Sequence
atgc intronic sequence ATGC exonic sequence...tgcgcgttgtgcgagtgtgaggaatgcttgttcacctgtgtgttgtggtactttgtgaagttgtgctgaaatgcaatgtggtgaattttgaattgtccagGAATGGGAAGGTAGAATGAACGTGGGGATGTCAAATTCAGTGACGACTGCGATAAGGGACAGCATAAGGGAGACGGCAATTGGGAAAACAAGGAACACAG
Basic information
species | Oryza sativa |
transcript | LOC_Os07g06820.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g06820.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G166018_T01 (Zea mays), 3'ss of exon 1
--tgcgcgttgtgcgagtgtgaggaatgcttgttcacctgtgtgttgtggtactttgtgaagttgtgctgaaatgcaatgtggtgaattttgaattgtcca--gGAATGGGAAGGTAGAATGAACGTGGGGATGTCAAATTCAGTGACGACTGCGATAAGGGACAGCATAAGGGAGACGGCAATTGGGAAAACAAGGAACACAG
|||| || | || ||| ||| || | || || | | | | | || || || || ||||| | | |||| |||| ||| ||||||||||| |||||||||| |||||||||||| || || ||||| || ||||| ||||||||||| || || |||||||||| ||||||||| |
aaagcgcttta-actcatgggagatttgcgaattgaa-tgaatgcaaagttgagtgttcatgtggt-ttgtgttg-aatgtttcttgtctggaatgatccacagGAGTGGGAAGGTAGGATGAACGTGGCGATGTCAAATTCCGTCACAACTGCAATCAGGGATAGCATAAGGGACACAGCTATTGGGAAAATAAGGAACACTG
upper sequence: LOC_Os07g06820.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G035098_T01 (Zea mays), 3'ss of exon 1
----tgcgcgttgtgcgagtgtgaggaatgcttgttcacctgtgtgttgtggtactttgtgaagttgtgctgaaatgcaatgtggtgaattttgaattgtccagGAATGGGAAGGTAGAATGAACGTGGGGATGTCAAATTCAGTGACGACTGCGATAAGGGACAGCATAAGGGAGACGGCAATTGGGAAAACAAGGAACACAG
|||| || | || ||| ||| || | || || | | | | || || || || ||||| | | |||| ||||||| ||||||||||| |||||||||| |||||||||||| || || ||||| || ||||| ||||||||||| || || |||||||||| ||||||||| |
ttaaagcgcttta-actcatgggagatttgcgaattgaa-tgaatgcaaatttgagtgttcatgtggt-ttgtgttg-aatgtttcttgtctggaatgatccagGAGTGGGAAGGTAGGATGAACGTGGCGATGTCAAATTCCGTCACAACTGCAATCAGGGATAGCATAAGGGACACAGCTATTGGGAAAATAAGGAACACTG
upper sequence: LOC_Os07g06820.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G120329_T01 (Zea mays), 3'ss of exon 1
----tgcgcgttgtgcgagtgtgaggaatgcttgttcacctgtgtgt---tgtggtactttgtgaagttgtgctgaaatgcaatgtggtgaattttgaattgtccagGAATGGGAAGGTAGAATGAACGTGGGGATGTCAAATTCAGTGACGACTGCGATAAGGGACAGCATAAGGGAGACGGCAATTGGGAAAACAAGGAACACAG
|||| || | || ||| ||| || | || || | || | || || ||| | |||| || | |||| ||||||| ||||||||||| |||||||| | |||||||||||| || || ||||| || ||||| ||||||||||| || || |||||||||| ||||||||| |
ttaaagcgcttta-actcttgggagatttgcgaattgaa-tgaatgcaaatttgagagttcatgtggtttctgttgaatgtttcttg-----tccggaatgatccagGAGTGGGAAGGTAGGATGAACGTTGCGATGTCAAATTCCGTCACAACTGCAATCAGGGATAGCATAAGGGACACAGCTATTGGGAAAATAAGGAACACTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggtactttgtgaagttgtgctgaaatgcaatgtggtgaattttgaattgtccagGAATGGGAAGGTAGAATGAACGTGGGGATGTCAAATTCAGTGACGACTGCGATAAGGGACAGCATAAGGGAGACGGCAATTGGGAAAACAAGGAACACAG
aattttgaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgcgcgttgtgcgagtgtgaggaatgcttgttcacctgtgtgttgtggtactttgtgaagttgtgctgaaatgcaatgtggtgaattttgaattgtccagGAATGGGAAGGTAGAATGAACGTGGGGATGTCAAATTCAGTGACGACTGCGATAAGGGACAGCATAAGGGAGACGGCAATTGGGAAAACAAGGAACACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - -gttgtgc
- - - - - - - - - - - -atgcttg
- - - - - - - - - - - - - - - -tcacctg
- - - - - - - - - - - - - - - - - - - tgtgttg
- - - - - - - - - - - - - - - - - - - - - - -tggtact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtggtg