Sequence
atgc intronic sequence ATGC exonic sequence...tgtttctagagttgacattatgcaatttagagtggtgtagtttttttattaagttggacaggtgttgaaatgaaataatttctcaaaattttctgttcagTATTATCTGAAGACTGGAACATGCAAGTTTGGGCCTACATGCAAATTCCATCATCCCAGAGAAAAAGCTGGAATTGCAGGGAGGGTGCAGCTAAACACAT
Basic information
species | Oryza sativa |
transcript | LOC_Os01g68860.3 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g68860.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G107491_T03 (Zea mays), 3'ss of exon 3
tgtttctagagttgacattatgcaattta--gagtggtgtagtttttt-tattaagttggacaggtgttgaaatgaaataatttctcaaaattttctgttcagTATTATCTGAAGACTGGAACATGCAAGTTTGGGCCTACATGCAAATTCCATCATCCCAGAGAAAAAGCTGGAATTGCAGGGAGGGTGCAGCTAAACACAT
|||| | | || | ||| || ||||| | || | | | | | | | || | | | |||| || |||| || | |||| | |||||||||||||||| ||||||||||||||||| |||||||||||||| || |||||||| ||||| || |||||||||||||||||||||||||||||||
cagatctacatctttgatcacataatctattgagtgcttgagctatatatgtcatgctgta-aaatactgaagctgaa-aattact-gatttttttcctatagTATTATCTGAAGACCGGAACATGCAAGTTTGGTCCTACATGCAAATTTCACCATCCCAGGGAAAAGGCCGGAATTGCAGGGAGGGTGCAGCTAAACACAT
upper sequence: LOC_Os01g68860.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G087032_T04 (Zea mays), 3'ss of exon 3
tgtttctagagttgacattatgcaattta--gagtggtgtagtttttttattaagttggacaggtgttgaaatgaaataatttctcaaaattttctgttcagTATTATCTGAAGACTGGAACATGCAAGTTTGGGCCTACATGCAAATTCCATCATCCCAGAGAAAAAGCTGGAATTGCAGGGAGGGTGCAGCTAAACACAT
|||| | | || | |||| | ||||| | ||| || | | | | | || || || ||||| || |||| || | |||| | |||||||||||||||||||||||||||||||||| |||||||||||||| || |||||||| ||||| ||||||||||||||||||||||||||||||||||
-agatctacatctttgatcacacaatccattgagtgctttagcttatatgtcatgctgtgcaagtattgaagctgaa-aattactgatcttttttcctgtagTATTATCTGAAGACTGGAACATGCAAGTTTGGCCCTACATGCAAATTTCACCATCCCAGGGAAAAGGCTGGAATTGCAGGGAGGGTGCAGCTAAACACAT
upper sequence: LOC_Os01g68860.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA20G36140.1 (Glycine max), 3'ss of exon 3
---------------------tgtttctagagttgacattatgcaatt-tagagtggtgtagtttttttattaagttggacaggtgttgaaatgaaataatttctcaaaattttctgttcagTATTATCTGAAGACTGGAACATGCAAGTTTGGGCCTACATGCAAATTCCATCATCCCAGAGAAAAAGCTGGAATTGCAGGGAGGGTGCAGCTAAACACAT
| | || ||| | | || | || || ||| | || |||||| | || | || | | | ||| | | | | | |||| ||||||||||| ||||| ||||| ||||| | ||||||||||| |||||||| | ||| | ||||| ||||| || || || |||| | |
gcacgtactagtttctcaaccttgtactgcagtgcagagcattaatttgtatcttggcatgcattctttatttaaacattcaccaatcatcataacagagttttttccccctgtttttctagTACTATCTGAAGACAGGAACGTGCAAATTTGGAGCCACATGCAAATTTCATCATCCTAAAGATCAGGCTGGGATTGCTGGAAGAGTTGCCTTAAATATTT
upper sequence: LOC_Os01g68860.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA10G31370.3 (Glycine max), 3'ss of exon 3
---------------------tgtttctagagttga---catta---tgcaatttagagt---ggtgtagtttttttattaag--ttggacaggtgttgaaatgaaataatttctcaaaattttctgttcagTATTATCTGAAGACTGGAACATGCAAGTTTGGGCCTACATGCAAATTCCATCATCCCAGAGAAAAAGCTGGAATTGCAGGGAGGGTGCAGCTAAACACAT
| || || ||| | || || || ||||| | | || | | ||| |||| || || || || || | ||| | | ||| | ||||| ||||||||||| ||||||||||| ||||| | ||||||||||| |||||||| | ||| | ||||||||||| || || || |||| | |
gcatgtactagtttctcaaccttttactgcagtgcagagcactaatttgtaattttgtatcttggcatgcatctttatttaaacattcaccaatcgtcataacaaagtgttttttttcccctgtctttccagTACTATCTGAAGACAGGAACATGCAAATTTGGAGCCACATGCAAATTTCATCATCCTAAAGATCAGGCTGGAATTGCTGGAAGAGTTGCCTTAAATATTT
upper sequence: LOC_Os01g68860.3 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv04s0023g00370.t01 (Vitis vinifera), 3'ss of exon 3
tgtttctagagttgacattatgc---aatttagagtggtgtagtttttttattaagttggacaggtgttgaaatgaaataatttctcaaaattttctgttcagTATTATCTGAAGACTGGAACATGCAAGTTTGGGCCTACATGCAAATTCCATCATCCCAGAGAAAAAGCTGGAATTGCAGGGAGGGTGCAGCTAAACACAT
||| | | | || ||| | | | | | |||||||| || ||| || || | | | ||||| | | | | ||||| || ||||||| ||||| ||||||||||| | |||||||| || |||||||| ||||| || ||||||||||| || || || |||| | |
--tttaatgtcctcatatcatgtgtaagatctctattttctcatttttttaatatgttctg-agttggaagagttgacaaatttgctttgaatggttctccagTACTACTTGAAGACAGGAACTTGCAAGTTTGGAGCCACATGCAAGTTTCATCATCCTAGAGACAAGGCTGGAATTGCTGGAAGAGTTTCTTTAAATATTTMapped 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|29643926|gb|CB648933.1|CB648933EST: CCAGAATGAAAGGAGAATACCCTGAGAGGATGGGGCAACCAGAATGTCAG TATTATCTGAAGACTGGAACATGCAAGTTTGGGCCTACATGCAAATTCCAT
genomic: CCAGAATGAAAGGAGAATACCCTGAGAGGATGGGGCAACCAGAATGTCAGgtaattatgg ... ttctgttcagTATTATCTGAAGACTGGAACATGCAAGTTTGGGCCTACATGCAAATTCCAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttattaagttggacaggtgttgaaatgaaataatttctcaaaattttctgttcagTATTATCTGAAGACTGGAACATGCAAGTTTGGGCCTACATGCAAATTCCATCATCCCAGAGAAAAAGCTGGAATTGCAGGGAGGGTGCAGCTAAACACAT
ttttctgttc CT-rich tract
ttgaaatgaaataatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtttctagagttgacattatgcaatttagagtggtgtagtttttttattaagttggacaggtgttgaaatgaaataatttctcaaaattttctgttcagTATTATCTGAAGACTGGAACATGCAAGTTTGGGCCTACATGCAAATTCCATCATCCCAGAGAAAAAGCTGGAATTGCAGGGAGGGTGCAGCTAAACACAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT