Sequence
atgc intronic sequence ATGC exonic sequencegtaggcgcggttttctcttcttatcagcagtcctttttgtgtgtgaaataaaagcatatgatattgtcattgcagACAATTGGTCAAGCATATGAAGACATGCAAACCCAAAATCAGCACCTTCTTCAACAGGTTGCTGATAGAGATGATTTTAACATAAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os10g41590.2 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os10g41590.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G341271_T02 (Zea mays), 3'ss of exon 15
gtaggcgcggttttctcttcttatcagcagtcctttttgtgtgtgaaataaaagcatatgatattgtcattgcagACAATTGGTCAAGCATATGAAGACATGCAAACCCAAAATCAGCACCTTCTTCAACAGGTTGCTGATAGAGATGATTTTAACATAAAG
||| | || | | |||| || ||| || || | ||| ||| ||||| || | |||||| |||||||||||||||||||||||||||| ||||||||||| |||||||||||| || ||||||||||||| ||||||||||||
---------gttcgtttttttatttgtcagtactgtttttgggtatgagtaaaatgtataatatttgcaatacagACAGTTGGTCAAGCATATGAAGACATGCAAACGCAAAATCAGCATCTTCTTCAACAGCTTACTGATAGAGATGACTTTAACATAAAG
upper sequence: LOC_Os10g41590.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA14G05490.1 (Glycine max), 3'ss of exon 4
gtaggcg---cggttttctcttcttatcagcagtc---ctttttgtgtgtgaaataaaagcatatgatattgtcattgcagACAATTGGTCAAGCATATGAAGACATGCAAACCCAAAATCAGCACCTTCTTCAACAGGTTGCTGATAGAGATGATTTTAACATAAAG
||| || | ||| ||||| | | || || || | || |||| || || |||| | ||||||| |||||||||||||||||||| ||||| || || || || | || | | ||||| || || ||||| | ||| || |||
gtatgctatctgactttttcttccccttcatactctaactcttatttcttgtaatataattat-tgattgctttggtgcagACTATTGGTCAAGCATATGAAGATATGCAGACACAGAACCAAAATCTGTTGAACCAGGTGATCGAGAGGGATGACTATAATATTAAG
upper sequence: LOC_Os10g41590.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA02G43490.1 (Glycine max), 3'ss of exon 15
gtaggcg---cggttttctcttcttatcagcagtcctttttgtgtgt---gaaataaaagcatatgatattgtcattgcagACAATTGGTCAAGCATATGAAGACATGCAAACCCAAAATCAGCACCTTCTTCAACAGGTTGCTGATAGAGATGATTTTAACATAAAG
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gtttgctatctgactttttcttccccttcatactcttactcttatttcttgtaatataattatttgatcgcttttatgcagACTATTGGTCAAGCATATGAAGATATGCAGACACAGAACCAAAATCTGTTGGACCAGGTGATCGAGAGGGATGACTATAATATTAAG
upper sequence: LOC_Os10g41590.1 (Oryza sativa), 3'ss of exon 14
lower sequence: EFJ11831 (Selaginella moellendorffii), 3'ss of exon 14
gtaggcgcggttttctcttcttatcagcagtcctttttgtgtg-tgaaataaaagcatatgatattgtcattg--cagACAATTGGTCAAGCATATGAAGACATGCAAACCCAAAATCAGCACCTTCTTCAACAGGTTGCTGATAGAGATGATTTTAACATAAAG
| | |||| || | | | || | | | | | || | || ||||| || || ||||||||||||||||||||||| ||||| || ||| | || ||| | | || || ||||||| || | ||||
--------------------------gtaagatttttagttttcttacatttatgtctgtagttttctttttaaacagACTATCGGGCAAGCATATGAAGACATGCAAACTCAAAACCAAAGGCTTTTGCAGCAGATATCCGAAAGGGATGATTACAATACAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatcagcagtcctttttgtgtgtgaaataaaagcatatgatattgtcattgcagACAATTGGTCAAGCATATGAAGACATGCAAACCCAAAATCAGCACCTTCTTCAACAGGTTGCTGATAGAGATGATTTTAACATAAAG
aaataaaagcatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggcgcggttttctcttcttatcagcagtcctttttgtgtgtgaaataaaagcatatgatattgtcattgcagACAATTGGTCAAGCATATGAAGACATGCAAACCCAAAATCAGCACCTTCTTCAACAGGTTGCTGATAGAGATGATTTTAACATAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG