Sequence
atgc intronic sequence ATGC exonic sequence...agttatgctggtttgtttagttatgccaatgcctgcaagtgttgaacaaactgtaccatagggcatagagcactattaatcattcccccaatcaatgcagGCCGAAACAGACAGAGAGGCGGGTGGTAACAAAGGTGTGTCAGATAAGCAGATACGACTGAAGATCTACTCACCAAATGTTCTAAACATTACGTTGGTTG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g69130.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g69130.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G129155_T02 (Zea mays), 3'ss of exon 1
------agttatgctggtttgtttagttatgccaatgcctgcaagtgttgaacaaactgtaccatagggcatagagcactattaatc-attcccccaatcaatgcagGCCGAAACAGACAGAGAGGCGGGTGGTAACAAAGGTGTGTCAGATAAGCAGATACGACTGAAGATCTACTCACCAAATGTTCTAAACATTACGTTGGTTG
| || | ||||| ||| || | || || | ||||| | || | ||| ||| || | |||| | | || | ||| |||||||| |||||||| | ||||| ||||||||||||||||| || |||| ||||||||| ||||||||| || || ||||| || |||||||| || || |
tgtttcacttcaattacgatgttttgttttgttagtgtgggctggagttgag--attagtgct-----gcacagaccattcttaaacgactctctgcatctatgcagGCTGAAACAGATCGTGAGGCAGGTGGTAACAAAGGTGTATCGGATAGGCAGATACGGTTGAAGATCTTTTCTCCGAATGTCCTTAACATTACTTTAGTCG
upper sequence: LOC_Os01g69130.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G180335_T01 (Zea mays), 3'ss of exon 1
----agttatgctggtttgtttagttatgccaatgcctgcaagtgttgaacaaactgtaccatagggcatagagcactattaatcattcccccaatcaatgcagGCCGAAACAGACAGAGAGGCGGGTGGTAACAAAGGTGTGTCAGATAAGCAGATACGACTGAAGATCTACTCACCAAATGTTCTAAACATTACGTTGGTTG
| ||| || || || || | | || | |||| | || | || ||| || | |||| | | | ||| |||||||| ||||||||| ||||||| ||||||||||||||||| || |||| |||||||||| ||||||| | || ||||||||||| |||||||| |||||||
tgtttggtattttgtttcacttcttttctttagttagtgtgggc-ttgagttgccatta--gtgctccacagaccattgttaaa-agactctgcatctatgcagGCAGAAACAGACCGAGAGGCAGGTGGTAACAAAGGTGTATCGGATAGGCAGATACGATTGAAGATTTTTTCTCCAAATGTTCTTAACATTACTTTGGTTG
upper sequence: LOC_Os01g69130.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA20G06670.1 (Glycine max), 3'ss of exon 1
-----agttatgctggtttgtttagttatgccaatgcctgcaagtgttgaacaaactgtaccatagggc-atagagcactat-taatcattcccccaatcaatgcagGCCGAAACAGACAGAGAGGCGGGTGGTAACAAAGGTGTGTCAGATAAGCAGATACGACTGAAGATCTACTCACCAAATGTTCTAAACATTACGTTGGTTG
| || || | || ||| | | || | ||| | || | | |||| | || || ||| | ||| | | || ||||||| |||| || || || | |||||| ||||||||||| ||| | |||||||| ||||| ||||| | |||||||||||||| | || || |||| |
ctcttgatggcaatgtactgataaggtatacg---gtctactagt--ttaatactccaccccatctctctattgacttgtatatcttcactttctttttc--tgcagGCTAAAACTGATAGGGAAGTGGGTGGGAACAAAGGTGTATCAAACAAGCAGATCCGACTTAAGATTTTTTCACCAAATGTTCTTGATATCACACTGGTAG
upper sequence: LOC_Os01g69130.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA15G06380.1 (Glycine max), 3'ss of exon 1
--agttatgctggtttgtttagttatgccaatgcctgcaagtgttgaacaaactgtaccatagggc-atagagcactat-taatcattcccccaatcaatgcagGCCGAAACAGACAGAGAGGCGGGTGGTAACAAAGGTGTGTCAGATAAGCAGATACGACTGAAGATCTACTCACCAAATGTTCTAAACATTACGTTGGTTG
|| || || || | | | || | | | |||| || | | | || | | || | ||| | ||| || | || ||||||| ||||| || || || || ||||| ||||||||||| ||||| |||||||| ||||||||||| | |||||||||||||| | || || ||||| |
aatgtaatactc-ttgatgccgatttgtatacggtc-tacttgtttaatcccccctcctatctctctgttgactagtatatcttcactcactttttc--tgcagGCTGAAACTGATAGGGAAGCAGGTGGGAACAAAGGTGTCTCAGACAAGCAGATTCGACTGAAGATTTTTTCACCAAATGTTCTTGATATCACCTTGGTAG
upper sequence: LOC_Os01g69130.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA13G32940.1 (Glycine max), 3'ss of exon 1
agttatgctggtt-tgtttagttatgccaatgcctgcaagtgttgaacaaactgtaccatagggcatagagcactattaatcattcccccaatcaatgcagGCCGAAACAGACAGAGAGGCGGGTGGTAACAAAGGTGTGTCAGATAAGCAGATACGACTGAAGATCTACTCACCAAATGTTCTAAACATTACGTTGGTTG
| | || ||| ||| | || | | | | ||| || | | | |||| | || | | | ||| | | | | ||||||| ||||| || || || |||||||| ||||||||||| ||||| |||||||| ||||| ||||| | |||||||||||||| | || || |||| |
actcttgatggcaatgtacggataaggtatgtggtctactagtttaatactccgccccatctctc-tattgacttgtatatcttcactctcttttctgcagGCTGAAACTGATAGGGAAGCGGGTGGGAACAAAGGTGTATCAGACAAGCAGATCCGACTTAAGATTTTTTCACCAAATGTTCTTGATATCACACTGGTAGMapped 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|88718784|gb|CI742294.1|CI742294EST: TCCCCGGCCGCCGCTTCTATGACTTCCGCGAAATCCGCCGCGAGATCCAG GCCGAAACAGACAGAGAGGCGGGTGGTAACAAAGGTGTGTCAGATAAGCAG
genomic: TCCCCGGCCGCCGCTTCTATGACTTCCGCGAAATCCGCCGCGAGATCCAGgttcccctcc ... atcaatgcagGCCGAAACAGACAGAGAGGCGGGTGGTAACAAAGGTGTGTCAGATAAGCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acaaactgtaccatagggcatagagcactattaatcattcccccaatcaatgcagGCCGAAACAGACAGAGAGGCGGGTGGTAACAAAGGTGTGTCAGATAAGCAGATACGACTGAAGATCTACTCACCAAATGTTCTAAACATTACGTTGGTTG
tattaat putative branch site (score: 2)
tattaatcatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agttatgctggtttgtttagttatgccaatgcctgcaagtgttgaacaaactgtaccatagggcatagagcactattaatcattcccccaatcaatgcagGCCGAAACAGACAGAGAGGCGGGTGGTAACAAAGGTGTGTCAGATAAGCAGATACGACTGAAGATCTACTCACCAAATGTTCTAAACATTACGTTGGTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA