Sequence
atgc intronic sequence ATGC exonic sequence...taaagtatgatctcagagaccgtattagagtttaaaaatatttatattttgttacgaaagagtactaatttaatttcatggtgacttgaatctattgcagGAACTACTACCGGTGCTCGACGGAGGGGTGCAACGTGAAGAAGAGGGTGGAGAGAGACAAGAACGACCCGCGGTACGTGGTGACGATGTACGAGGGGATC
Basic information
species | Oryza sativa |
transcript | LOC_Os01g51690.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g51690.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G101405_T01 (Zea mays), 3'ss of exon 2
----------------------------------taaagtatgatctcagagaccgtattagagtttaaaaata---tttatattttgttacgaaagagtactaatttaa-----tttcatggtgacttgaatctattgcagGAACTACTACCGGTGCTCGACGGAGGGGTGCAACGTGAAGAAGAGGGTGGAGAGAGACAAGAACGACCCGCGGTACGTGGTGACGATGTACGAGGGGATC
||| | | | || | ||| | | || | | | || | | || | | || || | | || || | | ||| |||||||||||||||||||||||||||||| |||||||| ||||| ||||||||| |||||| | |||||||| | ||||| ||||| ||||||||||| |
gtgaatttataaagtaattacgcagctgatagtttaatttgcaaac-cattaattatatcaaaagccaagagtgagctagatgtgtacatatatatgcgtgctggactgaagaaccttgcaaacgaacgaattggattccagGAACTACTACCGGTGCTCGACGGAGGGCTGCAACGTCAAGAAAAGGGTGGAGCGAGACAGGGACGACCCGAGATACGTTGTGACCATGTACGAGGGAGTG
upper sequence: LOC_Os01g51690.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA17G34210.1 (Glycine max), 3'ss of exon 4
----taaagtatgatctcagagaccg----tattagagtttaaaaatatttatattttgt-tacgaaagagtactaatttaatttcatggtgacttgaatctattgcagGAACTACTACCGGTGCTCGACGGAGGGGTGCAACGTGAAGAAGAGGGTGGAGAGAGACAAGAACGACCCGCGGTACGTGGTGACGATGTACGAGGGGATC
|| ||| | | | | | | | || | ||| || || | | | ||| || | ||| |||| ||| | | | |||| |||||| ||||| |||| || ||| || ||||||||||| ||||| ||||||||||||||| | ||||| |||| || | || | ||||| || | |
aatgcaatatattactacttaaattaaaaccacgatacttaagaaagatgcatgctatatatacaggagttttctattttatttttcttttta--tgaa-------cagGAATTACTATAGGTGTTCAGTGGATGGATGCAACGTGAAAAAGAGAGTGGAGAGAGACAAGGATGACCCAAGGTATGTAATAACAACCTACGAAGGCAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attttgttacgaaagagtactaatttaatttcatggtgacttgaatctattgcagGAACTACTACCGGTGCTCGACGGAGGGGTGCAACGTGAAGAAGAGGGTGGAGAGAGACAAGAACGACCCGCGGTACGTGGTGACGATGTACGAGGGGATC
tactaatttaatttca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taaagtatgatctcagagaccgtattagagtttaaaaatatttatattttgttacgaaagagtactaatttaatttcatggtgacttgaatctattgcagGAACTACTACCGGTGCTCGACGGAGGGGTGCAACGTGAAGAAGAGGGTGGAGAGAGACAAGAACGACCCGCGGTACGTGGTGACGATGTACGAGGGGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - -aaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttcatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgacttg