Sequence
atgc intronic sequence ATGC exonic sequenceACAATTCATCCATCAAAGGTAGCATATGTAGCTAAGGAGCTTTATGACATGGGTTGCTCGGAGATCTCACTCGGAGACACGATTGGTGTTGGTACACCAGgtattgattttgttgcctttactgctttcagcatgtcatttcctggtttatatatttttgcgcatttaaaactactttcaaaagcgatgatacgtttttt...
Basic information
species | Oryza sativa |
transcript | LOC_Os12g04020.2 |
intron # | 8 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g04020.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G095141_T03 (Zea mays), 5'ss of exon 7
ACAATTCATCCATCAAAGGTAGCATATGTAGCTAAGGAGCTTTATGACATGGGTTGCTCGGAGATCTCACTCGGAGACACGATTGGTGTTGGTACACCAGgtat-----tgattttgt-tgcctttactgctttcagcatgtcatttcctggtttatatatttttgc--gcatttaaaactactt-tcaaaagcgatgat----acgtttttt-----------------
|| |||| | ||||| || || |||||||||||||| ||| |||||| |||||||||||||| ||||| ||||||| |||||| || ||||||||| | || || | | ||||| | || | | || | || | || | | | | | | || ||||| | || | || |||
--AACCGATCCGGCGAAGGTGGCGTACGTAGCTAAGGAGCTGTATACCATGGGCTGCTCGGAGATCTCGCTCGGCGACACGACTGGTGTCGGGACACCAGGTgtactactggttctctctgcctatgctatgccgaacccgttcgtggctctcagtcgttttctggacagtacgtggagagaccggccaaaaactatactcactgcgatttgcaaacgtctctgcctcag
upper sequence: LOC_Os12g04020.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G095141_T01 (Zea mays), 5'ss of exon 5
ACAATTCATCCATCAAAGGTAGCATATGTAGCTAAGGAGCTTTATGACATGGGTTGCTCGGAGATCTCACTCGGAGACACGATTGGTGTTGGTACACCAGgtat-----tgattttgt-tgcctttactgctttcagcatgtcatttcctggtttatatatttttgc--gcatttaaaactactt-tcaaaagcgatgat----acgtttttt-----------------
||| |||| | ||||| || || |||||||||||||| ||| |||||| |||||||||||||| ||||| ||||||| |||||| || ||||||||| | || || | | ||||| | || | | || | || | || | | | | | | || ||||| | || | || |||
GCAACCGATCCGGCGAAGGTGGCGTACGTAGCTAAGGAGCTGTATACCATGGGCTGCTCGGAGATCTCGCTCGGCGACACGACTGGTGTCGGGACACCAGgtgtactactggttctctctgcctatgctatgccgaacccgttcgtggctctcagtcgttttctggacagtacgtggagagaccggccaaaaactatactcactgcgatttgcaaacgtctctgcctcag
upper sequence: LOC_Os12g04020.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA20G08360.1 (Glycine max), 5'ss of exon 8
ACAATTCATCCATCAAAGGTAGCATATGTAGCTAAGGAGCTTTATGACATGGGTTGCTCGGAGATCTCACTCGGAGACACGATTGGTGTTGGTACACCAGgtattgattttgttgcctttactgctttcagcatgtcatttcctggtttatatatttttgcgcatt-taaaactactttcaaaagcgatgatacgtttttt--------
|||| | ||||||||| || |||||||||||||| || || ||||| |||||||||| || |||||||| || ||||| ||||| |||||||| || |||| ||| || | | | | | |||| | | | || || | | | | | ||| ||| | | ||| || | | || |||
CCAATCCCTCCATCAAAAGTGGCATATGTAGCTAAAGAACTATATGATATGGGTTGCTTTGAAATCTCACTTGGGGACACAATTGGAGTTGGTACTCCCGgtaatgaattagctagatgtctttctttttgaaa---actttatgctacacaca-----gaacataataatatcagcctcatg-gcagcattcccttgtttggcatttg
upper sequence: LOC_Os12g04020.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA07G36340.1 (Glycine max), 5'ss of exon 6
ACAATTCATCCATCAAAGGTAGCATATGTAGCTAAGGAGCTTTATGACATGGGTTGCTCGGAGATCTCACTCGGAGACACGATTGGTGTTGGTACACCAGgtattgattttgttgcctttactgctttcagcatgtcatttcctggtttatatatttttg-cgcatttaaaactactttcaaaagcgatgatacgtttttt
|||| | ||| |||| || |||||||||||||| || || ||||| |||||||||| || ||||||||||| ||||| ||||| |||||||| || |||| ||| || | || |||| | | | | | | | | ||| | | | | | | | ||| | ||| | | | ||
CCAATCCCTCCGTCAAGAGTGGCATATGTAGCTAAAGAACTATATGATATGGGTTGCTTTGAAATCTCACTCGGGGACACAATTGGAGTTGGTACTCCCGgtaatgaattagatgtctttctttttgaaaactttatgctacacacagaacatactaatatcagcctcatgatagcattcccttgtt-tgacatttgtctt
upper sequence: LOC_Os12g04020.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA19G30880.1 (Glycine max), 5'ss of exon 6
ACAATTCATCCATCAAAGGTAGCATATGTAGCTAAGGAGCTTTATGACATGGGTTGCTCGGAGATCTCACTCGGAGACACGATTGGTGTTGGTACACCAGgtattgatttt---gttgcctttactgctttcagcatgtcatttcctggtttatata---tttttgcgcatttaaaactactttcaaaag-cgatgatacgtttttt
| ||| |||| |||| || |||||||| || || ||||||||| ||||||||||| ||||| ||||| || || || || |||||||| ||||| |||| || || | || || | || ||| | || | ||| | | | | | || || | | | ||||| | ||| |
AATATTGCTCCAGCAAAAGTTGCATATGTGGCAAAATCGCTTTATGAGATGGGTTGCTCAGAGATTTCACTGGGGGATACAATCGGTGTTGGCACACCTGgtaatgtttctttcattagctgtctcatgttttgcaaagctattttggctttggctgcagtgctggtgtatctatctcatttgttaaaaggcaatggatc-------Mapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|88985612|gb|CI016321.1|CI016321EST: CGGAGATCTCACTCGGAGACACGATTGGTGTTGGTACACCAG GTAGCGTACTTGCTATGCTTGAAGCTGTAATGTCTTTTGTTCCAGTGGACA
genomic: CGGAGATCTCACTCGGAGACACGATTGGTGTTGGTACACCAGgtattgattt ... tttgtttcagGTAGCGTACTTGCTATGCTTGAAGCTGTAATGTCTTTTGTTCCAGTGGACA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ACAATTCATCCATCAAAGGTAGCATATGTAGCTAAGGAGCTTTATGACATGGGTTGCTCGGAGATCTCACTCGGAGACACGATTGGTGTTGGTACACCAGgtattgattttgttgcctttactgctttcagcatgtcatttcctggtttatatatttttgcgcatttaaaactactttcaaaagcgatgatacgtttttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC