCATGGT
||| || | | | | | | | | ||| | | || | || || | | || ||||| | ||||| | ||||||||||| ||||| ||||||||||||||||||||||||||||||||||||||||||| | | ||||||| ||||||| |||||||||||||||||||||||| |
gtaacgccgcatcattccggccatgcatggtgcagcagcaacatttggttggttt--tttttttctgattgtaccgtcgcgcgcgagcttcgcgtgcagTGCAGGCGTTGATCGCCATCAGGCAGGGGCTGGTCGACCCGCACGGCGTGCTCAGGAGCTGGGACCAGGACTCGGTCGACCCCTGCAGCTGGGCCATGAT
upper sequence: LOC_Os08g34380.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA17G07810.1 (Glycine max), 3'ss of exon 1
gtacgtgcccttgtctgacgtttcttggaaccgaagatggctgcggctgatgagaccgcatgttggttgtatttggcgcggcgaat-gcgcgtgcagTGGAGGCGCTGATCGCCATCAGGCAGGGGCTGGTCGACCCGCACGGCGTGCTGAACAACTGGGACGAGGACTCCGTCGACCCCTGCAGCTGGGCCATGGT
|| | | | | | || | || | || | || | | | | | | | | || | |||| | |||||||||||||| ||||| ||| | || ||| ||||| |||||||| || ||||||||||| || ||||||||||| | ||||||||| ||||| |
----gtcaaccaaacacccttatttttcacattaaattctctaagtctaa--ggttcccttaattgacattttgttaacaatgaattgttcgtgcagTGGAGGCTTTGATCAACATTAAAGGAGGTCTGAATGACCCTCACGGCGTCCTCAACAACTGGGATGAATACTCCGTCGACGCTTGCAGCTGGACCATGAT
upper sequence: LOC_Os08g34380.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA02G36940.1 (Glycine max), 3'ss of exon 1
gtacgtgcccttgtctgacgtttcttggaaccgaagatggctgcggctgatga---gaccgcatgttggttgtatttggcgcggcgaatgcgcgtgcagTGGAGGCGCTGATCGCCATCAGGCAGGGGCTGGTCGACCCGCACGGCGTGCTGAACAACTGGGACGAGGACTCCGTCGACCCCTGCAGCTGGGCCATGGT
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-------------------gtctactaaacacgcttatttttcacattcattctccaagtctaagattcccttaattgatata-taattgtgcgtgcagTGGAGGCTTTGATGTACATTAAGGCAGCTCTCCATGACCCACACGGCGTCCTCAACAACTGGGATGAATACTCCGTCGACGCTTGCAGCTGGACCATGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcggctgatgagaccgcatgttggttgtatttggcgcggcgaatgcgcgtgcagTGGAGGCGCTGATCGCCATCAGGCAGGGGCTGGTCGACCCGCACGGCGTGCTGAACAACTGGGACGAGGACTCCGTCGACCCCTGCAGCTGGGCCATGGT
ggctgat putative branch site (score: 4)
ttgtattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgtgcccttgtctgacgtttcttggaaccgaagatggctgcggctgatgagaccgcatgttggttgtatttggcgcggcgaatgcgcgtgcagTGGAGGCGCTGATCGCCATCAGGCAGGGGCTGGTCGACCCGCACGGCGTGCTGAACAACTGGGACGAGGACTCCGTCGACCCCTGCAGCTGGGCCATGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG