Sequence
atgc intronic sequence ATGC exonic sequence...tcttcatacgtatttggttgatgtgaatattttctagaaagctgaaagactttattgttttcagaaaattgttgggagattcttatagtgtgctatgcagATCGTGGAGATCTTAAAAGACCGCCCATCTTGGTTCCGTGATTGTCGAAGTCTTGAAGTCTTCACAATGTTTCCAGCTGGAAATGGTGGCACGATCGAAC
Basic information
species | Oryza sativa |
transcript | LOC_Os10g33960.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os10g33960.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G469551_T02 (Zea mays), 3'ss of exon 6
--tcttcatacgtatttggttgatgtgaatattttctagaaagctgaaagactttattgttttcagaaaattgttgggagattctt----atagtgtgctatgcagATCGTGGAGATCTTAAAAGACCGCCCATCTTGGTTCCGTGATTGTCGAAGTCTTGAAGTCTTCACAATGTTTCCAGCTGGAAATGGTGGCACGATCGAAC
| || || | || | ||| ||||||| | | | | || || | | ||||| | |||| || | || | |||| |||| ||||| ||||| ||||| || ||||||||||| ||||||||||| ||||||||||||| |||||||| ||||||||||||||||| || || ||||
ttttttgccacatggttcaaaacttagaacattttctgaattttttggaca---tacagtct---gtaaattatctggaggtttcttacgattgcttgcttgatagATAGTGGAAATCTTGAAAGATCGTCCATCTTGGTTTCGTGATTGTCGGAGTCTTGAAGTCTATACAATGTTACCAGCTGGAAATGGTGGAACCATTGAAC
upper sequence: LOC_Os10g33960.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA12G08080.1 (Glycine max), 3'ss of exon 5
---tcttcat-acgtatttggttgatgtgaatattttctagaaagctgaaagacttta-ttgttttcagaaaattgttggga----gattcttatagtgtgctatg-----cagATCGTGGAGATCTTAAAAGACCGCCCATCTTGGTTCCGTGATTGTCGAAGTCTTGAAGTCTTCACAATGTTTCCAGCTGGAAATGGTGGCACGATCGAAC
|||| | ||| | || | || || |||| | | | | || | || | || |||| ||| || | | | || || ||||| | |||||| | ||||| || ||||||||||||||||| ||||| || || ||||| || || |||||||| ||||||||||| || || || ||||
gtaaattcaccaagtaaaagtatggtttggattttttttgtcatatcttggtatgccagttaatgtctggaatctgtttggaatttgaatttctgaatgcctgattttcaccagATTGCAGAGATCCTTAAAGATCGTCCATCTTGGTTCCGTGACTGTCGGAGCCTAGAAGTTTTTACTATGTTTCCTGCTGGAAATGGAGGAACCATTGAAC
upper sequence: LOC_Os10g33960.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA11G20520.1 (Glycine max), 3'ss of exon 5
-tcttcatacgtatttggttgatgtgaatattttctagaaagctgaaagactttattgttttcagaaaattgttggga----gattcttatagtgtgctat-----gcagATCGTGGAGATCTTAAAAGACCGCCCATCTTGGTTCCGTGATTGTCGAAGTCTTGAAGTCTTCACAATGTTTCCAGCTGGAAATGGTGGCACGATCGAAC
| || || | || | || || |||| | | || | | || | || |||| ||| || | | | || || ||||| | |||||| | ||||| || ||||||||||||||||| ||||| || || ||||| || || |||||||| ||||||||||| || || || ||||
gtaaattgacttagaagtatggtttggatttttttttcatttcttggtatgccagtgaatgtctgtaagctgtttggaatttgaatttctgaatgcctgattttcaacagATTGCAGAGATCCTTAAAGATCGTCCATCTTGGTTCCGTGACTGTCGGAGCCTAGAAGTTTTTACTATGTTTCCTGCTGGAAATGGAGGAACCATTGAAC
upper sequence: LOC_Os10g33960.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT5G60690.1 (Arabidopsis thaliana), 3'ss of exon 5
tcttcatacgtatttggttgatgtgaatattttctagaaagctgaaagactttattgttttcagaaaattgttgggagattcttatagtgtgctatgcagATCGTGGAGATCTTAAAAGACCGCCCATCTTGGTTCCGTGATTGTCGAAGTCTTGAAGTCTTCACAATGTTTCCAGCTGGAAATGGTGGCACGATCGAAC
||| || | | | |||| | ||| | | || || || | | | || || |||| || | ||||| | |||||| | ||||| || ||||||||||||||||| ||| | || |||||||| ||||| ||||| || ||||| ||||||||||| ||||| |
---------gtaagaaagggacactcttttcgttgctaaagatacaagtcataatgtttcattttcaaccagtttgggtttttt---gtgttct-tacagATTGCAGAGATCCTCAAAGATCGGCCATCTTGGTTCCGTGACTGTAGGAGCCTTGAAGTTTTCACTATGTTCCCGGCTGGTAATGGTGGCACAATCGAGC
upper sequence: LOC_Os10g33960.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv06s0004g02800.t01 (Vitis vinifera), 3'ss of exon 5
-----------------------------tcttcatacgtatttgg---ttgatgtgaatattttctagaaag-ctgaaagactttattgttttcagaaaattg-------ttgggagat--tcttatagtgtgctat--gcagATCGTGGAGATCTTAAAAGACCGCCCATCTTGGTTCCGTGATTGTCGAAGTCTTGAAGTCTTCACAATGTTTCCAGCTGGAAATGGTGGCACGATCGAAC
|| || ||||| || | | ||||||| | | | | | | ||| |||| | | || ||| ||| | | | || | || ||| | ||||| | |||||| | ||||| || |||||||||||||| || ||||| || |||||||| ||||| |||||||||||||||||||| || || | ||||
gtaagcttcagccaattatgtggtcaggtcatttatgaaaatttgaacatttttcttgatattttattgtaggacctttattttttcatgttataataatattagcatgctttgaaaagtaatatttttgtttgcgactgacagATTGCAGAGATCCTCAAAGATCGTCCATCTTGGTTCCGGGACTGTCGGAGCCTTGAAGTTTTCACCATGTTTCCAGCTGGAAATGGAGGAACTGTTGAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagactttattgttttcagaaaattgttgggagattcttatagtgtgctatgcagATCGTGGAGATCTTAAAAGACCGCCCATCTTGGTTCCGTGATTGTCGAAGTCTTGAAGTCTTCACAATGTTTCCAGCTGGAAATGGTGGCACGATCGAAC
tttattgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcttcatacgtatttggttgatgtgaatattttctagaaagctgaaagactttattgttttcagaaaattgttgggagattcttatagtgtgctatgcagATCGTGGAGATCTTAAAAGACCGCCCATCTTGGTTCCGTGATTGTCGAAGTCTTGAAGTCTTCACAATGTTTCCAGCTGGAAATGGTGGCACGATCGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - gttgatg
- - - - - - - - - - - - - - - - - - - -agctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -attgttg