Sequence
atgc intronic sequence ATGC exonic sequence...agtcacaaaagattaagagtagtctcaaaaacttatccttgaaactacgagattacggcctacttatgttaccatttgacacaccaaaactctaatgtagATATCAGGTGCAAGTGTTGGAGAAGTGAAAATTGTGTCTGACATGCATGAGAGGAAAGCTGAGATGGCACGCCAATCCGATGCCTTCATCGCTCTTCCTG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g51210.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g51210.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G008726_T01 (Zea mays), 3'ss of exon 3
agtcacaaaagattaagagtagtctc----aaaaacttatccttgaaactacgagattacggcctacttatgttaccatttgacacaccaaaactct-aatgtagATATCAGGTGCAAGTGTTGGAGAAGTGAAAATTGTGTCTGACATGCATGAGAGGAAAGCTGAGATGGCACGCCAATCCGATGCCTTCATCGCTCTTCCTG
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----accacaatctaaaattcgctcccatggaaagcaaatccatgac-ctgagaagtgctatatcaactcggctacaaacaaattttttcttcttctcaaactagATATCTGGTGCTAGCGTTGGAGAAGTTAAGGTTGTCTCCGACATGCACGAGAGGAAAGCTGAGATGGCACGGCAAGCTGATGCCTTCATAGCTCTTCCTG
upper sequence: LOC_Os01g51210.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv04s0008g01040.t01 (Vitis vinifera), 3'ss of exon 3
-agtcacaaaagattaagagtagtctcaaaaacttatc--cttgaaactacgagattacggcctacttatgttaccatttgacacaccaaaactctaatgtagATATCAGGTGCAAGTGTTGGAGAAGTGAAAATTGTGTCTGACATGCATGAGAGGAAAGCTGAGATGGCACGCCAATCCGATGCCTTCATCGCTCTTCCTG
||| | | ||| | |||| | | | | | |||| | | | | || ||||| || | | || |||| | | ||||||| || || |||||||||||| | ||||||||| |||||||||||| |||||||||| ||||| | || | ||||| || || ||||||||||
tagttccctatgatggaaagtacttcaatcttgtgagcagcttggagcatgtgaacaatggactactaatat-attgttaacatgggtaaaatggtgac--agATATCTGGCCAAACTGTTGGAGAAGTAAGAATTGTGTCGGACATGCATGAGCGGAAAGCTGAAATGGCTCAAGAAGCTGATGCTTTTATTGCTCTTCCTG
upper sequence: LOC_Os01g51210.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ26301 (Selaginella moellendorffii), 3'ss of exon 3
agtcacaaaagattaagagtagtctcaaaaacttatccttgaaactacgagattacggc-ctacttatgttaccatttgacacaccaaaactctaat---gtagATATCAGGTGCAAGTGTTGGAGAAGTGAAAATTGTGTCTGACATGCATGAGAGGAAAGCTGAGATGGCACGCCAATCCGATGCCTTCATCGCTCTTCCTG
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--ttttgttttgtttcttct-gcgttgccaagttgtggcttttctcatgcccctccggcgttggctactttcctgctcg-ctcacctctcgtccggttgaacagATATGCGGCCAAACGGTGGGAGAGGTGCGGCCGGTTGCCGATATGCACCAAAGGAAAGCCGAGATGGCACGCCAAGCCGACGCCTTCATTGCTCTTCCTG
upper sequence: LOC_Os01g51210.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ14638 (Selaginella moellendorffii), 3'ss of exon 3
agtcacaaaagattaagagtagtctcaaa----aacttatccttgaaactacgagattacggcctacttatgttaccatttgacacaccaaaactctaatgtagATATCAGGTGCAAGTGTTGGAGAAGTGAAAATTGTGTCTGACATGCATGAGAGGAAAGCTGAGATGGCACGCCAATCCGATGCCTTCATCGCTCTTCCTG
| | | | ||| ||| || | | | | || |||||| || || | | | | | || |||||| || || || ||||| ||| || | || ||||| | |||||||| ||||||||||||||| |||| |||||||| ||||||||||
ttttgttttgtttcttctgcgttgccaagttgtggcttttctcatgcccctccggcgttcg--ctactttcgtgcccgctcacctctcgtccggttgaac--agATATGCGGCCAAACGGTGGGAGAGGTGCGGCCGGTTGCCGATATGCACCAAAGGAAAGCCGAGATGGCACGCCAAGCCGACGCCTTCATTGCTCTTCCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacgagattacggcctacttatgttaccatttgacacaccaaaactctaatgtagATATCAGGTGCAAGTGTTGGAGAAGTGAAAATTGTGTCTGACATGCATGAGAGGAAAGCTGAGATGGCACGCCAATCCGATGCCTTCATCGCTCTTCCTG
ctctaat putative branch site (score: 3)
ttatgtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agtcacaaaagattaagagtagtctcaaaaacttatccttgaaactacgagattacggcctacttatgttaccatttgacacaccaaaactctaatgtagATATCAGGTGCAAGTGTTGGAGAAGTGAAAATTGTGTCTGACATGCATGAGAGGAAAGCTGAGATGGCACGCCAATCCGATGCCTTCATCGCTCTTCCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG