Sequence
atgc intronic sequence ATGC exonic sequencegtatgtatttcccagcaagttgagtgaagctatttgtgtcatgagttttgctacaattttttaccttttgttagtaaaggatgtcgcgaactttctgaactcttgtttcttgcagCGATTGATGCTCCTGGTGGTTTTCTTTTTGAGTGGTGGTCAGTTTTTTGGGATATTTTCATAGCAAGGACAAATGAGAAGCATTCAGATGTTGCGGCTTC
Basic information
species | Oryza sativa |
transcript | LOC_Os01g42260.3 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g42260.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G022383_T01 (Zea mays), 3'ss of exon 2
gtatgtatttcccagcaagttgagtgaagctatttgtgt---catgagttttgctacaattttttaccttttgttagtaaaggatgtcgcgaactttctgaactct---tgtttcttgcagCGATTGATGCTCCTGGTGGTTTTCTTTTTGAGTGGTGGTCAGTTTTTTGGGATATTTTCATAGCAAGGACAAATGAGAAGCATTCAGATGTTGCGGCTTC
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gtatgcatttgtctgcaagttgtgtggagttacttttcttttcttgagttcttcctgtccgttttgtctgttgcttgtcaagactattatttacttcccaaaaactgttcttttttttcagCCATTGATGCACCCGGTGGCTTTCTTTTCGAGTGGTGGTCGGTTTTCTGGGATATATTCATAGCAAGAACTAACGAGAAGCATTCAGATGTTGCAGCCTC
upper sequence: LOC_Os01g42260.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA05G08110.1 (Glycine max), 3'ss of exon 2
gtatgtatttcccagcaagttgagtgaagctatttgtgtcatgagttttgctacaattttttaccttttgttagtaaaggatgtcgcgaactttctgaactcttgtttcttgcagCGATTGATGCTCCTGGTGGTTTTCTTTTTGAGTGGTGGTCAGTTTTTTGGGATATTTTCATAGCAAGGACAAATGAGAAGCATTCAGATGTTGCGGCTTC
||| | || | | | | | | | | | | | | | | | | | || | || | ||||| || | | || | | ||| || ||||| ||||||||||||||||||||||||||||| || || ||||| || | || || | | |||| ||||||| |||| | || | |||
gtaag-ataataatataggcttttttaggggaaagaaattaggtatatgcaaatgcaactgctcttctaatttactgaatttgacctttacttt-tggccgcatgctcc----agCTATAGATGCACCTGGTGGTTTTCTTTTTGAGTGGTGGTCTGTCTTCTGGGACATATATATTGCCATGGTAAATCAGAAGCACCCAGAAGCAGCAGTTTC
upper sequence: LOC_Os01g42260.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA17G12900.1 (Glycine max), 3'ss of exon 2
gtatgtatttcccagcaagttgagtgaagctatttgtgtcatgagttttgctacaattttttaccttttgttagtaaaggatgtcgcgaactttctgaactcttgtttcttgcagCGATTGATGCTCCTGGTGGTTTTCTTTTTGAGTGGTGGTCAGTTTTTTGGGATATTTTCATAGCAAGGACAAATGAGAAGCATTCAGATGTTGCGGCTTC
||| | | | | | | | | | | | || || | | ||| || || | | | | || | | ||||| || | || | | || || ||||| ||| ||||||||||||||||||||||||| || || ||||| || | || || ||| ||||| |||||| |||| ||
gtaagataatgcatataggctttcttagggga---aagaaattaggtatatgcaaatgcaaatgctcttctaatttattgaatttg---actttttggctacatgctcc----agTTATAGATGCACCTAGTGGTTTTCTTTTTGAGTGGTGGTCTGTCTTCTGGGACATATATATTGCCAGGGCAAATCAGAAGCTCCAAGATACAGCTCAGAA
upper sequence: LOC_Os01g42260.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv11s0016g04550.t01 (Vitis vinifera), 3'ss of exon 2
gtatgtatttcccagcaagttgagtgaagctatttg--tgtcatgagttttgcta-caattttttaccttttgttagtaaaggatgtcgcgaactttctgaactcttgtttcttgcagCGATTGATGCTCCTGGTGGTTTTCTTTTTGAGTGGTGGTCAGTTTTTTGGGATATTTTCATAGCAAGGACAAATGAGAAGCATTCAGATGTTGCGGCTTC
|| | || | | | ||| | ||||||| | | | | | | ||| | |||| | | | ||| | | |||||| ||| | | |||| || ||||| |||||||| ||||| ||||| |||||||| |||||||||||||| || ||||| |||||||||||||| || || || | ||| || ||
--------gcaaaagaatgtatcgaggaatcattaaattttcatgagatgtccaaatgagctcttatcatttgattggtattgattttatg-----tctgaa---ttgaattt--cagCCATCGATGCACCTGGTGGCTTTCTCTTTGAATGGTGGTCTGTTTTTTGGGATATATTTATAGCTAGGACAAATGAGAAACACTCGGAGGCTGCTGCATC
upper sequence: LOC_Os01g42260.2 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ36173 (Selaginella moellendorffii), 3'ss of exon 2
gtatgtatttcccagcaagttgagtgaagctatttgtgtcatgagttttgctacaattttttaccttttgttagtaaaggat-gtcgcgaactttctgaactcttgtttct--tgcagCGATTGATGCTCCTGGTGGTTTTCTTTTTGAGTGGTGGTCAGTTTTTTGGGATATTTTCATAGCAAGGACAAATGAGAAGCATTCAGATGTTGCGGCTTC
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--------------------------------------gtaagagctcctctccgtagagattcttgtcctcataggagttccattgctcctttttttccctttttttttcgatgcagCGATTGATGCTCCTGGTGGTTTTTTGTTCGAGTGGTGGTCCGTGTTCTGGGACATTTTCATTGCTCGTACGAATGAAAAGCACTCAGAGGTGGCTGCTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaccttttgttagtaaaggatgtcgcgaactttctgaactcttgtttcttgcagCGATTGATGCTCCTGGTGGTTTTCTTTTTGAGTGGTGGTCAGTTTTTTGGGATATTTTCATAGCAAGGACAAATGAGAAGCATTCAGATGTTGCGGCTTC
ctcttgtttcttgc CT-rich tract
ttttgtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtatttcccagcaagttgagtgaagctatttgtgtcatgagttttgctacaattttttaccttttgttagtaaaggatgtcgcgaactttctgaactcttgtttcttgcagCGATTGATGCTCCTGGTGGTTTTCTTTTTGAGTGGTGGTCAGTTTTTTGGGATATTTTCATAGCAAGGACAAATGAGAAGCATTCAGATGTTGCGGCTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG